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    Xab2 XPA binding protein 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 245976, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Xab2provided by RGD
    Official Full Name
    XPA binding protein 2provided by RGD
    Primary source
    RGD:621217
    See related
    EnsemblRapid:ENSRNOG00000000988 AllianceGenome:RGD:621217
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Ath55
    Summary
    Involved in cerebral cortex development. Predicted to be located in nucleoplasm. Predicted to be part of Prp19 complex; U2-type catalytic step 2 spliceosome; and post-mRNA release spliceosomal complex. Orthologous to human XAB2 (XPA binding protein 2). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 124.4), Spleen (RPKM 108.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Xab2 in Genome Data Viewer
    Location:
    12p12
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (6465569..6477616, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (1667672..1679702, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (2158391..2170397, complement)

    Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120095868 Neighboring gene patatin-like phospholipase domain containing 6 Neighboring gene calmodulin regulated spectrin-associated protein family, member 3 Neighboring gene uncharacterized LOC103690858 Neighboring gene PET100 cytochrome c oxidase chaperone Neighboring gene Purkinje cell protein 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Disruption of mouse XAB2 gene involved in pre-mRNA splicing, transcription and transcription-coupled DNA repair results in preimplantation lethality. Yonemasu R, et al. DNA Repair (Amst), 2005 Apr 4. PMID 15725628
    2. A novel rat orthologue and homologue for the Drosophila crooked neck gene in neural stem cells and their immediate descendants. Amada N, et al. J Biochem, 2003 May. PMID 12801913
    3. XAB2, a novel tetratricopeptide repeat protein involved in transcription-coupled DNA repair and transcription. Nakatsu Y, et al. J Biol Chem, 2000 Nov 10. PMID 10944529
    4. Nucleotide excision repair: new tricks with old bricks. Kamileri I, et al. Trends Genet, 2012 Nov. PMID 22824526
    5. Splicing and beyond: the many faces of the Prp19 complex. Chanarat S, et al. Biochim Biophys Acta, 2013 Oct. PMID 23742842

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in blastocyst development IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within blastocyst development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cerebral cortex development IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in generation of catalytic spliceosome for first transesterification step IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in transcription-coupled nucleotide-excision repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription-coupled nucleotide-excision repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in transcription-coupled nucleotide-excision repair ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Prp19 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type catalytic step 2 spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of U2-type catalytic step 2 spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U2-type catalytic step 2 spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of catalytic step 2 spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of post-mRNA release spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    pre-mRNA-splicing factor SYF1
    Names
    adapter protein ATH-55

    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_139109.2 → NP_620809.1  pre-mRNA-splicing factor SYF1

      See identical proteins and their annotated locations for NP_620809.1

      Status: PROVISIONAL

      Source sequence(s)
      AF277899
      UniProtKB/Swiss-Prot
      Q99PK0
      UniProtKB/TrEMBL
      A0A8L2PZV6, A6KQ13
      Related
      ENSRNOP00000001309.4, ENSRNOT00000001309.6
      Conserved Domains (2) summary
      COG0457
      Location:272 → 549
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:389 → 424
      TPR; TPR repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086030.1 Reference GRCr8

      Range
      6465569..6477616 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039089058.2 → XP_038944986.1  pre-mRNA-splicing factor SYF1 isoform X1

      UniProtKB/TrEMBL
      A0A8I5XWU2, A6KQ14
      Conserved Domains (2) summary
      COG0457
      Location:167 → 444
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:284 → 319
      TPR; TPR repeat [structural motif]
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99PK0.1 GenPept UniProtKB/Swiss-Prot:Q99PK0

    Gene LinkOut

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

    Chemical Information
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