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Aliases for CRNKL1 Gene

Aliases for CRNKL1 Gene

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

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. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway. Gene Ontology (GO) annotations related to this gene include RNA binding.

UniProtKB/Swiss-Prot for CRNKL1 Gene

  • Involved in pre-mRNA splicing process.

Additional gene information for CRNKL1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CRNKL1 Gene

Genomics for CRNKL1 Gene

GeneHancer (GH) Regulatory Elements for CRNKL1 Gene

Promoters and enhancers for CRNKL1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20I020051 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 +3.5 3548 2.1 HDGF PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 CFAP61 CRNKL1 GC20P020024 GC20M020024
GH20I020016 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 12 +37.6 37588 4.1 HDGF PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 SLC30A9 NAA20 CRNKL1 CFAP61 LOC105372553
GH20I019782 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.8 +270.7 270746 5.3 PKNOX1 CLOCK FOXA2 ARID4B NEUROD1 SIN3A ZNF2 ZNF207 ZNF143 FOS ENSG00000232675 CRNKL1 RIN2 NAA20 PIR61811 LOC100421663 ENSG00000268628
GH20I019129 Enhancer 0.8 ENCODE 10.8 +925.8 925790 1.8 PKNOX1 CLOCK FOXA2 NFIB NEUROD1 SIN3A BMI1 ZBTB7B ZNF207 FOS GC20P019131 CRNKL1 ENSG00000274863
GH20I019679 Enhancer 0.7 FANTOM5 10.8 +376.2 376158 0.3 NCOA3 ZSCAN4 YBX1 E4F1 ZKSCAN1 CTBP1 LCORL ZNF207 ATF7 HES1 CRNKL1 PIR51262 PIR38492 SLC24A3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CRNKL1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CRNKL1 gene promoter:

Genomic Locations for CRNKL1 Gene

Genomic Locations for CRNKL1 Gene
21,686 bases
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:
    Recommended name:
    Crooked neck-like protein 1
    Protein Accession:
    Secondary Accessions:
    • A8K9T4
    • Q5JY64
    • Q8WYI5
    • Q9BZI9
    • Q9BZJ1
    • Q9BZJ2
    • Q9GZW7
    • Q9H8F8
    • Q9NQH5
    • Q9NYD8

    Protein attributes for CRNKL1 Gene

    848 amino acids
    Molecular mass:
    100452 Da
    Quaternary structure:
    • Identified in the spliceosome C complex. Present in a spliceosome complex assembled in vitro containing CRNKL1, HPRP8BP and SNRPB2. Isoform 2 seems to be predominant in the spliceosome complex. Interacts with PPIL2 (via the PPIase cyclophilin-type domain); they may form a trimeric complex with HSP90.
    • Sequence=BAB14303.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB14485.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CRNKL1 Gene

    Alternative splice isoforms for CRNKL1 Gene


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

Protein Domains for CRNKL1 Gene

Suggested Antigen Peptide Sequences for CRNKL1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the crooked-neck 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.

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

Animal Model Products

CRISPR Products

miRNA for CRNKL1 Gene

miRTarBase miRNAs that target CRNKL1

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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 speckle. Cytoplasm. Note=Colocalizes with core spliceosomal snRNP proteins. Also diffusely expressed in cytoplasm.

Subcellular locations from

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 --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IDA,IEA 11991638
GO:0005737 cytoplasm 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 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

Unigene Clusters for CRNKL1 Gene

Crooked neck pre-mRNA splicing factor-like 1 (Drosophila):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for CRNKL1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CRNKL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for CRNKL1 Gene

Protein tissue co-expression partners for CRNKL1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CRNKL1 Gene:


SOURCE GeneReport for Unigene cluster for CRNKL1 Gene:


mRNA Expression by UniProt/SwissProt for CRNKL1 Gene:

Tissue specificity: Widely expressed. Highly expressed in testis. Not expressed in brain and lung.

Evidence on tissue expression from TISSUES for CRNKL1 Gene

  • Blood(4.3)
  • Heart(4.3)
  • Nervous system(3.7)
genes like me logo Genes that share expression patterns with CRNKL1: view

Primer Products

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
(Pan troglodytes)
Mammalia CRNKL1 33 34
  • 99.68 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 92 (a)
-- 34
  • 86 (a)
(Canis familiaris)
Mammalia CRNKL1 33 34
  • 89.85 (n)
(Mus musculus)
Mammalia Crnkl1 33 16 34
  • 89.31 (n)
Gm4782 34
  • 85 (a)
(Rattus norvegicus)
Mammalia LOC102548514 33
  • 89.26 (n)
(Bos Taurus)
Mammalia CRNKL1 33 34
  • 88.65 (n)
(Ornithorhynchus anatinus)
Mammalia CRNKL1 34
  • 83 (a)
(Gallus gallus)
Aves CRNKL1 33 34
  • 81.62 (n)
(Anolis carolinensis)
Reptilia CRNKL1 34
  • 92 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia crnkl1 33
  • 80 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2975 33
(Danio rerio)
Actinopterygii crnkl1 33 34
  • 74.62 (n)
zgc55327 33
fruit fly
(Drosophila melanogaster)
Insecta crn 35 33 34
  • 64.66 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001879 33
  • 63.63 (n)
(Caenorhabditis elegans)
Secernentea M03F8.3 35 33 34
  • 63.52 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CLF1 34 36
  • 38 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G41770 33
  • 60.25 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.10127 33
(Oryza sativa)
Liliopsida Os05g0289400 33
  • 60.42 (n)
Os.8927 33
(Hordeum vulgare)
Liliopsida Hv.10575 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes cwf4 33
  • 58.04 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02717 33
  • 56.85 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.11208 33
Species where no ortholog for CRNKL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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

Gene Tree for CRNKL1 (if available)
Gene Tree for CRNKL1 (if available)

Paralogs for CRNKL1 Gene

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

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

No data available for Paralogs for CRNKL1 Gene

Variants for CRNKL1 Gene

Sequence variations from dbSNP and Humsavar for CRNKL1 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1057519885 likely-pathogenic, Malignant melanoma of skin, Squamous cell carcinoma of the skin 20,052,443(-) G/A 5_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant
rs1000188392 -- 20,055,753(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000380367 -- 20,049,910(-) C/T intron_variant
rs1000415849 -- 20,055,607(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000642457 -- 20,057,268(-) A/T upstream_transcript_variant

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

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

Disorders for CRNKL1 Gene

Additional Disease Information for CRNKL1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CRNKL1 Gene.

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

Publications for CRNKL1 Gene

  1. 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 44 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. An unappreciated role for RNA surveillance. (PMID: 14759258) Hillman RT … Brenner SE (Genome biology 2004) 3 4 58
  4. 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 58
  5. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. (PMID: 11991638) Jurica MS … Moore MJ (RNA (New York, N.Y.) 2002) 3 4 58

Products for CRNKL1 Gene

Sources for CRNKL1 Gene

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