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    CRNKL1 crooked neck pre-mRNA splicing factor 1 [ Homo sapiens (human) ]

    Gene ID: 51340, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CRNKL1provided by HGNC
    Official Full Name
    crooked neck pre-mRNA splicing factor 1provided by HGNC
    Primary source
    HGNC:HGNC:15762
    See related
    Ensembl:ENSG00000101343 MIM:610952; AllianceGenome:HGNC:15762
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CLF; CRN; Clf1; HCRN; SYF3; MSTP021
    Summary
    The crooked neck (crn) gene of Drosophila is essential for embryogenesis and is thought to be involved in cell cycle progression and pre-mRNA splicing. A protein encoded by this human locus has been found to localize to pre-mRNA splicing complexes in the nucleus and is necessary for pre-mRNA splicing. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2013]
    Expression
    Ubiquitous expression in bone marrow (RPKM 8.6), testis (RPKM 8.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CRNKL1 in Genome Data Viewer
    Location:
    20p11.23
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (20034368..20056046, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (20088648..20110326, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (20015012..20036690, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene Ras and Rab interactor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:19819023-19819524 Neighboring gene ribosomal protein L12 pseudogene 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:19866384-19866884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:19938653-19939384 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:19939385-19940116 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:19961489-19961988 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:19960987-19961488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:19973649-19974520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:19998307-19998807 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:19999269-20000468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17605 Neighboring gene N-alpha-acetyltransferase 20, NatB catalytic subunit Neighboring gene uncharacterized LOC124904880 Neighboring gene cilia and flagella associated protein 61 Neighboring gene NANOG hESC enhancer GRCh37_chr20:20086826-20087390 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:20146043-20146208 Neighboring gene uncharacterized LOC105372554

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. CRNKL1 Is a Highly Selective Regulator of Intron-Retaining HIV-1 and Cellular mRNAs. Xiao H, et al. mBio, 2021 Jan 19. PMID 33468685, Free PMC Article
    2. Corin I555(P568) allele is associated with enhanced cardiac hypertrophic response to increased systemic afterload. Rame JE, et al. Hypertension, 2007 Apr. PMID 17296875
    3. 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
    4. Identification of the human crooked neck gene by comparative gene identification. Lai CH, et al. Biochim Biophys Acta, 2001 Feb 16. PMID 11342225
    5. Interaction of U-box-type ubiquitin-protein ligases (E3s) with molecular chaperones. Hatakeyama S, et al. Genes Cells, 2004 Jun. PMID 15189447

    See all (94) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CRNKL1 Is a Highly Selective Regulator of Intron-Retaining HIV-1 and Cellular mRNAs.
      Title: CRNKL1 Is a Highly Selective Regulator of Intron-Retaining HIV-1 and Cellular mRNAs.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Corin I555(P568) allele is associated with enhanced cardiac hypertrophic response to increased systemic afterload.
    3. Data show that crooked neck activity appears essential as extracts depleted of hcrn fail to splice pre-mRNA. These and related data support the view that crooked neck is a phylogenetically conserved pre-mRNA splicing factor.
      Title: Crooked neck is a component of the human spliceosome and implicated in the splicing process.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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 GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in spliceosomal complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spliceosomal complex assembly IDA
    Inferred from Direct Assay
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of post-mRNA release spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    crooked neck-like protein 1
    Names
    Crn, crooked neck-like 1
    SYF3 pre-mRNA-splicing factor
    crooked neck homolog
    crooked neck pre-mRNA splicing factor-like 1
    crooked neck-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_001278625.2 → NP_001265554.1  crooked neck-like protein 1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform b), compared to isoform a.
      Source sequence(s)
      AA255987, AF255443, AL832435, BC144222
      Consensus CDS
      CCDS63239.1
      UniProtKB/TrEMBL
      Q5JY65, Q69YP1
      Related
      ENSP00000366544.4, ENST00000377327.8
      Conserved Domains (5) summary
      pfam02184
      Location:345 → 376
      HAT; HAT (Half-A-TPR) repeat
      smart00386
      Location:244 → 276
      HAT; HAT (Half-A-TPR) repeats
      sd00006
      Location:233 → 258
      TPR; TPR repeat [structural motif]
      pfam05843
      Location:381 → 471
      Suf; Suppressor of forked protein (Suf)
      pfam08424
      Location:467 → 682
      NRDE-2; NRDE-2, necessary for RNA interference

    2. NM_001278626.2 → NP_001265555.1  crooked neck-like protein 1 isoform c

      See identical proteins and their annotated locations for NP_001265555.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses two alternate splice sites in the 5' UTR, compared to variant 1. These differences result in predicted translation initiation at a downstream in-frame start site through ribosomal re-initiation and/or leaky scanning. The encoded isoform (c) is shorter than isoform a. Both variants 3 and 4 encode the same isoform (c).
      Source sequence(s)
      AA255987, AF318304, AL832435, BC144222
      UniProtKB/Swiss-Prot
      Q9BZJ0
      UniProtKB/TrEMBL
      Q69YP1
      Conserved Domains (5) summary
      pfam02184
      Location:73 → 104
      HAT; HAT (Half-A-TPR) repeat
      smart00386
      Location:370 → 404
      HAT; HAT (Half-A-TPR) repeats
      COG5107
      Location:7 → 402
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:289 → 317
      TPR; TPR repeat [structural motif]
      pfam05843
      Location:109 → 199
      Suf; Suppressor of forked protein (Suf)

    3. NM_001278627.2 → NP_001265556.1  crooked neck-like protein 1 isoform c

      See identical proteins and their annotated locations for NP_001265556.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses two alternate splice sites in the 5' UTR, compared to variant 1. These differences result in predicted translation initiation at a downstream in-frame start site through ribosomal re-initiation and/or leaky scanning. The encoded isoform (c) is shorter than isoform a. Both variants 3 and 4 encode the same isoform (c).
      Source sequence(s)
      AA255987, AF318305, AL832435, BC144222
      UniProtKB/Swiss-Prot
      Q9BZJ0
      UniProtKB/TrEMBL
      Q69YP1
      Conserved Domains (5) summary
      pfam02184
      Location:73 → 104
      HAT; HAT (Half-A-TPR) repeat
      smart00386
      Location:370 → 404
      HAT; HAT (Half-A-TPR) repeats
      COG5107
      Location:7 → 402
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:289 → 317
      TPR; TPR repeat [structural motif]
      pfam05843
      Location:109 → 199
      Suf; Suppressor of forked protein (Suf)

    4. NM_001278628.2 → NP_001265557.1  crooked neck-like protein 1 isoform d

      See identical proteins and their annotated locations for NP_001265557.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. This variant represents use of an alternate promoter, compared to variant 1. The encoded isoform (d) is shorter than isoform a.
      Source sequence(s)
      AA255987, AL832435, BI550198, DB040881
      Consensus CDS
      CCDS63238.1
      UniProtKB/TrEMBL
      Q8IXG0
      Related
      ENSP00000440733.1, ENST00000536226.2
      Conserved Domains (4) summary
      pfam02184
      Location:196 → 227
      HAT; HAT (Half-A-TPR) repeat
      smart00386
      Location:95 → 127
      HAT; HAT (Half-A-TPR) repeats
      sd00006
      Location:84 → 109
      TPR; TPR repeat [structural motif]
      pfam05843
      Location:232 → 322
      Suf; Suppressor of forked protein (Suf)

    5. NM_016652.6 → NP_057736.4  crooked neck-like protein 1 isoform a

      See identical proteins and their annotated locations for NP_057736.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AA255987, AF318303, AL035454, AL832435, BC144222
      Consensus CDS
      CCDS33446.1
      UniProtKB/Swiss-Prot
      A8K9T4, Q5JY64, Q8WYI5, Q9BZI9, Q9BZJ0, Q9BZJ1, Q9BZJ2, Q9GZW7, Q9H8F8, Q9NQH5, Q9NYD8
      UniProtKB/TrEMBL
      Q69YP1
      Related
      ENSP00000366557.2, ENST00000377340.6
      Conserved Domains (5) summary
      pfam02184
      Location:357 → 388
      HAT; HAT (Half-A-TPR) repeat
      COG5107
      Location:479 → 688
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:245 → 270
      TPR; TPR repeat [structural motif]
      pfam05843
      Location:393 → 483
      Suf; Suppressor of forked protein (Suf)
      cl26712
      Location:219 → 356
      U3_assoc_6; U3 small nucleolar RNA-associated protein 6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      20034368..20056046 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440187.1 → XP_047296143.1  crooked neck-like protein 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      20088648..20110326 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323479.1 → XP_054179454.1  crooked neck-like protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BZJ0.4 GenPept UniProtKB/Swiss-Prot:Q9BZJ0

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