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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 (1,025) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 114,462 318,313 138
Proteins 83,107 233,604 130


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

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0.00000000004189Least InformativeDirect
Enzyme Commission (EC)Isomerases0.000002211Least 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)Methyltransferases0.000000000000009651Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0.00000004046Moderately 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 ribonuclease0.00000000000004272Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)muscle tissue disease0.01924InformativeInherited
Disease Ontology (DO)ischemia0.29Highly InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Gonosomal inheritance0.00009495InformativeDirect
Mode of Inheritance (MI)Y-linked inheritance0.0002908Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the musculature0.3016Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.3036Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.3138Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.4454Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.5922Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.1511Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.4299Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.4681Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0.6358Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.6593Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.006885InformativeInherited
Phenotypic Abnormality (PA)Fatigable weakness0.008145InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle fiber morphology0.02703InformativeInherited
Phenotypic Abnormality (PA)Neurological speech impairment0.3269InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.5491InformativeInherited
Phenotypic Abnormality (PA)Abnormal motor neuron morphology0.0000001776Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of swallowing muscles0.000001378Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of respiratory muscles0.00003611Highly InformativeDirect
Phenotypic Abnormality (PA)Agitation0.0003308Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of salivation0.0004453Highly InformativeDirect
Phenotypic Abnormality (PA)Azoospermia0.003321Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal larynx physiology0.02392Highly InformativeInherited
Phenotypic Abnormality (PA)Atrophy/Degeneration affecting the central nervous system0.04107Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.2854Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.9999Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.7554Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.8892Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell differentiation0.7837InformativeInherited
Mammalian Phenotype (MP)premature neuronal precursor differentiation0.000629Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant8.918e-16Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.000001009Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0001738Least InformativeDirect
Worm Phenotype (WP)blast cell physiology variant0.003303Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.003329Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.004577Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.007605Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.9215Least InformativeInherited
Worm Phenotype (WP)neuron development variant0.00004918Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0003279Moderately InformativeDirect
Worm Phenotype (WP)body region morphology variant0.001467Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.001467Moderately InformativeInherited
Worm Phenotype (WP)developmental morphology variant0.001485Moderately InformativeInherited
Worm Phenotype (WP)adult body morphology variant0.001502Moderately InformativeInherited
Worm Phenotype (WP)body morphology variant0.001986Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.00865Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.5817Moderately InformativeInherited
Worm Phenotype (WP)germ cell development variant0.9878Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant1Moderately InformativeInherited
Worm Phenotype (WP)sterile progeny1Moderately InformativeInherited
Worm Phenotype (WP)RNA expression variant0.0000000002011InformativeDirect
Worm Phenotype (WP)sick0.0000003053InformativeDirect
Worm Phenotype (WP)brood size variant0.000007256InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00002962InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.00041InformativeDirect
Worm Phenotype (WP)cell number increased0.001846InformativeInherited
Worm Phenotype (WP)pericellular component morphology variant0.00188InformativeInherited
Worm Phenotype (WP)egg laying variant0.0118InformativeInherited
Worm Phenotype (WP)vulva development variant0.01535InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.03288InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.06954InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.2047InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.5664InformativeInherited
Worm Phenotype (WP)cell proliferation increased4.465e-16Highly InformativeDirect
Worm Phenotype (WP)sex determination variant0.00000001869Highly InformativeDirect
Worm Phenotype (WP)neurite development variant0.0000002302Highly InformativeDirect
Worm Phenotype (WP)embryonic lethal late emb0.000002025Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.00000719Highly InformativeDirect
Worm Phenotype (WP)egg morphology variant0.00001393Highly InformativeDirect
Worm Phenotype (WP)no induction of antimicrobial peptide expression after infection0.00001956Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.0003678Highly InformativeDirect
Worm Phenotype (WP)P granule defective0.05144Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.01376Least InformativeInherited
Fly Phenotype (FP)lethal0.0001359Moderately InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA 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)embryo0.0000000000001449Least InformativeDirect
Xenopus ANatomical entity (XAN)urogenital system0.0000004691Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.000005767Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0.002091Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.00725Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01604Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.4117Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.00000000000659Moderately InformativeDirect
Xenopus ANatomical entity (XAN)testis0.0000002838Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.000001788Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.000004397Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00001051Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.00012Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.001311Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.0123Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.01505Moderately InformativeInherited
Xenopus ANatomical entity (XAN)germ cell0.02379Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect
Xenopus ANatomical entity (XAN)immune system0.00000000001097InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0.00000000007695InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0.0000000541InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.0000007082InformativeDirect
Xenopus ANatomical entity (XAN)intestine0.000007944InformativeDirect
Xenopus ANatomical entity (XAN)eye0.00002239InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0004632InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.0006598InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0000854Highly InformativeDirect
Xenopus ANatomical entity (XAN)marginal zone0.001318Highly InformativeInherited
Xenopus ANatomical entity (XAN)vegetal hemisphere0.008617Highly InformativeInherited
Xenopus DEvelopment stage (XDE)post-embryonic stage0.00266Least InformativeInherited
Xenopus DEvelopment stage (XDE)unspecified stage0.0001914Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)climax stage0.009096Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 660.0007218InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0.00000008591Least InformativeDirect
Plant ANatomical entity (PAN)seed0.00000613Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0.0001151Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.002607Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.005049Least InformativeInherited
Plant ANatomical entity (PAN)inflorescence0.009978Least InformativeInherited
Plant ANatomical entity (PAN)whole plant0.02106Least InformativeInherited
Plant ANatomical entity (PAN)flower0.1693Least InformativeInherited
Plant ANatomical entity (PAN)collective phyllome structure0.2001Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.2113Least InformativeInherited
Plant ANatomical entity (PAN)gamete0.00005335InformativeDirect
Plant ANatomical entity (PAN)cultured plant cell0.0001439Highly InformativeDirect
Plant ANatomical entity (PAN)bud0.03197Highly InformativeInherited
Plant structure DEvelopment stage (PDE)D bilateral stage0.00001302Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0.00004978Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0.0001063Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0.0001151Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.02003Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.000000000479Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.0000001907Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.00007309Moderately InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases0.007976Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0.01978Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.05217Moderately InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)RNA helicase0.00000000000001945InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0.00000003487InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0006699InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0.00000000000000376Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0.0000000000004255Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationRNA-binding0InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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 194 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 194 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]