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Arid4b AT rich interactive domain 4B (RBP1-like) [ Mus musculus (house mouse) ]

Gene ID: 94246, updated on 8-Dec-2022

Summary

Official Symbol
Arid4bprovided by MGI
Official Full Name
AT rich interactive domain 4B (RBP1-like)provided by MGI
Primary source
MGI:MGI:2137512
See related
Ensembl:ENSMUSG00000039219 AllianceGenome:MGI:2137512
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
BCAA; BRCAA1; Rbp1l1; SAP180; RBBP1L1
Summary
Predicted to enable transcription cis-regulatory region binding activity. Acts upstream of or within several processes, including establishment of Sertoli cell barrier; peptidyl-lysine trimethylation; and regulation of gene expression. Predicted to be located in cytosol; mitochondrion; and nucleoplasm. Predicted to be active in nucleus. Is expressed in testis. Orthologous to human ARID4B (AT-rich interaction domain 4B). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 10.1), CNS E14 (RPKM 7.3) and 26 other tissues See more
Orthologs
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Genomic context

See Arid4b in Genome Data Viewer
Location:
13 A1; 13 5.29 cM
Exon count:
27
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 13 NC_000079.7 (14238334..14374188)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (14063609..14199603)

Chromosome 13 - NC_000079.7Genomic Context describing neighboring genes Neighboring gene UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 2 Neighboring gene tubulin-specific chaperone E Neighboring gene geranylgeranyl diphosphate synthase 1 Neighboring gene predicted gene, 26129 Neighboring gene zinc finger and SCAN domain containing 5B pseudogene Neighboring gene HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 Neighboring gene predicted gene, 30893

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (4)  1 citation
  • Endonuclease-mediated (2) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • 5930400I17, 6330417L24Rik, 6720480E17Rik

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
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
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within establishment of Sertoli cell barrier IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within histone H3-K9 trimethylation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within histone H4-K20 trimethylation IGI
Inferred from Genetic Interaction
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 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of gene expression by genomic imprinting IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within spermatogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
part_of Sin3 complex NAS
Non-traceable Author Statement
more info
PubMed 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in mitochondrion ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
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

Preferred Names
AT-rich interactive domain-containing protein 4B
Names
180 kDa Sin3-associated polypeptide
ARID domain-containing protein 4B
breast cancer-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.

mRNA and Protein(s)

  1. NM_194262.2NP_919238.1  AT-rich interactive domain-containing protein 4B isoform 1

    See identical proteins and their annotated locations for NP_919238.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK034400, AK041414, BC137783, BY720039
    Consensus CDS
    CCDS36599.1
    UniProtKB/Swiss-Prot
    A2CG63, Q8BYA5
    Related
    ENSMUSP00000106163.2, ENSMUST00000110534.8
    Conserved Domains (4) summary
    smart00333
    Location:58113
    TUDOR; Tudor domain
    cd16883
    Location:308399
    ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
    pfam08169
    Location:168263
    RBB1NT; RBB1NT (NUC162) domain
    cl28914
    Location:573630
    CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains
  2. NM_198122.2NP_937755.1  AT-rich interactive domain-containing protein 4B isoform 2

    See identical proteins and their annotated locations for NP_937755.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AK034400, AK041414, BC137783, BY720039
    Consensus CDS
    CCDS36600.1
    UniProtKB/Swiss-Prot
    A2CG63
    Related
    ENSMUSP00000043889.9, ENSMUST00000039538.15
    Conserved Domains (3) summary
    smart00333
    Location:58113
    TUDOR; Tudor domain
    smart01014
    Location:311394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:169262
    RBB1NT; RBB1NT (NUC162) domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000079.7 Reference GRCm39 C57BL/6J

    Range
    14238334..14374188
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006516808.4XP_006516871.1  AT-rich interactive domain-containing protein 4B isoform X2

    Conserved Domains (4) summary
    cd16883
    Location:308399
    ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
    pfam08169
    Location:168263
    RBB1NT; RBB1NT (NUC162) domain
    cd20460
    Location:161
    Tudor_ARID4B_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
    cd20462
    Location:62118
    Tudor_ARID4B_rpt2; second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
  2. XM_006516806.4XP_006516869.1  AT-rich interactive domain-containing protein 4B isoform X1

    See identical proteins and their annotated locations for XP_006516869.1

    UniProtKB/Swiss-Prot
    A2CG63, Q8BYA5
    Conserved Domains (4) summary
    smart00333
    Location:58113
    TUDOR; Tudor domain
    cd16883
    Location:308399
    ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
    pfam08169
    Location:168263
    RBB1NT; RBB1NT (NUC162) domain
    cl28914
    Location:573630
    CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains
  3. XM_036158231.1XP_036014124.1  AT-rich interactive domain-containing protein 4B isoform X2

    Conserved Domains (4) summary
    cd16883
    Location:308399
    ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
    pfam08169
    Location:168263
    RBB1NT; RBB1NT (NUC162) domain
    cd20460
    Location:161
    Tudor_ARID4B_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
    cd20462
    Location:62118
    Tudor_ARID4B_rpt2; second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
  4. XM_006516807.4XP_006516870.1  AT-rich interactive domain-containing protein 4B isoform X1

    See identical proteins and their annotated locations for XP_006516870.1

    UniProtKB/Swiss-Prot
    A2CG63, Q8BYA5
    Conserved Domains (4) summary
    smart00333
    Location:58113
    TUDOR; Tudor domain
    cd16883
    Location:308399
    ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
    pfam08169
    Location:168263
    RBB1NT; RBB1NT (NUC162) domain
    cl28914
    Location:573630
    CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains
  5. XM_030247479.2XP_030103339.1  AT-rich interactive domain-containing protein 4B isoform X3

    Conserved Domains (2) summary
    cl28902
    Location:180
    ARID; ARID/BRIGHT DNA binding domain family
    cl28914
    Location:254311
    CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains
  6. XM_030247480.2XP_030103340.1  AT-rich interactive domain-containing protein 4B isoform X4

    Conserved Domains (1) summary
    cl28902
    Location:180
    ARID; ARID/BRIGHT DNA binding domain family

RNA

  1. XR_003950495.2 RNA Sequence