SUPERFAMILY 1.75 HMM library and genome assignments server


RNA-binding domain, RBD superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   RNA-binding domain, RBD [ 54928] (5)
Families:   Canonical RBD [ 54929] (67)
  Non-canonical RBD domain [ 54954]
  Splicing factor U2AF subunits [ 64276]
  Smg-4/UPF3 [ 102987]
  GUCT domain [ 160314]


Superfamily statistics
Genomes (848) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 97,201 81,527 138
Proteins 70,499 59,803 130


Functional annotation
General category Regulation
Detailed category RNA binding, metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)heterocycle metabolic process6.165e-060Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process7.882e-060Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process2.491e-050Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process4.179e-050Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.00051220Least InformativeDirect
Biological Process (BP)regulation of cellular process0.50770.3191Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.11280Least InformativeInherited
Biological Process (BP)localization0.56061Least InformativeInherited
Biological Process (BP)single-organism cellular process0.96221Least InformativeInherited
Biological Process (BP)gene expression3.099e-150Moderately InformativeDirect
Biological Process (BP)RNA metabolic process3.456e-140Moderately InformativeDirect
Biological Process (BP)organic substance transport0.048410.7566Moderately InformativeInherited
Biological Process (BP)regulation of localization0.0071321Moderately InformativeInherited
Biological Process (BP)cellular localization0.039730.1472Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.16760Moderately InformativeInherited
Biological Process (BP)regulation of cellular metabolic process0.1130Moderately InformativeInherited
Biological Process (BP)regulation of biosynthetic process0.69051Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process0.73040.03755Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.010930.007093Moderately InformativeInherited
Biological Process (BP)nucleocytoplasmic transport1.348e-070InformativeDirect
Biological Process (BP)cytoplasmic transport0.0001553.659e-10InformativeDirect
Biological Process (BP)nitrogen compound transport0.00064817.261e-07InformativeDirect
Biological Process (BP)posttranscriptional regulation of gene expression0.00087440InformativeDirect
Biological Process (BP)regulation of intracellular transport1.739e-070.003274InformativeInherited
Biological Process (BP)positive regulation of transport4.873e-061InformativeInherited
Biological Process (BP)RNA export from nucleus7.298e-111.342e-07Highly InformativeDirect
Biological Process (BP)positive regulation of intracellular transport4.792e-108.196e-05Highly InformativeDirect
Biological Process (BP)mRNA processing8.868e-070Highly InformativeDirect
Biological Process (BP)regulation of translation0.000530Highly InformativeDirect
Biological Process (BP)regulation of nucleocytoplasmic transport1.095e-090.008018Highly InformativeInherited
Molecular Function (MF)binding0.00016490Least InformativeDirect
Molecular Function (MF)heterocyclic compound binding8.152e-110Moderately InformativeDirect
Molecular Function (MF)organic cyclic compound binding2.741e-100Moderately InformativeDirect
Molecular Function (MF)RNA binding00InformativeDirect
Cellular Component (CC)protein complex11Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.020220Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.035875.87e-07Least InformativeInherited
Cellular Component (CC)nuclear part7.083e-070Moderately InformativeDirect
Cellular Component (CC)ribonucleoprotein complex5.549e-060Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen0.020050Moderately InformativeInherited
Cellular Component (CC)nucleoplasm part0.63091InformativeInherited
Cellular Component (CC)nuclear body1.877e-060Highly InformativeDirect
Cellular Component (CC)RNA cap binding complex3.477e-062.933e-05Highly InformativeDirect
Cellular Component (CC)spliceosomal complex0.00014430Highly InformativeDirect
Cellular Component (CC)small nuclear ribonucleoprotein complex0.0046623.759e-10Highly InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.3191 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 3.8e-05 Moderately Informative Direct
Biological Process (BP) reproduction 0.0007756 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.0001285 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 7.66e-05 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.2499 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.1472 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.2386 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.007093 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.7566 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.2931 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.03755 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.4221 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) nucleocytoplasmic transport 0 Informative Direct
Biological Process (BP) cytoplasmic transport 3.659e-10 Informative Direct
Biological Process (BP) nitrogen compound transport 7.261e-07 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0 Informative Direct
Biological Process (BP) cellular process involved in reproduction 6.961e-08 Informative Direct
Biological Process (BP) sexual reproduction 9.36e-14 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 1.981e-09 Informative Direct
Biological Process (BP) single organism reproductive process 9.231e-10 Informative Direct
Biological Process (BP) developmental process involved in reproduction 1.319e-06 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 3.878e-09 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0.000385 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.0004401 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.2322 Informative Inherited
Biological Process (BP) positive regulation of phosphorus metabolic process 1 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 1 Informative Inherited
Biological Process (BP) cardiovascular system development 1 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 1 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) cell proliferation 0.3217 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.9015 Informative Inherited
Biological Process (BP) regulation of reproductive process 0.556 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.8523 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of cell death 1 Informative Inherited
Biological Process (BP) regulation of apoptotic process 1 Informative Inherited
Biological Process (BP) response to light stimulus 0.9743 Informative Inherited
Biological Process (BP) response to oxidative stress 0.01579 Informative Inherited
Biological Process (BP) proteolysis 1 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.003274 Informative Inherited
Biological Process (BP) positive regulation of transport 1 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of cellular metabolic process 0.006359 Informative Inherited
Biological Process (BP) cellular response to nitrogen compound 0.0199 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.8711 Informative Inherited
Biological Process (BP) ncRNA processing 1 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.6121 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) negative regulation of molecular function 1 Informative Inherited
Biological Process (BP) regulation of cell development 1 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.5011 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.05014 Informative Inherited
Biological Process (BP) response to external stimulus 1 Informative Inherited
Biological Process (BP) single-organism behavior 1 Informative Inherited
Biological Process (BP) cytoskeleton organization 1 Informative Inherited
Biological Process (BP) microtubule-based process 1 Informative Inherited
Biological Process (BP) organ morphogenesis 1 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.8764 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 1 Informative Inherited
Biological Process (BP) transcription, DNA-dependent 1 Informative Inherited
Biological Process (BP) RNA export from nucleus 1.342e-07 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 8.196e-05 Highly Informative Direct
Biological Process (BP) mRNA processing 0 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) response to cold 7.04e-05 Highly Informative Direct
Biological Process (BP) RNA splicing, via transesterification reactions 1.742e-11 Highly Informative Direct
Biological Process (BP) translational initiation 0 Highly Informative Direct
Biological Process (BP) germ cell development 0 Highly Informative Direct
Biological Process (BP) regulation of mitochondrion organization 0 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0 Highly Informative Direct
Biological Process (BP) negative regulation of neuron death 8.872e-12 Highly Informative Direct
Biological Process (BP) respiratory electron transport chain 1.128e-11 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 2.314e-09 Highly Informative Direct
Biological Process (BP) regulation of neuron apoptotic process 1.778e-08 Highly Informative Direct
Biological Process (BP) positive regulation of organelle organization 5.02e-07 Highly Informative Direct
Biological Process (BP) negative regulation of cellular catabolic process 1.584e-06 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.0003908 Highly Informative Direct
Biological Process (BP) mRNA transport 0.0007841 Highly Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0.04044 Highly Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 1 Highly Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 1 Highly Informative Inherited
Biological Process (BP) regulation of nucleocytoplasmic transport 0.008018 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.09328 Highly Informative Inherited
Biological Process (BP) negative regulation of apoptotic process 0.5078 Highly Informative Inherited
Biological Process (BP) cell division 0.217 Highly Informative Inherited
Biological Process (BP) positive regulation of cell cycle process 0.00231 Highly Informative Inherited
Biological Process (BP) cellular response to organic cyclic compound 0.03251 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.8804 Highly Informative Inherited
Biological Process (BP) negative regulation of gene expression 1 Highly Informative Inherited
Biological Process (BP) feeding behavior 0.3739 Highly Informative Inherited
Biological Process (BP) adult behavior 0.5977 Highly Informative Inherited
Biological Process (BP) establishment or maintenance of cell polarity 0.9219 Highly Informative Inherited
Biological Process (BP) microtubule cytoskeleton organization 0.4923 Highly Informative Inherited
Biological Process (BP) post-embryonic organ development 0.1992 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.5253 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 0.285 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.09047 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.9653 Highly Informative Inherited
Biological Process (BP) epithelial cell development 0.03965 Highly Informative Inherited
Biological Process (BP) RNA 3'-end processing 0.01917 Highly Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 0.06032 Highly Informative Inherited
Biological Process (BP) multi-organism behavior 0.06575 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 0 Moderately Informative Direct
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) transporter activity 1 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.8698 Informative Inherited
Molecular Function (MF) phosphoric ester hydrolase activity 1 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 1 Informative Inherited
Molecular Function (MF) structure-specific DNA binding 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 3.07e-15 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 0.9281 Highly Informative Inherited
Molecular Function (MF) chromatin binding 0.2337 Highly Informative Inherited
Molecular Function (MF) adenylyltransferase activity 0.02304 Highly Informative Inherited
Molecular Function (MF) translation factor activity, nucleic acid binding 1 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 5.87e-07 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 1.227e-05 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) vesicle 1 Moderately Informative Inherited
Cellular Component (CC) extracellular region 1 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) chromosome 1 Informative Inherited
Cellular Component (CC) nuclear body 0 Highly Informative Direct
Cellular Component (CC) RNA cap binding complex 2.933e-05 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 3.759e-10 Highly Informative Direct
Cellular Component (CC) cytoplasmic mRNA processing body 3.339e-07 Highly Informative Direct
Cellular Component (CC) CCR4-NOT complex 0.0002235 Highly Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.01084 Highly Informative Inherited
Cellular Component (CC) chromatin 0.4711 Highly Informative Inherited
Cellular Component (CC) nuclear chromosome part 1 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups4.189e-11Least InformativeDirect
Enzyme Commission (EC)Isomerases2.211e-06Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.01123Least InformativeInherited
Enzyme Commission (EC)Acting on ester bonds0.003436Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.02837Least InformativeInherited
Enzyme Commission (EC)Methyltransferases9.651e-15Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an4.046e-08Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.02062Moderately InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)RNA uridylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease4.272e-14Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant1.008e-05Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.04874Least InformativeInherited
Worm Phenotype (WP)larval development variant0.883Least InformativeInherited
Worm Phenotype (WP)growth variant0.9964Least InformativeInherited
Worm Phenotype (WP)organ system development variant4.967e-09Moderately InformativeDirect
Worm Phenotype (WP)locomotion variant6.171e-05Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.001356Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.004062Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.2825Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.7465Moderately InformativeInherited
Worm Phenotype (WP)sterile progeny1Moderately InformativeInherited
Worm Phenotype (WP)RNA expression variant3.456e-09InformativeDirect
Worm Phenotype (WP)sick3.371e-08InformativeDirect
Worm Phenotype (WP)brood size variant9.047e-06InformativeDirect
Worm Phenotype (WP)alimentary system development variant5.507e-05InformativeDirect
Worm Phenotype (WP)VPC competence variant0.01983InformativeInherited
Worm Phenotype (WP)vulva development variant0.08108InformativeInherited
Worm Phenotype (WP)egg laying variant0.3289InformativeInherited
Worm Phenotype (WP)cell proliferation increased0Highly InformativeDirect
Worm Phenotype (WP)developmental morphology variant4.306e-06Highly InformativeDirect
Worm Phenotype (WP)P granule defective0.0002637Highly InformativeDirect
Worm Phenotype (WP)germline proliferation variant0.005875Highly InformativeInherited
Worm Phenotype (WP)mRNA expression variant0.7726Highly InformativeInherited

Document: WP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)cell1.414e-12Least InformativeDirect
Xenopus ANatomical entity (XAN)embryo3.211e-10Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue1.084e-05Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0.00109Least InformativeInherited
Xenopus ANatomical entity (XAN)central nervous system0.006491Least InformativeInherited
Xenopus ANatomical entity (XAN)gonad0.008412Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01382Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.01686Least InformativeInherited
Xenopus ANatomical entity (XAN)gamete1.063e-13Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure2.022e-13Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm8.313e-07Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system9.765e-07Moderately InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm1.005e-05Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure1.144e-05Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system1.899e-05Moderately InformativeDirect
Xenopus ANatomical entity (XAN)intestine4.492e-05Moderately InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.0001523Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ovary0.000943Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.00128Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro4.172e-15InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system2.401e-09InformativeDirect
Xenopus ANatomical entity (XAN)heart8.866e-07InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region6.577e-06InformativeDirect
Xenopus ANatomical entity (XAN)lung3.901e-05InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord8.652e-05InformativeDirect
Xenopus ANatomical entity (XAN)skeletal muscle0.0001104InformativeDirect
Xenopus ANatomical entity (XAN)spleen0.0004275InformativeDirect
Xenopus ANatomical entity (XAN)solid compound organ0.0006992InformativeDirect
Xenopus ANatomical entity (XAN)liver and biliary system0.0007127InformativeDirect
Xenopus ANatomical entity (XAN)otic vesicle0.0008046InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.04148InformativeInherited
Xenopus ANatomical entity (XAN)stomach4.571e-06Highly InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal arch1.891e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0004425Highly InformativeDirect
Xenopus ANatomical entity (XAN)ventral blood island0.0004865Highly InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)seed1.601e-10Least InformativeDirect
Plant ANatomical entity (PAN)pedicel2.906e-09Least InformativeDirect
Plant ANatomical entity (PAN)shoot apex7.518e-09Least InformativeDirect
Plant ANatomical entity (PAN)plant cell3.389e-07Least InformativeDirect
Plant ANatomical entity (PAN)stalk2.436e-06Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex4.522e-06Least InformativeDirect
Plant ANatomical entity (PAN)sepal5.621e-06Least InformativeDirect
Plant ANatomical entity (PAN)petal1.525e-05Least InformativeDirect
Plant ANatomical entity (PAN)gynoecium2.01e-05Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina2.82e-05Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll4.044e-05Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo6.632e-05Least InformativeDirect
Plant ANatomical entity (PAN)root7.217e-05Least InformativeDirect
Plant ANatomical entity (PAN)androecium0.0001638Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0.0004333Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0.05213Least InformativeInherited
Plant ANatomical entity (PAN)microgametophyte0.1404Least InformativeInherited
Plant ANatomical entity (PAN)vascular leaf0.6763Least InformativeInherited
Plant ANatomical entity (PAN)guard cell1.728e-05Moderately InformativeDirect
Plant ANatomical entity (PAN)cultured plant cell0.0003761Highly InformativeDirect
Plant ANatomical entity (PAN)bud0.02504Highly InformativeInherited
Plant structure DEvelopment stage (PDE)D bilateral stage1.421e-05Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage5.469e-05Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0.0001084Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0.0001241Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.02605Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups4.354e-11Moderately InformativeDirect
Enzyme Commission (EC)Isomerases2.631e-06Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.01103Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0.02133Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.02816Moderately InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)RNA helicase8.921e-13InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters3.012e-08InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)RNA uridylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease3.707e-14Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processDifferentiation0Moderately InformativeDirect
Biological processTranscription regulation0.0003385Moderately InformativeDirect
Biological processInitiation factor0InformativeDirect
Biological processmRNA splicing0InformativeDirect
Biological processTranslation regulation0InformativeDirect
Biological processMeiosis1.388e-12InformativeDirect
Biological processRibosome biogenesis1.066e-06InformativeDirect
Biological processrRNA processing4.326e-05InformativeDirect
Biological processmRNA transport0Highly InformativeDirect
Biological processNonsense-mediated mRNA decay0Highly InformativeDirect
Biological processRNA-mediated gene silencing0Highly InformativeDirect
Biological processSpermatogenesis6.395e-06Highly InformativeDirect
Biological processOogenesis2.605e-05Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome9.342e-08InformativeDirect
Coding sequence diversityAlternative splicing0Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainCoiled coil2.136e-08Moderately InformativeDirect
DomainWD repeat3.033e-07InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionZinc-finger0Moderately InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationIsomerase1Moderately InformativeInherited
Post-translational modificationChromatin regulator8.186e-06InformativeDirect
Post-translational modificationRotamase6.418e-06Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0Moderately InformativeDirect
Post-translational modificationMethylation1.644e-13Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein ubiquitination0Moderately InformativeDirect

Document: UP annotation of SCOP domains

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Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 98 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a RNA-binding domain, RBD domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 98 hidden Markov models representing the RNA-binding domain, RBD superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]