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    crnkl1 crooked neck pre-mRNA splicing factor 1 [ Danio rerio (zebrafish) ]

    Gene ID: 393920, updated on 27-Mar-2024

    Summary

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    Official Symbol
    crnkl1provided by ZNC
    Official Full Name
    crooked neck pre-mRNA splicing factor 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-694
    See related
    Ensembl:ENSDARG00000007901 AllianceGenome:ZFIN:ZDB-GENE-040426-694
    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:55327
    Summary
    Predicted to be involved in spliceosomal complex assembly. 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. Human ortholog(s) of this gene implicated in basal cell carcinoma. Orthologous to human CRNKL1 (crooked neck pre-mRNA splicing factor 1). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See crnkl1 in Genome Data Viewer
    Location:
    chromosome: 20
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 20 NC_007131.7 (49081967..49103320)
    105 previous assembly GRCz10 (GCF_000002035.5) 20 NC_007131.6 (49274034..49293902)

    Chromosome 20 - NC_007131.7Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 61 Neighboring gene 5'-3' exoribonuclease 2 Neighboring gene uncharacterized LOC110438201 Neighboring gene uncharacterized LOC110438204 Neighboring gene microRNA mir-2193 Neighboring gene N-alpha-acetyltransferase 20, NatB catalytic subunit Neighboring gene CD109 molecule

    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. Rbfox-regulated alternative splicing is critical for zebrafish cardiac and skeletal muscle functions. Gallagher TL, et al. Dev Biol, 2011 Nov 15. PMID 21925157, Free PMC Article
    2. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    3. 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
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
    5. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC55327

    Gene Ontology Provided by ZFIN

    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA 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
    		  
    involved_in spliceosomal complex assembly IBA
    Inferred from Biological aspect of Ancestor
    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
    		  

    General protein information

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    Preferred Names
    crooked neck-like protein 1
    Names
    crooked neck pre-mRNA splicing factor-like 1

    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_200946.1 → NP_957240.1  crooked neck-like protein 1

      See identical proteins and their annotated locations for NP_957240.1

      Status: PROVISIONAL

      Source sequence(s)
      BC044369
      UniProtKB/TrEMBL
      A0A8M1PFB6, E7FGM7, Q803R7
      Related
      ENSDARP00000100660.3, ENSDART00000112689.4
      Conserved Domains (4) summary
      pfam02184
      Location:195 → 226
      HAT; HAT (Half-A-TPR) repeat
      smart00386
      Location:94 → 126
      HAT; HAT (Half-A-TPR) repeats
      sd00006
      Location:83 → 108
      TPR; TPR repeat [structural motif]
      pfam05843
      Location:231 → 321
      Suf; Suppressor of forked protein (Suf)

    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_007131.7 Reference GRCz11 Primary Assembly

      Range
      49081967..49103320
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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