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

Gene ID: 51340, updated on 12-Oct-2019

Summary

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
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

Genomic context

See CRNKL1 in Genome Data Viewer
Location:
20p11.23
Exon count:
15
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (20034361..20056046, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (20015005..20036690, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene Ras and Rab interactor 2 Neighboring gene ribosomal protein L12 pseudogene 12 Neighboring gene uncharacterized LOC105372553 Neighboring gene N(alpha)-acetyltransferase 20, NatB catalytic subunit Neighboring gene cilia and flagella associated protein 61 Neighboring gene uncharacterized LOC105372554 Neighboring gene uncharacterized LOC107985413 Neighboring gene ribosomal protein L17 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • 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

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, 35S U5-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, 35S U5-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, 35S U5-snRNP, conserved biosystem (from KEGG)
    Spliceosome, 35S U5-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome IC
Inferred by Curator
more info
PubMed 
mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
spliceosomal complex assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spliceosomal complex assembly IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Prp19 complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2-type catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2-type catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
nuclear speck IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
post-mRNA release spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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_001278625.1NP_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/Swiss-Prot
    Q9BZJ0
    UniProtKB/TrEMBL
    Q5JY65, Q69YP1
    Related
    ENSP00000366544.4, ENST00000377327.8
    Conserved Domains (5) summary
    pfam02184
    Location:345376
    HAT; HAT (Half-A-TPR) repeat
    smart00386
    Location:244276
    HAT; HAT (Half-A-TPR) repeats
    sd00006
    Location:233258
    TPR; TPR repeat [structural motif]
    pfam05843
    Location:381471
    Suf; Suppressor of forked protein (Suf)
    pfam08424
    Location:467682
    NRDE-2; NRDE-2, necessary for RNA interference
  2. NM_001278626.1NP_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:73104
    HAT; HAT (Half-A-TPR) repeat
    smart00386
    Location:370404
    HAT; HAT (Half-A-TPR) repeats
    COG5107
    Location:7402
    RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
    sd00006
    Location:289317
    TPR; TPR repeat [structural motif]
    pfam05843
    Location:109199
    Suf; Suppressor of forked protein (Suf)
  3. NM_001278627.1NP_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:73104
    HAT; HAT (Half-A-TPR) repeat
    smart00386
    Location:370404
    HAT; HAT (Half-A-TPR) repeats
    COG5107
    Location:7402
    RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
    sd00006
    Location:289317
    TPR; TPR repeat [structural motif]
    pfam05843
    Location:109199
    Suf; Suppressor of forked protein (Suf)
  4. NM_001278628.1NP_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/Swiss-Prot
    Q9BZJ0
    UniProtKB/TrEMBL
    Q69YP1
    Related
    ENSP00000440733.1, ENST00000536226.1
    Conserved Domains (4) summary
    pfam02184
    Location:196227
    HAT; HAT (Half-A-TPR) repeat
    smart00386
    Location:95127
    HAT; HAT (Half-A-TPR) repeats
    sd00006
    Location:84109
    TPR; TPR repeat [structural motif]
    pfam05843
    Location:232322
    Suf; Suppressor of forked protein (Suf)
  5. NM_016652.5NP_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
    Q9BZJ0
    UniProtKB/TrEMBL
    Q69YP1
    Related
    ENSP00000366557.2, ENST00000377340.6
    Conserved Domains (5) summary
    pfam02184
    Location:357388
    HAT; HAT (Half-A-TPR) repeat
    COG5107
    Location:479688
    RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
    sd00006
    Location:245270
    TPR; TPR repeat [structural motif]
    pfam05843
    Location:393483
    Suf; Suppressor of forked protein (Suf)
    cl26712
    Location:219356
    U3_assoc_6; U3 small nucleolar RNA-associated protein 6

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    20034361..20056046 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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