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    xab2 XPA binding protein 2 [ Danio rerio (zebrafish) ]

    Gene ID: 387600, updated on 25-Apr-2024

    Summary

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    Official Symbol
    xab2provided by ZNC
    Official Full Name
    XPA binding protein 2provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-685
    See related
    Ensembl:ENSDARG00000007092 AllianceGenome:ZFIN:ZDB-GENE-040426-685
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    zgc:63498; zgc:63949
    Summary
    Predicted to be involved in generation of catalytic spliceosome for first transesterification step. Predicted to act upstream of or within RNA processing. 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, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See xab2 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (53317040..53350547)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (53062377..53095884)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene syntaxin binding protein 2 Neighboring gene uncharacterized LOC556170 Neighboring gene calmodulin regulated spectrin-associated protein family, member 3 Neighboring gene nuclear receptor subfamily 5, group A, member 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Cellular responses to ionizing radiation change quickly over time during early development in zebrafish. Honjo Y, et al. Cell Biol Int, 2019 May. PMID 30791195, Free PMC Article
    2. BTLA-HVEM Checkpoint Axis Regulates Hepatic Homeostasis and Inflammation in a ConA-Induced Hepatitis Model in Zebrafish. Shi W, et al. J Immunol, 2019 Nov 1. PMID 31562209
    3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC198247

    Gene Ontology Provided by ZFIN

    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in generation of catalytic spliceosome for first transesterification step IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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

    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_001044783.1 → NP_001038248.1  pre-mRNA-splicing factor SYF1

      See identical proteins and their annotated locations for NP_001038248.1

      Status: PROVISIONAL

      Source sequence(s)
      BX005479
      UniProtKB/TrEMBL
      B7ZVB1, Q1LY92
      Related
      ENSDARP00000010070.4, ENSDART00000011780.5
      Conserved Domains (4) summary
      TIGR02521
      Location:427 → 613
      type_IV_pilW; type IV pilus biogenesis/stability protein PilW
      sd00006
      Location:384 → 419
      TPR; TPR repeat [structural motif]
      pfam08424
      Location:25 → 135
      NRDE-2; NRDE-2, necessary for RNA interference
      pfam13424
      Location:391 → 457
      TPR_12; Tetratricopeptide repeat

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007114.7 Reference GRCz11 Primary Assembly

      Range
      53317040..53350547
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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