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    Crnkl1 crooked neck pre-mRNA splicing factor 1 [ Mus musculus (house mouse) ]

    Gene ID: 66877, updated on 4-Jan-2025

    Summary

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    Official Symbol
    Crnkl1provided by MGI
    Official Full Name
    crooked neck pre-mRNA splicing factor 1provided by MGI
    Primary source
    MGI:MGI:1914127
    See related
    Ensembl:ENSMUSG00000001767 AllianceGenome:MGI:1914127
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    crn; 1200013P10Rik; 5730590A01Rik
    Summary
    Predicted to enable RNA binding activity. Predicted to be involved in spliceosomal complex assembly. Predicted to be located in nucleus. Predicted to be part of Prp19 complex; U2-type catalytic step 2 spliceosome; and post-mRNA release spliceosomal complex. Is expressed in several structures, including central nervous system and sensory organ. 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, Jan 2025]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 12.8), liver E14 (RPKM 8.1) and 24 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Crnkl1 in Genome Data Viewer
    Location:
    2 G1; 2 71.28 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (145759402..145776620, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (145917482..145934700, complement)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_05933 Neighboring gene STARR-positive B cell enhancer ABC_E8796 Neighboring gene predicted gene, 39954 Neighboring gene TM2 domain containing 1 pseudogene Neighboring gene N(alpha)-acetyltransferase 20, NatB catalytic subunit Neighboring gene STARR-positive B cell enhancer ABC_E5996 Neighboring gene STARR-positive B cell enhancer mm9_chr2:145783203-145783504 Neighboring gene cilia and flagella associated protein 61 Neighboring gene STARR-seq mESC enhancer starr_05934 Neighboring gene STARR-seq mESC enhancer starr_05935 Neighboring gene predicted gene, 34629 Neighboring gene STARR-seq mESC enhancer starr_05936 Neighboring gene insulinoma-associated 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Crooked neck is a component of the human spliceosome and implicated in the splicing process. Chung S, et al. Biochim Biophys Acta, 2002 Jul 19. PMID 12084575
    2. Interaction of U-box-type ubiquitin-protein ligases (E3s) with molecular chaperones. Hatakeyama S, et al. Genes Cells, 2004 Jun. PMID 15189447
    3. Microarray analysis of Foxa2 mutant mouse embryos reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives. Tamplin OJ, et al. BMC Genomics, 2008 Oct 30. PMID 18973680, Free PMC Article
    4. A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. McKee AE, et al. BMC Dev Biol, 2005 Jul 20. PMID 16033648, Free PMC Article
    5. Irisin Mediates Effects on Bone and Fat via αV Integrin Receptors. Kim H, et al. Cell, 2018 Dec 13. PMID 30550785, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    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 spliceosomal complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spliceosomal complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spliceosomal complex assembly ISS
    Inferred from Sequence or Structural Similarity
    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 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 nuclear speck IEA
    Inferred from Electronic Annotation
    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 ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    part_of spliceosomal complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    crooked neck-like protein 1
    Names
    Crn, crooked neck-like 1
    crooked neck homolog

    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_025820.3 → NP_080096.1  crooked neck-like protein 1

      Status: PROVISIONAL

      Source sequence(s)
      AL672100
      Consensus CDS
      CCDS16828.1
      UniProtKB/Swiss-Prot
      P63154, Q542E8, Q9CQC1
      Related
      ENSMUSP00000001818.5, ENSMUST00000001818.5
      Conserved Domains (4) summary
      pfam02184
      Location:196 → 227
      HAT; HAT (Half-A-TPR) repeat
      COG5107
      Location:130 → 525
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:84 → 109
      TPR; TPR repeat [structural motif]
      cl26712
      Location:64 → 195
      U3_assoc_6; U3 small nucleolar RNA-associated protein 6

    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_000068.8 Reference GRCm39 C57BL/6J

      Range
      145759402..145776620 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P63154.1 GenPept UniProtKB/Swiss-Prot:P63154

    Gene LinkOut

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