ARID4B AT-rich interaction domain 4B [Homo sapiens (human)] - Gene

Summary

Official Symbol: ARID4Bprovided by HGNC
Official Full Name: AT-rich interaction domain 4Bprovided by HGNC
Primary source: HGNC:HGNC:15550
See related: Ensembl:ENSG00000054267 MIM:609696; AllianceGenome:HGNC:15550
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: BCAA; BRCAA1; RBP1L1; SAP180; RBBP1L1
Summary: This gene encodes a protein with sequence similarity to retinoblastoma-binding protein-1. The encoded protein is a subunit of the histone deacetylase-dependant SIN3A transcriptional corepressor complex, which functions in diverse cellular processes including proliferation, differentiation, apoptosis, oncogenesis, and cell fate determination. The gene product is recognized by IgG antibody isolated from a breast cancer patient and appears to be a molecular marker associated with a broad range of human malignancies. Alternate transcriptional splice variants encoding different isoforms have been characterized. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 12.1), lymph node (RPKM 11.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q42.3

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (235166902..235328179, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (234558607..234719910, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (235330217..235491494, complement)

Chromosome 1 - NC_000001.11 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
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?

Circ-SMARCA5 suppresses colorectal cancer progression via downregulating miR-39-3p and upregulating ARID4B.
Title: Circ-SMARCA5 suppresses colorectal cancer progression via downregulating miR-39-3p and upregulating ARID4B.
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.
our results suggest that ARID4B acts as an oncogene in hepatocellular carcinoma and can therefore serve as a biomarker for the prognoses of patients with hepatocellular carcinoma
Title: Overexpression of ARID4B predicts poor survival in patients with hepatocellular carcinoma.
miR-519b-3p directly binds to the 3' UTR of ARID4B mRNA whose expression was inversely correlated with miR-519b-3p expression.
Title: miR-519b-3p promotes responsiveness to preoperative chemoradiotherapy in rectal cancer patients by targeting ARID4B.
ARID4B overexpression presented in most of primary brain tumors, rather than non-neoplastic brain tissue, and correlated with WHO grades in meningiomas and gliomas.
Title: ARID4B is a good biomarker to predict tumour behaviour and decide WHO grades in gliomas and meningiomas.
ARID4B was significantly elevated in the serum of excessive alcohol users.
Title: Novel serum biomarkers for detection of excessive alcohol use.
Consistent with our genetic analysis and in vivo experiments in our mouse model system, ARID4B expression was also an independent predictor of distant metastasis-free survival in breast cancer patients with ER+ tumors
Title: Allelic variation and differential expression of the mSIN3A histone deacetylase complex gene Arid4b promote mammary tumor growth and metastasis.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: MicroRNAs and target site screening reveals a pre-microRNA-30e variant associated with schizophrenia.
Immunohistochemistry analysis showed that the antigen epitope exhibited positive expression in 65% (39 of 60) breast cancer specimens and negative expression in 60 non-cancerous tissues. A novel breast cancer antigen epitope, SSKKQKRSHK, is identified
Title: Characterization of BRCAA1 and its novel antigen epitope identification.

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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

SHGC-76545 (e-PCR)
- UniSTS:63744

D11S2921 (e-PCR)
- UniSTS:152074

D1S3341 (e-PCR)
- UniSTS:15641

PMC156606P1 (e-PCR)
- UniSTS:271408

D8S2279 (e-PCR)
- UniSTS:473907

sY3084 (e-PCR)
- UniSTS:515126

L18426 (e-PCR)
- UniSTS:34648

D1S2649 (e-PCR), detects polymorphism
- UniSTS:65711

HSC1CA092 (e-PCR)
- UniSTS:17105

Homology

Homologs of the ARID4B gene: The ARID4B gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 479 organisms have orthologs with human gene ARID4B
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription cis-regulatory region binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in establishment of Sertoli cell barrier	IEA Inferred from Electronic Annotation more info
involved_in histone H3-K9 trimethylation	IEA Inferred from Electronic Annotation more info
involved_in histone H4-K20 trimethylation	IEA Inferred from Electronic Annotation more info
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 gene expression by genomic imprinting	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	PubMed
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 complex	NAS Non-traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in mitochondrion	IDA Inferred from Direct Assay more info
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	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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

Names: 180 kDa Sin3-associated polypeptide; ARID domain-containing protein 4B; AT rich interactive domain 4B (RBP1-like); Rb-binding protein homolog; SIN3A-associated protein 180; breast cancer-associated antigen 1; breast cancer-associated antigen BRCAA1; breast carcinoma-associated antigen; histone deacetylase complex subunit SAP180; retinoblastoma-binding protein 1-like 1; sin3-associated polypeptide p180

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_029484.1 RefSeqGene

Range

5039..166316

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001206794.2 → NP_001193723.1 AT-rich interactive domain-containing protein 4B isoform 1

See identical proteins and their annotated locations for NP_001193723.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1 and 3 encode the same protein (isoform 1).

Source sequence(s)

AB210032, AF208045, AL391994

Consensus CDS

CCDS31061.1

UniProtKB/Swiss-Prot

Q4LE39, Q9Y6E1

UniProtKB/TrEMBL

A0A024R3R1

Related

ENSP00000355562.2, ENST00000366603.6

Conserved Domains (4) summary

smart00333
Location:58 → 113

TUDOR; Tudor domain

smart01014
Location:311 → 394

ARID; ARID/BRIGHT DNA binding domain

pfam08169
Location:170 → 262

RBB1NT; RBB1NT (NUC162) domain

pfam11717
Location:571 → 624

Tudor-knot; RNA binding activity-knot of a chromodomain
NM_016374.6 → NP_057458.4 AT-rich interactive domain-containing protein 4B isoform 1

See identical proteins and their annotated locations for NP_057458.4

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 3 encode the same isoform.

Source sequence(s)

AB210032, AL133418, AL391994

Consensus CDS

CCDS31061.1

UniProtKB/Swiss-Prot

Q4LE39, Q9Y6E1

UniProtKB/TrEMBL

A0A024R3R1

Related

ENSP00000264183.3, ENST00000264183.9

Conserved Domains (4) summary

smart00333
Location:58 → 113

TUDOR; Tudor domain

smart01014
Location:311 → 394

ARID; ARID/BRIGHT DNA binding domain

pfam08169
Location:170 → 262

RBB1NT; RBB1NT (NUC162) domain

pfam11717
Location:571 → 624

Tudor-knot; RNA binding activity-knot of a chromodomain
NM_031371.4 → NP_112739.2 AT-rich interactive domain-containing protein 4B isoform 2

See identical proteins and their annotated locations for NP_112739.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1 but maintains the reading frame. The resulting protein (isoform 2) is shorter than isoform 1.

Source sequence(s)

AB210032, AL133418, AL391994, BC048959

Consensus CDS

CCDS31060.1

UniProtKB/Swiss-Prot

Q4LE39

Related

ENSP00000264184.4, ENST00000349213.7

Conserved Domains (4) summary

smart00333
Location:58 → 113

TUDOR; Tudor domain

smart01014
Location:311 → 394

ARID; ARID/BRIGHT DNA binding domain

pfam08169
Location:173 → 262

RBB1NT; RBB1NT (NUC162) domain

cl26761
Location:451 → 728

MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

RNA

NR_135074.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB210032, AY220790, BC130418, CB048003, DB100845

Related

ENST00000421364.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

235166902..235328179 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024447626.2 → XP_024303394.1 AT-rich interactive domain-containing protein 4B isoform X3

Conserved Domains (4) summary

smart00333
Location:58 → 113

TUDOR; Tudor domain

smart01014
Location:311 → 394

ARID; ARID/BRIGHT DNA binding domain

pfam08169
Location:173 → 262

RBB1NT; RBB1NT (NUC162) domain

cl26761
Location:451 → 728

MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
XM_047422531.1 → XP_047278487.1 AT-rich interactive domain-containing protein 4B isoform X2
XM_011544212.4 → XP_011542514.1 AT-rich interactive domain-containing protein 4B isoform X1

See identical proteins and their annotated locations for XP_011542514.1

UniProtKB/Swiss-Prot

Q4LE39, Q9Y6E1

UniProtKB/TrEMBL

A0A024R3R1

Conserved Domains (4) summary

smart00333
Location:58 → 113

TUDOR; Tudor domain

smart01014
Location:311 → 394

ARID; ARID/BRIGHT DNA binding domain

pfam08169
Location:170 → 262

RBB1NT; RBB1NT (NUC162) domain

pfam11717
Location:571 → 624

Tudor-knot; RNA binding activity-knot of a chromodomain
XM_006711781.4 → XP_006711844.1 AT-rich interactive domain-containing protein 4B isoform X2

Conserved Domains (3) summary

smart00333
Location:58 → 113

TUDOR; Tudor domain

smart01014
Location:311 → 394

ARID; ARID/BRIGHT DNA binding domain

pfam08169
Location:170 → 262

RBB1NT; RBB1NT (NUC162) domain
XM_017001472.2 → XP_016856961.1 AT-rich interactive domain-containing protein 4B isoform X5

Conserved Domains (2) summary

smart01014
Location:14 → 101

ARID; ARID/BRIGHT DNA binding domain

pfam11717
Location:278 → 331

Tudor-knot; RNA binding activity-knot of a chromodomain
XM_047422533.1 → XP_047278489.1 AT-rich interactive domain-containing protein 4B isoform X6
XM_047422532.1 → XP_047278488.1 AT-rich interactive domain-containing protein 4B isoform X4

Related

ENST00000491632.5

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

234558607..234719910 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054337003.1 → XP_054192978.1 AT-rich interactive domain-containing protein 4B isoform X3
XM_054337002.1 → XP_054192977.1 AT-rich interactive domain-containing protein 4B isoform X2
XM_054337000.1 → XP_054192975.1 AT-rich interactive domain-containing protein 4B isoform X1
XM_054337001.1 → XP_054192976.1 AT-rich interactive domain-containing protein 4B isoform X2
XM_054337005.1 → XP_054192980.1 AT-rich interactive domain-containing protein 4B isoform X5
XM_054337006.1 → XP_054192981.1 AT-rich interactive domain-containing protein 4B isoform X6
XM_054337004.1 → XP_054192979.1 AT-rich interactive domain-containing protein 4B isoform X4