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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CRNKL1 Gene

protein-coding   GIFtS: 54
GCID: GC20M019963

crooked neck pre-mRNA splicing factor-like 1 (Drosophila)

(Previous names: crooked neck (Drosophila Crn homolog)-like 1, Crn, crooked...)
 Explore 1 disease affiliated with
CRNKL1 via our new
 Human Malady Compendium 
Biological research products
for CRNKL1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Crooked Neck Pre-MRNA Splicing Factor-Like 1 (Drosophila)1 2     Crooked Neck (Drosophila Crn Homolog)-Like 11
CRN1 2 3 5     HCRN2
CLF1 2     MSTP0212
Clf11 2     Crn, Crooked Neck-Like 12
SYF31 2     Crooked Neck-Like 12
Crooked Neck Homolog2 3     Crooked Neck-Like Protein 12
Crn, Crooked Neck-Like 1 (Drosophila)1     HCrn1

External Ids:    HGNC: 157621   Entrez Gene: 513402   Ensembl: ENSG000001013437   OMIM: 6109525   UniProtKB: Q9BZJ03   

Export aliases for CRNKL1 gene to outside databases

Previous GC identifers: GC20M020003 GC20M020010


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for CRNKL1:
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. This gene is similar in sequence to crn and encodes a protein which can localize to
pre-mRNA splicing complexes in the nucleus. The encoded protein, which contains many tetratricopeptide repeats, is
required for pre-mRNA splicing. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: CRNL1_HUMAN, Q9BZJ0
Function: Involved in pre-mRNA splicing process




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NC_018931.1  NT_011387.8  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CRNKL1 gene promoter:
         C/EBPbeta   STAT1   p53   Lmo2   STAT1beta   Nkx2-5   STAT1alpha   Ik-2   HNF-1   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): CRNKL1 promoter sequence
   Search SABiosciences Chromatin IP Primers for CRNKL1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CRNKL1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 20p11.2   Ensembl cytogenetic band:  20p11.23   HGNC cytogenetic band: 20p11.2

CRNKL1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CRNKL1 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20M019963:  view genomic region     (about GC identifiers)

Start:
20,015,012 bp from pter      End:
20,036,690 bp from pter
Size:
21,679 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CRNL1_HUMAN, Q9BZJ0 (See protein sequence)
Recommended Name: Crooked neck-like protein 1  
Size: 848 amino acids; 100452 Da
Subunit: 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
Subcellular location: Nucleus speckle. Cytoplasm. Note=Colocalizes with core spliceosomal snRNP proteins. Also
diffusely expressed in cytoplasm
Sequence caution: Sequence=BAB14303.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAB14485.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: A8K9T4 Q5JY64 Q8WYI5 Q9BZI9 Q9BZJ1 Q9BZJ2 Q9GZW7 Q9H8F8 Q9NQH5 Q9NYD8
Alternative splicing: 5 isoforms:  Q9BZJ0-1   Q9BZJ0-2   Q9BZJ0-3   Q9BZJ0-4   Q9BZJ0-5   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for CRNKL1: NX_Q9BZJ0

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9BZJ0

  • CRNKL1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_057736.4  
    ENSEMBL proteins: 
     ENSP00000366544   ENSP00000366557   ENSP00000429226   ENSP00000428436   ENSP00000440733  

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    Uscn Proteins for CRNKL1

    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005681spliceosomal complex IDA11991638
    GO:0005737cytoplasm IEA--
    GO:0016607nuclear speck IEA--
    GO:0071013catalytic step 2 spliceosome IDA11991638


    CRNKL1 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    CRNKL1 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR011990 TPR-like_helical
     IPR003107 HAT
     IPR013026 TPR-contain_dom

    Graphical View of Domain Structure for InterPro Entry Q9BZJ0

    ProtoNet protein and cluster: Q9BZJ0

    1 Blocks protein family: IPB003107 RNA-processing protein

    UniProtKB/Swiss-Prot: CRNL1_HUMAN, Q9BZJ0
    Similarity: Belongs to the crooked-neck family
    Similarity: Contains 17 HAT repeats


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: CRNL1_HUMAN, Q9BZJ0
    Function: Involved in pre-mRNA splicing process

    miRNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003723RNA binding IDA12084575


    CRNKL1 for ontologies           About GeneDecksing


    4 GenomeRNAi human phenotypes for CRNKL1:
     Abundance of large cells with   Decreased influenza A virus in  Increased gamma-H2AX phosphory  Synthetic lethal with Ras 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1mRNA Splicing - Major Pathway
    Spliceosome0.31

    Pathway sources
    See GeneCards unified pathways
    Show all pathways



    1         Kegg Pathway  (Kegg details for CRNKL1):
        Spliceosome


    CRNKL1 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CRNKL1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/91 Interacting proteins for CRNKL1 (Q9BZJ02, 3 ENSP000003665574) via UniProtKB, MINT, STRING, and/or I2D (see all 91)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    BIDP559572, 3, ENSP000003188224MINT-8249509 I2D: score=2 STRING: ENSP00000318822
    CCDC12Q8WUD42, ENSP000002923144MINT-8337101 MINT-8332064 STRING: ENSP00000292314
    CDC5LQ994593, ENSP000003605324I2D: score=8 STRING: ENSP00000360532
    PLRG1O436603, ENSP000003031914I2D: score=7 STRING: ENSP00000303191
    XAB2Q9HCS73, ENSP000003511374I2D: score=7 STRING: ENSP00000351137
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000245spliceosomal complex assembly IDA12084575
    GO:0000398mRNA splicing, via spliceosome IC11991638
    GO:0006396RNA processing ----


    CRNKL1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CRNKL1
    Search CenterWatch for drugs/clinical trials and news about CRNKL1 / CRNL1 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CRNKL1 gene: 
    NM_016652.4  

    Unigene Cluster for CRNKL1:

    Crooked neck pre-mRNA splicing factor-like 1 (Drosophila)
    Hs.171342  [show with all ESTs]
    Unigene Representative Sequence: NM_016652
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000377327(uc002wrt.1) ENST00000377340(uc002wrs.3) ENST00000490910
    ENST00000496549 ENST00000536226 ENST00000521379 ENST00000490258

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    hsa-miR-498 hsa-miR-3163 hsa-miR-545 hsa-miR-340 hsa-miR-1305 hsa-miR-1262 hsa-miR-335 hsa-miR-3662
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    Additional cDNA sequence: 

    AB016840.1 AF111802.1 AF255443.2 AF318302.1 AF318303.1 AF318304.1 AF318305.1 AK022908.1 
    AK023246.1 AK023728.1 AK026342.1 AK292799.1 AL832435.1 BC144222.1 

    7 DOTS entries:

    DT.452702  DT.95353451  DT.100791876  DT.100791878  DT.97845114  DT.95375156  DT.439584 

    24/164 AceView cDNA sequences (see all 164):

    BQ681478 AA344681 BM846705 AV718167 BM770812 AA195126 BM460482 BF056996 
    AI872341 CB242683 BM462141 AK022908 AU132316 Z39888 AA195019 AA825980 
    CD644346 AF111802 AU118295 AK023728 BP345645 NM_016652 AL570166 BM756354 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CRNKL1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GCCAAACTGT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See CRNKL1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CRNKL1

    SOURCE GeneReport for Unigene cluster: Hs.171342

    UniProtKB/Swiss-Prot: CRNL1_HUMAN, Q9BZJ0
    Tissue specificity: Widely expressed. Highly expressed in testis. Not expressed in brain and lung

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for CRNKL1 gene from 8/33 species (see all 33)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves CRNKL11 crooked neck pre-mRNA splicing factor-like 1 (Drosophila) 81.61(n)
    93.43(a)
      421243  XM_419315.3  XP_419315.2 
    lizard
    (Anolis carolinensis)
    Reptilia CRNKL16
    --
    91(a)
    1 ↔ 1
    4(80521890-80539077)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.29752 Xenopus laevis transcribed sequence with strong similarity more 81.63(n)    CA790594.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc553272 similar to crooked neck protein 77.09(n)   393920  BC044369.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta crn1 , 3 mRNA splicing pre-mRNA splicing factor3
    crooked neck1
    68(a)3
    64.66(n)1
    70.03(a)1
      2F23
    312081  NM_057770.41  NP_477118.11 
    worm
    (Caenorhabditis elegans)
    Secernentea M03F8.31 , 3 Protein M03F8.31 62(a)3
    63.26(n)1
    63.51(a)1
      V(5942558-5944788)3
    1789791  NM_001129507.11  NP_001122979.11 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G417701 putative crooked neck protein / cell cycle protein 60.2(n)
    60.46(a)
      834182  NM_123542.2  NP_198992.2 
    rice
    (Oryza sativa)
    Liliopsida Os.89272 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 74.37(n)    AK100478.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/370 NCBI SNPs in CRNKL1 are shown (see all 370    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2001781,2
    H--20014805(-) TTTTAG/AAAGGG 1 -- ds50015Minor allele frequency- A:0.00EA NS 434
    rs114762971,2
    C--20014840(+) TGAGGT/-TTTTT 1 -- ds50011Minor allele frequency- -:0.00NA 2
    rs1462494381,2
    --20014870(+) GAACA-/TAAT  
            
    TAATT
    1 -- ds50010--------
    rs1135843751,2
    C,--20014892(+) GCCATA/GTAACT 1 -- ds50012Minor allele frequency- G:0.10CSA WA 120
    rs1835685051,2
    --20014898(+) TAACTA/GTATCA 1 -- ds50010--------
    rs61322611,2
    C,F,H,--20014955(+) TGAAAA/CTATCC 1 -- ds500132Minor allele frequency- N:0.00NS EA NA CSA WA 3406
    rs762982961,2
    C,F,--20014988(+) TTAACG/AAAAGA 1 -- ds50012Minor allele frequency- A:0.31WA EA 238
    rs1393737231,2
    --20015052(+) GAGTT-/GAG   
       GGTGG
    GAGAG
    1 -- ut310--------
    rs802533531,2
    C,F,--20015107(+) TTTTCC/TTTCCA 1 -- ut311Minor allele frequency- T:0.07EA 120
    rs1463457171,2
    C,--20015192(+) AACAT-/AAAC  
            
    AAACA
    1 -- ut310--------

    HapMap Linkage Disequilibrium report for CRNKL1 (20015012 - 20036690 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for CRNKL1
         2 CNVs: 59020 50631
         1 Indel: 50630

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    CRNKL1 for disorders           About GeneDecksing

    OMIM gene information: 610952    OMIM disorders: --

    1 disease for CRNKL1:    About MalaCards
    malaria

    Human Genome Epidemiology (HuGE) Navigator: CRNKL1 (1 document)

    Export disorders for CRNKL1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for CRNKL1 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with CRNKL1)
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    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    2. An unappreciated role for RNA surveillance. (PubMed id 14759258)1, 2 Hillman R.T.... Brenner S.E. (2004)
    3. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. (PubMed id 11991638)1, 2 Jurica M.S.... Moore M.J. (2002)
    4. Crooked neck is a component of the human spliceosome and implicated in the splicing process. (PubMed id 12084575)1, 2 Chung S.... Rymond B.C. (2002)
    5. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (2001)
    6. Identification of the human crooked neck gene by comparative gene identification. (PubMed id 11342225)1, 2 Lai C.-H.... Lin W.-C. (2001)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    8. Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)
    9. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    10. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 51340 HGNC: 15762 AceView: CRNKL1 Ensembl:ENSG00000101343 euGenes: HUgn51340
    ECgene: CRNKL1 Kegg: 51340 H-InvDB: CRNKL1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CRNKL1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CRNKL1 gene:
    Search GeneIP for patents involving CRNKL1

    GeneCards and IP:
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