ARID4A AT-rich interaction domain 4A [Homo sapiens (human)] - Gene

Summary

Official Symbol: ARID4Aprovided by HGNC
Official Full Name: AT-rich interaction domain 4Aprovided by HGNC
Primary source: HGNC:HGNC:9885
See related: Ensembl:ENSG00000032219 MIM:180201; AllianceGenome:HGNC:9885
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RBP1; RBBP1; RBP-1; RBBP-1
Summary: The protein encoded by this gene is a ubiquitously expressed nuclear protein. It binds directly, with several other proteins, to retinoblastoma protein (pRB) which regulates cell proliferation. pRB represses transcription by recruiting the encoded protein. This protein, in turn, serves as a bridging molecule to recruit HDACs and, in addition, provides a second HDAC-independent repression function. The encoded protein possesses transcriptional repression activity. Multiple alternatively spliced transcripts have been observed for this gene, although not all transcript variants have been fully described. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in bone marrow (RPKM 9.9), lymph node (RPKM 6.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q23.1

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (58298555..58373876)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (52505552..52580897)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (58765273..58840594)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A novel heterozygous missense variant of the ARID4A gene identified in Han Chinese families with schizophrenia-diagnosed siblings that interferes with DNA-binding activity.
Title: A novel heterozygous missense variant of the ARID4A gene identified in Han Chinese families with schizophrenia-diagnosed siblings that interferes with DNA-binding activity.
Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1.
Title: Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1.
ARID4A and ARID4B may play the role as tumor suppressor gene in prostate cancer by inhibiting cell proliferation, migration, and invasion. Moreover, co-downregulation of ARID4A and ARID4B can predict poorer prognosis in prostate cancer, suggesting they might be the novel marker of prognosis and potential therapeutic targets for prostate cancer in human.
Title: Downregulation of ARID4A and ARID4B promote tumor progression and directly regulated by microRNA-30d in patient with prostate cancer.
Consistently, our ITC assays also showed that DNA does not significantly enhance the histone binding ability of the chromo barrel domain of RBBP1.
Title: Crystal structure of chromo barrel domain of RBBP1.
The RBBP1 Tudor domain binds both double- and single-stranded DNA with an affinity of 10-100 muM; no apparent DNA sequence specificity was detected.
Title: Retinoblastoma-binding protein 1 has an interdigitated double Tudor domain with DNA binding activity.
ARID4a (AT-rich interacting domain 4a, also known as RBP1) and CCL5 (C-C motif ligand 5) are targets for miR-302.
Title: Reactive oxygen species mediate microRNA-302 regulation of AT-rich interacting domain 4a and C-C motif ligand 5 expression during transitions between quiescence and proliferation.
chromobarrel domain of RBBP1 is responsible for recognizing methylated histone tails in chromatin remodeling and epigenetic regulation
Title: Structural insight into recognition of methylated histone tails by retinoblastoma-binding protein 1.
Alterations of BRMS1-ARID4A interaction modify gene expression but still suppress metastasis in human breast cancer cells.
Title: Alterations of BRMS1-ARID4A interaction modify gene expression but still suppress metastasis in human breast cancer cells.
RBP1 and the mSin3 histone deacetylase complex bind to BRMS1 and repress transcription
Title: Breast cancer metastasis suppressor 1 (BRMS1) forms complexes with retinoblastoma-binding protein 1 (RBP1) and the mSin3 histone deacetylase complex and represses transcription.
there is an E2-dependent, ER isoform-specific transcriptional activation of the RBBP1 gene, which in part, is explained by the differential activity of ER AF1 and enhancer element binding
Title: Estrogen receptor isoform-specific regulation of the retinoblastoma-binding protein 1 (RBBP1) gene: roles of AF1 and enhancer elements.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW466107 (e-PCR)
- UniSTS:519208

A010A22 (e-PCR)
- UniSTS:31806

SHGC-132583 (e-PCR)
- UniSTS:170858

G35710 (e-PCR)
- UniSTS:64619

G33047 (e-PCR)
- UniSTS:117624

D14S1330 (e-PCR)
- UniSTS:33668

SHGC-36294 (e-PCR)
- UniSTS:58564

SHGC-36874 (e-PCR)
- UniSTS:20941

ARID4A_3852 (e-PCR)
- UniSTS:462037

GDB:196872 (e-PCR)
- UniSTS:155893

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in erythrocyte development	IEA Inferred from Electronic Annotation more info
involved_in establishment of Sertoli cell barrier	IEA Inferred from Electronic Annotation more info
involved_in genomic imprinting	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cell migration	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of transforming growth factor beta receptor signaling pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of Sin3-type complex	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info
part_of transcription repressor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: AT-rich interactive domain-containing protein 4A

Names: ARID domain-containing protein 4A; AT rich interactive domain 4A (RBP1-like); retinoblastoma-binding protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_052999.1 RefSeqGene

Range

5171..80492

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_002892.4 → NP_002883.3 AT-rich interactive domain-containing protein 4A isoform I

See identical proteins and their annotated locations for NP_002883.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the full length isoform.

Source sequence(s)

AL139021, BC026230, BX279740, DB218466, S57153

Consensus CDS

CCDS9732.1

UniProtKB/Swiss-Prot

P29374, Q15991, Q15992, Q15993

Related

ENSP00000347602.3, ENST00000355431.8

Conserved Domains (4) summary

smart00501
Location:312 → 401

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00333
Location:58 → 113

TUDOR; Tudor domain

pfam08169
Location:171 → 261

RBB1NT; RBB1NT (NUC162) domain

pfam11717
Location:575 → 629

Tudor-knot; RNA binding activity-knot of a chromodomain
NM_023000.3 → NP_075376.2 AT-rich interactive domain-containing protein 4A isoform II

See identical proteins and their annotated locations for NP_075376.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks 162 bp in the coding region, as compared to variant 1, but maintains the same reading frame. The encoded protein lacks 54 internal codons and is thought to lack phosphorylation sites.

Source sequence(s)

AL139021, BC026230, BX279740, DB218466, S57160

Consensus CDS

CCDS45114.1

Related

ENSP00000378597.3, ENST00000395168.7

Conserved Domains (5) summary

cd16882
Location:311 → 397

ARID_ARID4A; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins

cd18641
Location:577 → 635

CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins

pfam08169
Location:170 → 262

RBB1NT; RBB1NT (NUC162) domain

cd20390
Location:62 → 114

Tudor_ARID4_rpt2; second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family

cd20459
Location:4 → 61

Tudor_ARID4A_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins
NM_023001.3 → NP_075377.2 AT-rich interactive domain-containing protein 4A isoform III

See identical proteins and their annotated locations for NP_075377.2

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks 207 bp in the coding region, as compared to variant 1, but maintains the same reading frame. The encoded protein lacks 69 internal codons and is thought to lack phosphorylation sites.

Source sequence(s)

AL139021, BC026230, BX279740, DB218466, S57162

Consensus CDS

CCDS9733.1

Related

ENSP00000344556.3, ENST00000348476.7

Conserved Domains (4) summary

smart00501
Location:312 → 401

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00333
Location:58 → 113

TUDOR; Tudor domain

pfam08169
Location:171 → 261

RBB1NT; RBB1NT (NUC162) domain

pfam11717
Location:575 → 629

Tudor-knot; RNA binding activity-knot of a chromodomain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

58298555..58373876

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005267964.3 → XP_005268021.1 AT-rich interactive domain-containing protein 4A isoform X1

See identical proteins and their annotated locations for XP_005268021.1

Conserved Domains (4) summary

smart00501
Location:312 → 401

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00333
Location:58 → 113

TUDOR; Tudor domain

pfam08169
Location:171 → 261

RBB1NT; RBB1NT (NUC162) domain

pfam11717
Location:575 → 629

Tudor-knot; RNA binding activity-knot of a chromodomain
XM_005267965.3 → XP_005268022.1 AT-rich interactive domain-containing protein 4A isoform X2

Conserved Domains (4) summary

smart00501
Location:312 → 401

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00333
Location:58 → 113

TUDOR; Tudor domain

pfam08169
Location:171 → 261

RBB1NT; RBB1NT (NUC162) domain

pfam11717
Location:575 → 629

Tudor-knot; RNA binding activity-knot of a chromodomain
XM_047431656.1 → XP_047287612.1 AT-rich interactive domain-containing protein 4A isoform X6
XM_047431652.1 → XP_047287608.1 AT-rich interactive domain-containing protein 4A isoform X1
XM_047431653.1 → XP_047287609.1 AT-rich interactive domain-containing protein 4A isoform X3
XM_047431654.1 → XP_047287610.1 AT-rich interactive domain-containing protein 4A isoform X4
XM_047431655.1 → XP_047287611.1 AT-rich interactive domain-containing protein 4A isoform X5

RNA

XR_001750495.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060938.1 Alternate T2T-CHM13v2.0

Range

52505552..52580897

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054376532.1 → XP_054232507.1 AT-rich interactive domain-containing protein 4A isoform X1
XM_054376534.1 → XP_054232509.1 AT-rich interactive domain-containing protein 4A isoform X2
XM_054376538.1 → XP_054232513.1 AT-rich interactive domain-containing protein 4A isoform X6
XM_054376533.1 → XP_054232508.1 AT-rich interactive domain-containing protein 4A isoform X1
XM_054376535.1 → XP_054232510.1 AT-rich interactive domain-containing protein 4A isoform X3
XM_054376536.1 → XP_054232511.1 AT-rich interactive domain-containing protein 4A isoform X4
XM_054376537.1 → XP_054232512.1 AT-rich interactive domain-containing protein 4A isoform X5