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

Gene ID: 245976, updated on 2-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 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
  

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

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