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

Gene ID: 51340, updated on 7-Apr-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
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Genomic context

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Location:
20p11.23
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (20034368..20056046, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (20088648..20110326, complement)
105.20220307 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 (81) 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)

Genotypes

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_2023_10

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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