U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

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

    Gene ID: 68675, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    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. Used to study CHARGE syndrome. Orthologous to human ARB2A (ARB2 cotranscriptional regulator A). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in CNS E14 (RPKM 5.4), CNS E11.5 (RPKM 5.0) and 28 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Arb2a in Genome Data Viewer
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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. The CHARGE syndrome-associated protein FAM172A controls AGO2 nuclear import. Sallis S, et al. Life Sci Alliance, 2023 Aug. PMID 37221016, Free PMC Article
    3. 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
    4. 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
    5. 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

    See all (21) 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

    Go to the top of the page Help

    Alleles

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

    General gene information

    Go to the top of the page Help

    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
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in 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

    Go to the top of the page Help
    Preferred Names
    cotranscriptional regulator ARB2A
    Names
    cotranscriptional regulator FAM172A
    family with sequence similarity 172, member A
    protein FAM172A

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools