SUPERFAMILY 1.75 HMM library and genome assignments server


CCCH zinc finger superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   CCCH zinc finger [ 90228]
Superfamily:   CCCH zinc finger [ 90229]
Families:   CCCH zinc finger [ 90230] (4)


Superfamily statistics
Genomes (446) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 14,882 11,616 7
Proteins 9,583 7,773 4


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) heterocycle metabolic process 2.278e-13 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 5.55e-13 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1.764e-12 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.929e-11 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.681e-09 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.188e-07 Least Informative Direct
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.2873 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) macromolecule catabolic process 1.831e-08 Moderately Informative Direct
Biological Process (BP) gene expression 2.926e-08 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 3.85e-06 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 6.53e-06 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0001107 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.3988 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.4464 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.5924 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1104 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.1364 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.8805 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.1453 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.9697 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.7299 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.7367 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.1429 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.06259 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.4388 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 3.324e-10 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 1.622e-07 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 5.042e-06 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 5.837e-06 Informative Direct
Biological Process (BP) negative regulation of developmental process 6.078e-06 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 1.299e-05 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 2.52e-05 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0001919 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 0.0008934 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.2805 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.1835 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.2147 Informative Inherited
Biological Process (BP) regulation of establishment of protein localization 0.7594 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.06847 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.1095 Informative Inherited
Biological Process (BP) negative regulation of gene expression 1 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.04657 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.001044 Informative Inherited
Biological Process (BP) positive regulation of transport 0.4356 Informative Inherited
Biological Process (BP) cell activation 0.00701 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.02882 Informative Inherited
Biological Process (BP) regulation of kinase activity 0.09164 Informative Inherited
Biological Process (BP) immune effector process 0.04029 Informative Inherited
Biological Process (BP) immune response 0.2257 Informative Inherited
Biological Process (BP) RNA processing 0.001416 Informative Inherited
Biological Process (BP) RNA catabolic process 0 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 7.434e-12 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 2.476e-10 Highly Informative Direct
Biological Process (BP) positive regulation of cellular catabolic process 1.42e-06 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 2.022e-06 Highly Informative Direct
Biological Process (BP) T cell differentiation 2.383e-06 Highly Informative Direct
Biological Process (BP) negative regulation of phosphorylation 1.327e-05 Highly Informative Direct
Biological Process (BP) RNA splicing 3.648e-05 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 6.577e-05 Highly Informative Direct
Biological Process (BP) alpha-beta T cell activation 7.043e-05 Highly Informative Direct
Biological Process (BP) mRNA processing 0.0001964 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0.0003186 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 0.0009079 Highly Informative Direct
Biological Process (BP) regulation of T cell activation 0.0009187 Highly Informative Direct
Biological Process (BP) positive regulation of protein transport 0.001721 Highly Informative Inherited
Biological Process (BP) regulation of intracellular protein transport 0.03697 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.002294 Highly Informative Inherited
Biological Process (BP) negative regulation of immune system process 0.002559 Highly Informative Inherited
Biological Process (BP) gene silencing 0.009784 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.9462 Highly Informative Inherited
Biological Process (BP) cell proliferation 0.0198 Highly Informative Inherited
Biological Process (BP) stem cell development 0.01103 Highly Informative Inherited
Biological Process (BP) cell division 0.04234 Highly Informative Inherited
Molecular Function (MF) binding 1.151e-05 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.9686 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 4.418e-05 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 4.201e-05 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.7342 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.9565 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 1.534e-12 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.5284 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.1169 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.1223 Informative Inherited
Cellular Component (CC) protein serine/threonine phosphatase complex 5.754e-07 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 1.239e-06 Highly Informative Direct

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.143Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1834Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.6797Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.006788Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal protein level0.05594Moderately InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.0593Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.09739Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology3.623e-05InformativeDirect
Mammalian Phenotype (MP)abnormal spleen morphology0.002124InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.002205InformativeInherited
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.002579InformativeInherited
Mammalian Phenotype (MP)abnormal circulating cytokine level0.003623InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.006036InformativeInherited
Mammalian Phenotype (MP)enlarged lymph nodes9.122e-07Highly InformativeDirect
Mammalian Phenotype (MP)increased T cell derived lymphoma incidence9.969e-05Highly InformativeDirect
Mammalian Phenotype (MP)enlarged spleen0.0001157Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus development0.0002582Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.02055Least InformativeInherited
Worm Phenotype (WP)organ system development variant0.0002533Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.01352Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.4851Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.8275Moderately InformativeInherited
Worm Phenotype (WP)transgene expression reduced0.01127InformativeInherited
Worm Phenotype (WP)alimentary system development variant0.01322InformativeInherited
Worm Phenotype (WP)P granule defective2.951e-10Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene1.035e-05Highly InformativeDirect
Worm Phenotype (WP)lineage variant0.001341Highly InformativeInherited
Worm Phenotype (WP)pharyngeal development variant0.01199Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

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ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)head0Least InformativeDirect
Zebrafish Anatomy (ZA)cavitated compound organ0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0.005688Moderately InformativeInherited
Biological processUbl conjugation pathway1.544e-13InformativeDirect
Biological processNeurogenesis0.0001943InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Cellular componentHost cytoplasm6.815e-06InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil7.434e-06Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionRNA-binding2.182e-12Moderately InformativeDirect
Post-translational modificationDevelopmental protein2.491e-07Moderately InformativeDirect
Post-translational modificationRepressor9.108e-06Moderately InformativeDirect
Post-translational modificationPhosphoprotein9.085e-16Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 6 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 CCCH zinc finger 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 6 hidden Markov models representing the CCCH zinc finger 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-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]