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ARID3B AT-rich interaction domain 3B [ Homo sapiens (human) ]

Gene ID: 10620, updated on 27-Nov-2024

Summary

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Official Symbol
ARID3Bprovided by HGNC
Official Full Name
AT-rich interaction domain 3Bprovided by HGNC
Primary source
HGNC:HGNC:14350
See related
Ensembl:ENSG00000179361 MIM:612457; AllianceGenome:HGNC:14350
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
BDP; DRIL2
Summary
This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA-binding proteins. The encoded protein is homologous with two proteins that bind to the retinoblastoma gene product, and also with the mouse Bright and Drosophila dead ringer proteins. A pseudogene on chromosome 1p31 exists for this gene. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and possibly in chromatin structure modification. [provided by RefSeq, Jul 2008]
Expression
Broad expression in testis (RPKM 16.7), placenta (RPKM 10.6) and 19 other tissues See more
Orthologs
mouse all
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Genomic context

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See ARID3B in Genome Data Viewer
Location:
15q24.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (74541220..74598131)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72408943..72468032)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74833561..74890472)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9779 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9780 Neighboring gene MPRA-validated peak2387 silencer Neighboring gene uncharacterized LOC124903528 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74832881-74833422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6652 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:74834323-74834507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9783 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:74838363-74838905 Neighboring gene VISTA enhancer hs1510 Neighboring gene uncharacterized LOC124903527 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74880397-74881182 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74881183-74881968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74886857-74887357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74889350-74889850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74890466-74891354 Neighboring gene uncharacterized LOC102723750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6654 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74908320-74908931 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74908932-74909542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74921666-74922166 Neighboring gene CDC like kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9787 Neighboring gene enhancer of mRNA decapping 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9788

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. ARID3B: a Novel Regulator of the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle. Wood JJ, et al. J Virol, 2016 Oct 15. PMID 27512077, Free PMC Article
  2. Genotype-Based Gene Expression in Colon Tissue-Prediction Accuracy and Relationship with the Prognosis of Colorectal Cancer Patients. Deutelmoser H, et al. Int J Mol Sci, 2020 Oct 31. PMID 33142733, Free PMC Article
  3. ARID3B increases ovarian tumor burden and is associated with a cancer stem cell gene signature. Roy L, et al. Oncotarget, 2014 Sep 30. PMID 25327563, Free PMC Article
  4. ARID3B expression in primary breast cancers and breast cancer-derived cell lines. Oguz Erdogan AS, et al. Cell Oncol (Dordr), 2014 Aug. PMID 25120063
  5. ARID3B induces tumor necrosis factor alpha mediated apoptosis while a novel ARID3B splice form does not induce cell death. Joseph S, et al. PLoS One, 2012. PMID 22860069, Free PMC Article

See all (77) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Distinct and overlapping roles of ARID3A and ARID3B in regulating E2Fdependent transcription via direct binding to E2F target genes.
    Title: Distinct and overlapping roles of ARID3A and ARID3B in regulating E2F‑dependent transcription via direct binding to E2F target genes.
  2. Harnessing stemness and PD-L1 expression by AT-rich interaction domain-containing protein 3B in colorectal cancer.
    Title: Harnessing stemness and PD-L1 expression by AT-rich interaction domain-containing protein 3B in colorectal cancer.
  3. Genotype-Based Gene Expression in Colon Tissue-Prediction Accuracy and Relationship with the Prognosis of Colorectal Cancer Patients.
    Title: Genotype-Based Gene Expression in Colon Tissue-Prediction Accuracy and Relationship with the Prognosis of Colorectal Cancer Patients.
  4. Knockout of LIN28A and LIN28B in ACH-3P cells not only significantly increased amounts of let-7 miRNAs but also led to significant reduction in ARID3B-complex proteins, potentially because of increased targeting by let-7 miRNAs.
    Title: LIN28-let-7 axis regulates genes in immortalized human trophoblast cells by targeting the ARID3B-complex.
  5. Study provides a comprehensive list of genes and pathways regulated by ARID3A and ARID3B in ovarian cancer cells.
    Title: ARID3A and ARID3B induce stem promoting pathways in ovarian cancer cells.
  6. A novel cellular protein (AT-rich interacting domain protein 3B [ARID3B]) that we show is able to temper lytic reactivation.
    Title: ARID3B: a Novel Regulator of the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle.
  7. Data indicate that the most prominent proteins associating with Gab2 are PTPN11, PIK3R1 and ARID3B.
    Title: Changes in Gab2 phosphorylation and interaction partners in response to interleukin (IL)-2 stimulation in T-lymphocytes.
  8. Although ARID3B and ARID3A share overlapping functions, ARID3B play a key role in the expression of pro-apoptotic p53-target genes and apoptosis.
    Title: Critical role of ARID3B in the expression of pro-apoptotic p53-target genes and apoptosis.
  9. ARID3B boosts production CD133+ tumor stem cells and increases ovarian cancer progression in vivo.
    Title: ARID3B increases ovarian tumor burden and is associated with a cancer stem cell gene signature.
  10. Data report a positive correlation between ER positivity and nuclear ARID3B expression in primary breast cancers, along with a negative correlation with the ERBB2 status.
    Title: ARID3B expression in primary breast cancers and breast cancer-derived cell lines.
Submit: New GeneRIF Correction See all GeneRIFs (16)

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

EBI GWAS Catalog

Description
Genome-wide association study identifies eight loci associated with blood pressure.
EBI GWAS Catalog

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
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
  
Component Evidence Code Pubs
located_in nucleoplasm IDA
Inferred from Direct Assay
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 

General protein information

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Preferred Names
AT-rich interactive domain-containing protein 3B
Names
ARID domain-containing protein 3B
AT rich interactive domain 3B (BRIGHT- like)
Bright-derived protein
bright and dead ringer protein
bright-like protein

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.

mRNA and Protein(s)

  1. NM_001307939.2 → NP_001294868.1  AT-rich interactive domain-containing protein 3B isoform 1

    See identical proteins and their annotated locations for NP_001294868.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC100835, AF116846, BC041792, DC396899
    Consensus CDS
    CCDS76777.1
    UniProtKB/Swiss-Prot
    O95443, Q59HC9, Q6P9C9, Q8IVW6
    UniProtKB/TrEMBL
    B4DQB0
    Related
    ENSP00000477878.1, ENST00000622429.1
    Conserved Domains (1) summary
    smart00501
    Location:216 → 305
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

  2. NM_006465.4 → NP_006456.1  AT-rich interactive domain-containing protein 3B isoform 2

    See identical proteins and their annotated locations for NP_006456.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.
    Source sequence(s)
    AC100835, AF116846, DC396899
    Consensus CDS
    CCDS10264.1
    UniProtKB/TrEMBL
    B4DQB0
    Related
    ENSP00000343126.5, ENST00000346246.10
    Conserved Domains (1) summary
    smart00501
    Location:216 → 305
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

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

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    74541220..74598131
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_007064418.1 RNA Sequence

  2. XR_007064419.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    72408943..72468032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_008488912.1 RNA Sequence

  2. XR_008488913.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IVW6.2 GenPept UniProtKB/Swiss-Prot:Q8IVW6

Gene LinkOut

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