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Arb2a ARB2 cotranscriptional regulator A [ Mus musculus (house mouse) ]

Gene ID: 68675, updated on 21-Apr-2024

Summary

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Official Symbol
Arb2aprovided by MGI
Official Full Name
ARB2 cotranscriptional regulator Aprovided by MGI
Primary source
MGI:MGI:1915925
See related
Ensembl:ENSMUSG00000064138 AllianceGenome:MGI:1915925
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
53-E6; pEN87; Fam172a; 1110033M05Rik; 2610318O14Rik; 9430037D06Rik
Summary
Predicted to contribute to siRNA binding activity. Involved in neural crest cell development and regulation of alternative mRNA splicing, via spliceosome. Located in endoplasmic reticulum and nucleus. Is expressed in telencephalon ventricular layer. Orthologous to human FAM172A (family with sequence similarity 172 member A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E14 (RPKM 5.4), CNS E11.5 (RPKM 5.0) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
13 C1; 13 41.29 cM
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 13 NC_000079.7 (77856799..78314359)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (77708677..78166240)

Chromosome 13 - NC_000079.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_35071 Neighboring gene ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1, pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E11549 Neighboring gene predicted gene, 26088 Neighboring gene STARR-seq mESC enhancer starr_35072 Neighboring gene STARR-seq mESC enhancer starr_35073 Neighboring gene POU domain class 5, transcription factor 2 Neighboring gene STARR-seq mESC enhancer starr_35075 Neighboring gene ATPase, H+ transporting, lysosomal V1 subunit A pseudogene Neighboring gene STARR-seq mESC enhancer starr_35076 Neighboring gene RIKEN cDNA 3110006O06 gene Neighboring gene predicted gene, 38604 Neighboring gene RIKEN cDNA A830082K12 gene Neighboring gene nuclear receptor subfamily 2, group F, member 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Gene trap insertional mutagenesis in mice: new vectors and germ line mutations in two novel genes. Neilan EG, et al. Transgenic Res, 1999. PMID 10767988
  2. CHARGE syndrome-associated proteins FAM172A and CHD7 influence male sex determination and differentiation through transcriptional and alternative splicing mechanisms. Bélanger C, et al. FASEB J, 2022 Mar. PMID 35129866, Free PMC Article
  3. Dysregulation of cotranscriptional alternative splicing underlies CHARGE syndrome. Bélanger C, et al. Proc Natl Acad Sci U S A, 2018 Jan 23. PMID 29311329, Free PMC Article
  4. Characterization of an exchangeable gene trap using pU-17 carrying a stop codon-beta geo cassette. Taniwaki T, et al. Dev Growth Differ, 2005 Apr. PMID 15840001
  5. Exchangeable gene trap using the Cre/mutated lox system. Araki K, et al. Cell Mol Biol (Noisy-le-grand), 1999 Jul. PMID 10512203

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CHARGE syndrome-associated proteins FAM172A and CHD7 influence male sex determination and differentiation through transcriptional and alternative splicing mechanisms.
    Title: CHARGE syndrome-associated proteins FAM172A and CHD7 influence male sex determination and differentiation through transcriptional and alternative splicing mechanisms.
  2. key role in the regulation of cotranscriptional alternative splicing in CHARGE syndrome model
    Title: Dysregulation of cotranscriptional alternative splicing underlies CHARGE syndrome.
Submit: New GeneRIF Correction

Variation

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Alleles

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

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
contributes_to siRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in neural crest cell development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of alternative mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulatory ncRNA-mediated heterochromatin formation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
cotranscriptional regulator ARB2A
Names
cotranscriptional regulator FAM172A
family with sequence similarity 172, member A
protein FAM172A

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_001163419.1 → NP_001156891.1  cotranscriptional regulator ARB2A isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon and uses a downstream start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC167171, AW060304, BC057380
    Consensus CDS
    CCDS49318.1
    UniProtKB/TrEMBL
    E9QMA2, Q6PFX1
    Related
    ENSMUSP00000089038.5, ENSMUST00000091459.12
    Conserved Domains (1) summary
    pfam09757
    Location:32 → 184
    Arb2; Arb2 domain

  2. NM_001163420.1 → NP_001156892.1  cotranscriptional regulator ARB2A isoform 3

    See identical proteins and their annotated locations for NP_001156892.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two alternate exons and uses a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus and lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AC154548, AC154584, AC167171, AW060304, CT025642
    Consensus CDS
    CCDS49319.1
    UniProtKB/Swiss-Prot
    Q3TNH5
    Related
    ENSMUSP00000096960.4, ENSMUST00000099358.5
    Conserved Domains (1) summary
    pfam09757
    Location:32 → 120
    Arb2; Arb2 domain

  3. NM_138312.1 → NP_612185.1  cotranscriptional regulator ARB2A isoform 1 precursor

    See identical proteins and their annotated locations for NP_612185.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC154548, AC154584, AC167171, AW060304, CT025642
    Consensus CDS
    CCDS49317.1
    UniProtKB/Swiss-Prot
    Q3TLW0, Q3TNH5
    UniProtKB/TrEMBL
    Q6PFX1
    Related
    ENSMUSP00000133140.2, ENSMUST00000163257.9
    Conserved Domains (1) summary
    pfam09757
    Location:78 → 230
    Arb2; Arb2 domain

RNA

  1. NR_028109.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks one alternate exon and includes an additional exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC167171, AK165273, AW060304, BC057380

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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
    77856799..78314359
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006517352.4 → XP_006517415.1  cotranscriptional regulator ARB2A isoform X1

    UniProtKB/TrEMBL
    Q9Z106
    Conserved Domains (1) summary
    pfam09757
    Location:290 → 339
    Arb2; Arb2 domain

  2. XM_017315582.3 → XP_017171071.1  cotranscriptional regulator ARB2A isoform X8

  3. XM_036158146.1 → XP_036014039.1  cotranscriptional regulator ARB2A isoform X9

  4. XM_006517353.5 → XP_006517416.1  cotranscriptional regulator ARB2A isoform X2

    UniProtKB/TrEMBL
    Q6PFX1

  5. XM_006517355.5 → XP_006517418.1  cotranscriptional regulator ARB2A isoform X4

    Conserved Domains (1) summary
    pfam09757
    Location:204 → 253
    Arb2; Arb2 domain

  6. XM_017315581.3 → XP_017171070.1  cotranscriptional regulator ARB2A isoform X5

    Conserved Domains (1) summary
    pfam09757
    Location:171 → 220
    Arb2; Arb2 domain

  7. XM_030247391.2 → XP_030103251.1  cotranscriptional regulator ARB2A isoform X3

    UniProtKB/TrEMBL
    Q6PFX1

  8. XM_030247392.2 → XP_030103252.1  cotranscriptional regulator ARB2A isoform X7

  9. XM_036158145.1 → XP_036014038.1  cotranscriptional regulator ARB2A isoform X6

  10. XM_036158144.1 → XP_036014037.1  cotranscriptional regulator ARB2A isoform X5

    Conserved Domains (1) summary
    pfam09757
    Location:171 → 220
    Arb2; Arb2 domain

RNA

  1. XR_001780804.3 RNA Sequence

    Related
    ENSMUST00000224217.2

  2. XR_003950473.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q3TNH5.2 GenPept UniProtKB/Swiss-Prot:Q3TNH5

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