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

Gene ID: 51742, updated on 1-Aug-2020

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
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

Genomic context

See ARID4B in Genome Data Viewer
Location:
1q42.3
Exon count:
28
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (235166895..235328224, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (235330210..235491532, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379283 Neighboring gene translocase of outer mitochondrial membrane 20 Neighboring gene small nucleolar RNA, H/ACA box 14B Neighboring gene RNA binding motif protein 34 Neighboring gene microRNA 4753 Neighboring gene ribosomal protein L23a pseudogene 23 Neighboring gene geranylgeranyl diphosphate synthase 1 Neighboring gene atrophin 1 pseudogene Neighboring gene tubulin folding cofactor E Neighboring gene ribosomal protein S21 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC163290, DKFZp313M2420

Gene Ontology Provided by GOA

Function Evidence Code Pubs
molecular_function ND
No biological Data available
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
biological_process ND
No biological Data available
more info
 
establishment of Sertoli cell barrier IEA
Inferred from Electronic Annotation
more info
 
histone H3-K9 trimethylation IEA
Inferred from Electronic Annotation
more info
 
histone H4-K20 trimethylation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression by genetic imprinting IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cellular_component ND
No biological Data available
more info
 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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)

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

  1. NG_029484.1 RefSeqGene

    Range
    5039..166316
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206794.1NP_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, AI431949, AL391994
    Consensus CDS
    CCDS31061.1
    UniProtKB/Swiss-Prot
    Q4LE39
    UniProtKB/TrEMBL
    A0A024R3R1
    Related
    ENSP00000355562.2, ENST00000366603.6
    Conserved Domains (4) summary
    smart00333
    Location:58113
    TUDOR; Tudor domain
    smart01014
    Location:311394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:170262
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:571624
    Tudor-knot; RNA binding activity-knot of a chromodomain
  2. NM_016374.6NP_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
    UniProtKB/TrEMBL
    A0A024R3R1
    Related
    ENSP00000264183.3, ENST00000264183.9
    Conserved Domains (4) summary
    smart00333
    Location:58113
    TUDOR; Tudor domain
    smart01014
    Location:311394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:170262
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:571624
    Tudor-knot; RNA binding activity-knot of a chromodomain
  3. NM_031371.4NP_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:58113
    TUDOR; Tudor domain
    smart01014
    Location:311394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:173262
    RBB1NT; RBB1NT (NUC162) domain
    cl26761
    Location:451728
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

RNA

  1. 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: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    235166895..235328224 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011544212.3XP_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
    UniProtKB/TrEMBL
    A0A024R3R1
    Conserved Domains (4) summary
    smart00333
    Location:58113
    TUDOR; Tudor domain
    smart01014
    Location:311394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:170262
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:571624
    Tudor-knot; RNA binding activity-knot of a chromodomain
  2. XM_024447626.1XP_024303394.1  AT-rich interactive domain-containing protein 4B isoform X3

    Conserved Domains (4) summary
    smart00333
    Location:58113
    TUDOR; Tudor domain
    smart01014
    Location:311394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:173262
    RBB1NT; RBB1NT (NUC162) domain
    cl26761
    Location:451728
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
  3. XM_006711781.3XP_006711844.1  AT-rich interactive domain-containing protein 4B isoform X2

    Conserved Domains (3) summary
    smart00333
    Location:58113
    TUDOR; Tudor domain
    smart01014
    Location:311394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:170262
    RBB1NT; RBB1NT (NUC162) domain
  4. XM_017001472.1XP_016856961.1  AT-rich interactive domain-containing protein 4B isoform X5

    Conserved Domains (2) summary
    smart01014
    Location:14101
    ARID; ARID/BRIGHT DNA binding domain
    pfam11717
    Location:278331
    Tudor-knot; RNA binding activity-knot of a chromodomain
  5. XM_024447628.1XP_024303396.1  AT-rich interactive domain-containing protein 4B isoform X4

    Related
    ENST00000491632.5
    Conserved Domains (4) summary
    smart00333
    Location:58113
    TUDOR; Tudor domain
    smart01014
    Location:311394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:173262
    RBB1NT; RBB1NT (NUC162) domain
    cl26761
    Location:451728
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

RNA

  1. XR_002956802.1 RNA Sequence

  2. XR_001737227.2 RNA Sequence

  3. XR_001737226.2 RNA Sequence

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