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 R... See more...

Aliases for CRNKL1 Gene

Aliases for CRNKL1 Gene

  • Crooked Neck Pre-MRNA Splicing Factor 1 2 3 5
  • CRN 2 3 4
  • SYF3 Pre-MRNA-Splicing Factor 2 3
  • Crooked Neck-Like Protein 1 3 4
  • Crooked Neck Homolog 3 4
  • Clf1 2 3
  • SYF3 2 3
  • CLF 2 3
  • Crooked Neck Pre-MRNA Splicing Factor-Like 1 (Drosophila) 2
  • Crooked Neck (Drosophila Crn Homolog)-Like 1 2
  • Crooked Neck Pre-MRNA Splicing Factor-Like 1 3
  • Crn, Crooked Neck-Like 1 (Drosophila) 2
  • Crn, Crooked Neck-Like 1 3
  • Crooked Neck-Like 1 3
  • MSTP021 3
  • CRNKL1 5
  • HCRN 3
  • HCrn 4

External Ids for CRNKL1 Gene

Previous GeneCards Identifiers for CRNKL1 Gene

  • GC20M020003
  • GC20M020010
  • GC20M019963

Summaries for CRNKL1 Gene

Entrez Gene Summary for CRNKL1 Gene

  • 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]

GeneCards Summary for CRNKL1 Gene

CRNKL1 (Crooked Neck Pre-MRNA Splicing Factor 1) is a Protein Coding gene. Diseases associated with CRNKL1 include Skin Squamous Cell Carcinoma and Skin Melanoma. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. Gene Ontology (GO) annotations related to this gene include RNA binding. An important paralog of this gene is XAB2.

UniProtKB/Swiss-Prot Summary for CRNKL1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CRNKL1 Gene

Genomics for CRNKL1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CRNKL1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CRNKL1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CRNKL1

Top Transcription factor binding sites by QIAGEN in the CRNKL1 gene promoter:
  • ATF6
  • C/EBPbeta
  • HNF-1
  • Ik-2
  • Lmo2
  • Nkx2-5
  • p53
  • STAT1
  • STAT1alpha
  • STAT1beta

Genomic Locations for CRNKL1 Gene

Latest Assembly
chr20:20,034,368-20,056,046
(GRCh38/hg38)
Size:
21,679 bases
Orientation:
Minus strand

Previous Assembly
chr20:20,015,012-20,036,690
(GRCh37/hg19 by Entrez Gene)
Size:
21,679 bases
Orientation:
Minus strand

chr20:20,015,012-20,036,690
(GRCh37/hg19 by Ensembl)
Size:
21,679 bases
Orientation:
Minus strand

Genomic View for CRNKL1 Gene

Genes around CRNKL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CRNKL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CRNKL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CRNKL1 Gene

Proteins for CRNKL1 Gene

  • Protein details for CRNKL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BZJ0-CRNL1_HUMAN
    Recommended name:
    Crooked neck-like protein 1
    Protein Accession:
    Q9BZJ0
    Secondary Accessions:
    • A8K9T4
    • Q5JY64
    • Q8WYI5
    • Q9BZI9
    • Q9BZJ1
    • Q9BZJ2
    • Q9GZW7
    • Q9H8F8
    • Q9NQH5
    • Q9NYD8

    Protein attributes for CRNKL1 Gene

    Size:
    848 amino acids
    Molecular mass:
    100452 Da
    Quaternary structure:
    • Identified in the spliceosome C complex (PubMed:11991638, PubMed:28502770, PubMed:28076346). Present in a spliceosome complex assembled in vitro containing CRNKL1, HPRP8BP and SNRPB2 (PubMed:12084575). Isoform 2 seems to be predominant in the spliceosome complex (PubMed:12084575). Interacts with PPIL2 (via the PPIase cyclophilin-type domain); they may form a trimeric complex with HSP90 (PubMed:15189447).
    SequenceCaution:
    • Sequence=BAB14303.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB14485.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
    Miscellaneous:
    • [Isoform 4]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    • [Isoform 5]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Three dimensional structures from OCA and Proteopedia for CRNKL1 Gene

    Alternative splice isoforms for CRNKL1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CRNKL1 Gene

Post-translational modifications for CRNKL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CRNKL1 Gene

Domains & Families for CRNKL1 Gene

Gene Families for CRNKL1 Gene

Protein Domains for CRNKL1 Gene

InterPro:
Blocks:
  • RNA-processing protein, HAT helix
ProtoNet:

Suggested Antigen Peptide Sequences for CRNKL1 Gene

GenScript: Design optimal peptide antigens:
  • Crooked neck homolog (CRNL1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BZJ0

UniProtKB/Swiss-Prot:

CRNL1_HUMAN :
  • Belongs to the crooked-neck family.
Family:
  • Belongs to the crooked-neck family.
genes like me logo Genes that share domains with CRNKL1: view

Function for CRNKL1 Gene

Molecular function for CRNKL1 Gene

UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing process.

Phenotypes From GWAS Catalog for CRNKL1 Gene

Gene Ontology (GO) - Molecular Function for CRNKL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 12084575
GO:0005515 protein binding IPI 22365833
genes like me logo Genes that share ontologies with CRNKL1: view
genes like me logo Genes that share phenotypes with CRNKL1: view

miRNA for CRNKL1 Gene

miRTarBase miRNAs that target CRNKL1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CRNKL1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CRNKL1 Gene

Localization for CRNKL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CRNKL1 Gene

Nucleus. Nucleus speckle. Note=Colocalizes with core spliceosomal snRNP proteins (PubMed:12084575). {ECO:0000269 PubMed:12084575}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CRNKL1 gene
Compartment Confidence
nucleus 5
cytoskeleton 1
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CRNKL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000974 Prp19 complex IBA 21873635
GO:0005634 nucleus IEA,IDA 28076346
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA,IDA 11991638
GO:0016607 nuclear speck IEA --
genes like me logo Genes that share ontologies with CRNKL1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CRNKL1 Gene

Pathways & Interactions for CRNKL1 Gene

genes like me logo Genes that share pathways with CRNKL1: view

Pathways by source for CRNKL1 Gene

Gene Ontology (GO) - Biological Process for CRNKL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000245 spliceosomal complex assembly IBA,IDA 12084575
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006396 RNA processing IEA --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with CRNKL1: view

No data available for SIGNOR curated interactions for CRNKL1 Gene

Drugs & Compounds for CRNKL1 Gene

No Compound Related Data Available

Transcripts for CRNKL1 Gene

mRNA/cDNA for CRNKL1 Gene

5 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CRNKL1

Alternative Splicing Database (ASD) splice patterns (SP) for CRNKL1 Gene

No ASD Table

Relevant External Links for CRNKL1 Gene

GeneLoc Exon Structure for
CRNKL1

Expression for CRNKL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CRNKL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CRNKL1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (23.7) and Plasma (9.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CRNKL1 Gene



Protein tissue co-expression partners for CRNKL1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CRNKL1

SOURCE GeneReport for Unigene cluster for CRNKL1 Gene:

Hs.171342

mRNA Expression by UniProt/SwissProt for CRNKL1 Gene:

Q9BZJ0-CRNL1_HUMAN
Tissue specificity: Widely expressed (PubMed:11342225). Highly expressed in testis (PubMed:12084575). Not detected in brain and lung (PubMed:12084575).

Evidence on tissue expression from TISSUES for CRNKL1 Gene

  • Blood(4.4)
  • Heart(4.3)
  • Nervous system(3.9)
genes like me logo Genes that share expression patterns with CRNKL1: view

Primer products for research

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CRNKL1 Gene

Orthologs for CRNKL1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CRNKL1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CRNKL1 30 31
  • 99.68 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 92 (a)
OneToMany
-- 31
  • 86 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia CRNKL1 30 31
  • 89.85 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Crnkl1 30 17 31
  • 89.31 (n)
OneToMany
Gm4782 31
  • 85 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Crnkl1 30
  • 89.26 (n)
Cow
(Bos Taurus)
Mammalia CRNKL1 30 31
  • 88.65 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CRNKL1 31
  • 83 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CRNKL1 30 31
  • 81.62 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CRNKL1 31
  • 92 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia crnkl1 30
  • 80 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2975 30
Zebrafish
(Danio rerio)
Actinopterygii crnkl1 30 31
  • 74.62 (n)
OneToOne
zgc55327 30
Fruit Fly
(Drosophila melanogaster)
Insecta crn 30 31 32
  • 64.66 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001879 30
  • 63.63 (n)
Worm
(Caenorhabditis elegans)
Secernentea M03F8.3 30 31 32
  • 63.52 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CLF1 31 33
  • 38 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT5G41770 30
  • 60.25 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.10127 30
Rice
(Oryza sativa)
Liliopsida Os05g0289400 30
  • 60.42 (n)
Os.8927 30
Barley
(Hordeum vulgare)
Liliopsida Hv.10575 30
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes cwf4 30
  • 58.04 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU02717 30
  • 56.85 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.11208 30
Species where no ortholog for CRNKL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for CRNKL1 Gene

ENSEMBL:
Gene Tree for CRNKL1 (if available)
TreeFam:
Gene Tree for CRNKL1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CRNKL1: view image

Paralogs for CRNKL1 Gene

Paralogs for CRNKL1 Gene

(2) SIMAP similar genes for CRNKL1 Gene using alignment to 2 proteins:

  • CRNL1_HUMAN
  • Q5JY65_HUMAN
genes like me logo Genes that share paralogs with CRNKL1: view

Variants for CRNKL1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CRNKL1 Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
rs1057519885 Likely Pathogenic: Squamous cell carcinoma of the skin; Malignant melanoma of skin 20,052,443(-) G/A
NM_001278626.1(CRNKL1):c.-319+36C>T
MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON
rs2255255 - p.Thr158Ala
rs2255258 - p.Gln111His
rs2273058 - p.Phe51Leu
rs35201190 - p.Val843Ile

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CRNKL1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CRNKL1 Gene

Variant ID Type Subtype PubMed ID
nsv3320 CNV insertion 18451855
nsv517467 CNV loss 19592680
nsv525682 CNV loss 19592680
nsv819555 CNV loss 19587683

Variation tolerance for CRNKL1 Gene

Residual Variation Intolerance Score: 17.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.20; 69.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CRNKL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CRNKL1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CRNKL1 Gene

Disorders for CRNKL1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CRNKL1 Gene - From: CVR and COP

Disorder Aliases PubMed IDs
skin squamous cell carcinoma
  • epidermoid skin carcinoma
skin melanoma
  • cutaneous melanoma
fanconi anemia, complementation group g
  • fancg
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CRNKL1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CRNKL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CRNKL1 Gene

Publications for CRNKL1 Gene

  1. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. (PMID: 28076346) Bertram K … Lührmann R (Nature 2017) 3 4
  2. Corin I555(P568) allele is associated with enhanced cardiac hypertrophic response to increased systemic afterload. (PMID: 17296875) Rame JE … Dries DL (Hypertension (Dallas, Tex. : 1979) 2007) 3 41
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. An unappreciated role for RNA surveillance. (PMID: 14759258) Hillman RT … Brenner SE (Genome biology 2004) 3 4
  5. Interaction of U-box-type ubiquitin-protein ligases (E3s) with molecular chaperones. (PMID: 15189447) Hatakeyama S … Nakayama KI (Genes to cells : devoted to molecular & cellular mechanisms 2004) 3 4

Products for CRNKL1 Gene

Sources for CRNKL1 Gene