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Crnkl1 crooked neck pre-mRNA splicing factor 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 100910202, updated on 14-Nov-2024

Summary

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Symbol
Crnkl1provided by RGD
Full Name
crooked neck pre-mRNA splicing factor 1provided by RGD
Primary source
RGD:620507
See related
EnsemblRapid:ENSRNOG00000010587 AllianceGenome:RGD:620507
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Crn
Summary
Predicted to enable RNA binding activity. Involved in cellular response to brain-derived neurotrophic factor stimulus; cellular response to leukemia inhibitory factor; and cerebral cortex development. 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. 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, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See Crnkl1 in Genome Data Viewer
Location:
3q41
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (153764718..153807973, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (133338593..133354329, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (18349226..18351540, complement)

Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene Ras and Rab interactor 2 Neighboring gene probable rRNA-processing protein EBP2 pseudogene Neighboring gene transfer RNA threonine (anticodon AGU) 15 Neighboring gene N(alpha)-acetyltransferase 20, NatB catalytic subunit Neighboring gene cilia and flagella associated protein 61 Neighboring gene eukaryotic translation initiation factor 4A1, pseudogene 3 Neighboring gene INSM transcriptional repressor 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Mutational landscape of basal cell carcinomas by whole-exome sequencing. Jayaraman SS, et al. J Invest Dermatol, 2014 Jan. PMID 23774526
  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. Drosophila crooked-neck protein co-fractionates in a multiprotein complex with splicing factors. Raisin-Tani S, et al. Biochem Biophys Res Commun, 2002 Aug 16. PMID 12163015
  4. 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
  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

General gene information

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Markers

Homology

Clone Names

  • MGC93283

Gene Ontology Provided by RGD

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 cellular response to brain-derived neurotrophic factor stimulus IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in cellular response to leukemia inhibitory factor IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in cerebral cortex development IEP
Inferred from Expression Pattern
more info
 PubMed 
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 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 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
  
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
crooked neck pre-mRNA splicing factor-like 1
crooked neck-like 1 protein-like
crooked neck-like protein 1-like

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_053797.2 → NP_446249.1  crooked neck-like protein 1

    See identical proteins and their annotated locations for NP_446249.1

    Status: VALIDATED

    Source sequence(s)
    BC085718
    UniProtKB/Swiss-Prot
    P63155
    UniProtKB/TrEMBL
    A0A0G2K5Q2, A6H999
    Related
    ENSRNOP00000014632.7, ENSRNOT00000014632.9
    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_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086021.1 Reference GRCr8

    Range
    153764718..153807973 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063282973.1 → XP_063139043.1  crooked neck-like protein 1 isoform X1

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P63155.1 GenPept UniProtKB/Swiss-Prot:P63155

Gene LinkOut

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