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ARID-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   DNA/RNA-binding 3-helical bundle [ 46688] (14)
Superfamily:   ARID-like [ 46774]
Families:   ARID domain [ 46775] (4)


Superfamily statistics
Genomes (471) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 3,267 9,686 5
Proteins 3,264 9,654 5


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the musculature0.09379Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1154Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.1226Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.1238Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.1396Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.146Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.2381Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.2478Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.2486Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal ocular adnexa morphology0.004775Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.009318Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebrum0.01446Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.03128Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skull morphology0.03235Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.04178Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.04836Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.0498Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.05175Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.0554Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0.07471Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal physiology0.0947Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.1117Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.2335Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.3646Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.3782Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.4248Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.6407Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the palm0.0002315InformativeDirect
Phenotypic Abnormality (PA)Abnormal testis morphology0.0006323InformativeDirect
Phenotypic Abnormality (PA)Abnormal lip morphology0.0008542InformativeDirect
Phenotypic Abnormality (PA)Abnormal eyelid morphology0.002316InformativeInherited
Phenotypic Abnormality (PA)Abnormal hair quantity0.002574InformativeInherited
Phenotypic Abnormality (PA)Abnormal finger phalanx morphology0.002597InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia of the extremities0.002671InformativeInherited
Phenotypic Abnormality (PA)Abnormal lower limb bone morphology0.002746InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral white matter0.00649InformativeInherited
Phenotypic Abnormality (PA)Abnormality of eye movement0.008873InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.01025InformativeInherited
Phenotypic Abnormality (PA)Regional abnormality of skin0.0125InformativeInherited
Phenotypic Abnormality (PA)Joint hypermobility0.03208InformativeInherited
Phenotypic Abnormality (PA)Abnormal cerebellum morphology0.03645InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb joint0.0554InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.06019InformativeInherited
Phenotypic Abnormality (PA)Joint dislocation0.07006InformativeInherited
Phenotypic Abnormality (PA)Abnormality of toe0.07471InformativeInherited
Phenotypic Abnormality (PA)Generalized abnormality of skin0.1774InformativeInherited
Phenotypic Abnormality (PA)Slow-growing hair0.00000376Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal distal phalanx morphology of finger0.00001119Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the phalanges of the hand0.00004571Highly InformativeDirect
Phenotypic Abnormality (PA)Long eyelashes0.00006945Highly InformativeDirect
Phenotypic Abnormality (PA)Widened posterior fossa0.00008093Highly InformativeDirect
Phenotypic Abnormality (PA)Cerebellar cyst0.0001036Highly InformativeDirect
Phenotypic Abnormality (PA)Generalized hirsutism0.0001139Highly InformativeDirect
Phenotypic Abnormality (PA)Cryptorchidism0.0001661Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the phalanges of the toes0.0001879Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal hand morphology0.0002716Highly InformativeDirect
Phenotypic Abnormality (PA)Wide mouth0.0003405Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the diaphragm0.0003424Highly InformativeDirect
Phenotypic Abnormality (PA)Hypoplasia of the corpus callosum0.0004096Highly InformativeDirect
Phenotypic Abnormality (PA)Spinal dysraphism0.000463Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal renal pelvis morphology0.0005339Highly InformativeDirect
Phenotypic Abnormality (PA)Strabismus0.0006372Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the cerebellar vermis0.0006985Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the nasal bridge0.0007917Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the hand0.0008199Highly InformativeDirect
Phenotypic Abnormality (PA)Joint hyperflexibility0.0009264Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal dermatoglyphics0.001174Highly InformativeInherited
Phenotypic Abnormality (PA)Short digit0.001358Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the knee0.003072Highly InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of toe0.0136Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal 5th finger morphology0.08211Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of femur morphology0.08972Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal eyebrow morphology0.1067Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral ventricles0.1145Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the external nose0.1478Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the elbow0.1725Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skin of the palm0.258Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.005459Least InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic stem cell morphology0.0003411Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.00204Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.1495Least InformativeInherited
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)organism stress response variant0.000005336Moderately InformativeDirect
Worm Phenotype (WP)protein expression variant0.0006672Moderately InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive0.00000000007456Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect
Fly Phenotype (FP)lethal0Moderately InformativeDirect
Fly Phenotype (FP)modifier of variegation0.00006269InformativeDirect
Fly Phenotype (FP)some die during P-stage0.007885Highly InformativeInherited

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)adult segment0Moderately InformativeDirect
Fly Anatomy (FA)region of integument0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0Least InformativeDirect
Xenopus ANatomical entity (XAN)embryo0.09169Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.1028Least InformativeInherited
Xenopus ANatomical entity (XAN)urogenital system0.1898Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.3127Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.006828Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical space0.01199InformativeInherited
Xenopus ANatomical entity (XAN)urinary system0.02404InformativeInherited
Xenopus ANatomical entity (XAN)pronephric tubule0.0007247Highly 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)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect

Document: AP annotation of SCOP domains

InterPro annotation
Cross references IPR001606 SSF46774 Protein matches
Abstract

Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure [PubMed10838570]. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini.

The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 [PubMed10757798]. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [PubMed10757798].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) ]

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 10 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 ARID-like 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 10 hidden Markov models representing the ARID-like 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 · InterPro annotation · PDBeMotif links · Functional annotation · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Internal database links ]