SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 inheritance0.0001365InformativeDirect
Mode of Inheritance (MI)Y-linked inheritance0.000406Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.2791Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.3775Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.3778Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.4302Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.5746Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.16Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.2721Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of central motor function0.4055Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.4861Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.5409Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0.6013Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.009019InformativeInherited
Phenotypic Abnormality (PA)Fatigable weakness0.01247InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle fiber morphology0.02554InformativeInherited
Phenotypic Abnormality (PA)Neurological speech impairment0.2477InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.6185InformativeInherited
Phenotypic Abnormality (PA)Abnormal motor neuron morphology0.0000002101Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of swallowing muscles0.000001576Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of respiratory muscles0.00004059Highly InformativeDirect
Phenotypic Abnormality (PA)Paralysis0.0003328Highly InformativeDirect
Phenotypic Abnormality (PA)Agitation0.0003665Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of salivation0.0006842Highly InformativeDirect
Phenotypic Abnormality (PA)Azoospermia0.003577Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal larynx physiology0.02649Highly InformativeInherited
Phenotypic Abnormality (PA)Atrophy/Degeneration affecting the central nervous system0.04709Highly 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 variant0.000000000000005375Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0000004221Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.000001412Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0002923Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.006236Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.7999Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.8453Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.0001723Moderately InformativeDirect
Worm Phenotype (WP)neuron development variant0.0002278Moderately InformativeDirect
Worm Phenotype (WP)metabolic pathway variant0.003347Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.01071Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.04877Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.1634Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.2335Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.3051Moderately InformativeInherited
Worm Phenotype (WP)germ cell development variant0.9776Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant1Moderately InformativeInherited
Worm Phenotype (WP)sterile progeny1Moderately InformativeInherited
Worm Phenotype (WP)RNA expression variant0.0000000004612InformativeDirect
Worm Phenotype (WP)sick0.0000001154InformativeDirect
Worm Phenotype (WP)brood size variant0.00001452InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00003645InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.0003645InformativeDirect
Worm Phenotype (WP)cell number increased0.001248InformativeInherited
Worm Phenotype (WP)pericellular component morphology variant0.00204InformativeInherited
Worm Phenotype (WP)vulva development variant0.02087InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.03205InformativeInherited
Worm Phenotype (WP)egg laying variant0.03876InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.1131InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.1999InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.6164InformativeInherited
Worm Phenotype (WP)cell proliferation increased0Highly InformativeDirect
Worm Phenotype (WP)sex determination variant0.00000003257Highly InformativeDirect
Worm Phenotype (WP)neurite development variant0.0000004419Highly InformativeDirect
Worm Phenotype (WP)embryonic lethal late emb0.000002156Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.00000423Highly InformativeDirect
Worm Phenotype (WP)no induction of antimicrobial peptide expression after infection0.00002306Highly InformativeDirect
Worm Phenotype (WP)developmental morphology variant0.0001367Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.0004479Highly InformativeDirect
Worm Phenotype (WP)organism starvation response variant0.037Highly InformativeInherited
Worm Phenotype (WP)P granule abnormal0.05247Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.007762Least InformativeInherited
Fly Phenotype (FP)lethal0.00005157Moderately 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)embryo0.00000000000009439Least InformativeDirect
Xenopus ANatomical entity (XAN)urogenital system0.00000116Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.000004596Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0.00191Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.006186Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01595Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.4059Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.000000000003266Moderately InformativeDirect
Xenopus ANatomical entity (XAN)testis0.0000001861Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.000001372Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.000001939Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00002854Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.0001895Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.002486Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.01081Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.0207Moderately InformativeInherited
Xenopus ANatomical entity (XAN)germ cell0.02218Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect
Xenopus ANatomical entity (XAN)immune system0.000000000007961InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0.00000000005764InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0.00000004042InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.0000008482InformativeDirect
Xenopus ANatomical entity (XAN)intestine0.00001717InformativeDirect
Xenopus ANatomical entity (XAN)eye0.00005167InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0005639InformativeDirect
Xenopus ANatomical entity (XAN)neural crest0.0006508InformativeDirect
Xenopus ANatomical entity (XAN)limb0.0006975InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0001415Highly InformativeDirect
Xenopus ANatomical entity (XAN)marginal zone0.0009992Highly InformativeDirect
Xenopus ANatomical entity (XAN)vegetal hemisphere0.009251Highly InformativeInherited
Xenopus DEvelopment stage (XDE)post-embryonic stage0.002094Least InformativeInherited
Xenopus DEvelopment stage (XDE)unspecified stage0.0002316Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)climax stage0.008839Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 660.0005085InformativeDirect

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)Hydrolases0.01499Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.000000003457Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.0000001241Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.00007272Moderately InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases0.007358Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0.0197Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.04617Moderately InformativeInherited
Enzyme Commission (EC)RNA helicase0.00000000000001388InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0.00000003461InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0006119InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0.000000000000003019Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0.0000000000003649Highly 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 ]