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

CKLF Gene

protein-coding   GIFtS: 45
GCID: GC16P066586

chemokine-like factor

(Previous name: chemokine-like factor 1 )
(Previous symbol: CKLF1)
 Explore 8 diseases affiliated with
CKLF via our new
 Human Malady Compendium 
Biological research products
for CKLF
    

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

Aliases
Chemokine-Like Factor1 2     HSPC2241
C321 2 3     CKLF22
CKLF11 2 3     Chemokine-Like Factor 22
CKLF31 2     Chemokine-Like Factor 32
CKLF41 2     Chemokine-Like Factor 42
UCK-11 2     Transmembrane Proteolipid2
Chemokine-Like Factor 11 2     

External Ids:    HGNC: 132531   Entrez Gene: 511922   Ensembl: ENSG000002175557   UniProtKB: Q9UBR53   

Export aliases for CKLF gene to outside databases

Previous GC identifers: GC16P066964 GC16P066321 GC16P066362 GC16P065143 GC16P052462


(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 CKLF:
The product of this gene is a cytokine. Cytokines are small proteins that have an essential role in the immune and
inflammatory responses. This gene is one of several chemokine-like factor genes located in a cluster on chromosome 16.
The protein encoded by this gene is a potent chemoattractant for neutrophils, monocytes and lymphocytes. It also can
stimulate the proliferation of skeletal muscle cells. This protein may play important roles in inflammation and in the
regeneration of skeletal muscle. Alternatively spliced transcript variants encoding different isoforms have been
identified. Naturally occurring read-through transcription occurs between this locus and the neighboring locus CMTM1
(CKLF-like MARVEL transmembrane domain containing 1).(provided by RefSeq, Feb 2011)

UniProtKB/Swiss-Prot: CKLF_HUMAN, Q9UBR5
Function: May play an important role in inflammation and regeneration of skeletal muscle. Partly inhibited by
interleukin 10
Function: Isoform 1 has chemotactic response in rat monocytes, neutrophils, and lymphocytes

Gene Wiki entry for CKLF


(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_000016.9  NC_018927.1  NT_010498.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CKLF gene promoter:
         MyoD   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCKLF promoter sequence
   Search SABiosciences Chromatin IP Primers for CKLF

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


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

Entrez Gene cytogenetic band: 16q21   Ensembl cytogenetic band:  16q21   HGNC cytogenetic band: 16q22.1-q22.3

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

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P066586:  view genomic region     (about GC identifiers)

Start:
66,586,466 bp from pter      End:
66,600,331 bp from pter
Size:
13,866 bases      Orientation:
plus 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: CKLF_HUMAN, Q9UBR5 (See protein sequence)
Recommended Name: Chemokine-like factor  
Size: 152 amino acids; 17170 Da
Subcellular location: Isoform 1: Secreted
Subcellular location: Isoform 2: Membrane; Multi-pass membrane protein (Potential)
Subcellular location: Isoform 4: Membrane; Multi-pass membrane protein (Potential)
Secondary accessions: C9JE38 Q9UHM7 Q9UHN8 Q9UI41
Alternative splicing: 5 isoforms:  Q9UBR5-1   Q9UBR5-2   Q9UBR5-3   Q9UBR5-4   Q9UBR5-5   

Explore the universe of human proteins at neXtProt for CKLF: NX_Q9UBR5

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UBR5

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

    REFSEQ proteins (5 alternative transcripts): 
    NP_001035228.1  NP_057410.1  NP_058647.1  NP_857591.1  NP_857592.1  

    ENSEMBL proteins: 
     ENSP00000431270   ENSP00000264001   ENSP00000264003   ENSP00000290771   ENSP00000355417  
     ENSP00000416678   ENSP00000433857  

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    Uscn Proteins for CKLF

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IDA11415443
    GO:0005615extracellular space IEA--
    GO:0016021integral to membrane IDA11415443


    CKLF 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

    CKLF for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR008253 Marvel

    Graphical View of Domain Structure for InterPro Entry Q9UBR5

    ProtoNet protein and cluster: Q9UBR5

    1 Blocks protein family: IPB008253 Marvel

    UniProtKB/Swiss-Prot: CKLF_HUMAN, Q9UBR5
    Similarity: Belongs to the chemokine-like factor family
    Similarity: Contains 1 MARVEL domain


    (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: CKLF_HUMAN, Q9UBR5
    Function: May play an important role in inflammation and regeneration of skeletal muscle. Partly inhibited by
    interleukin 10
    Function: Isoform 1 has chemotactic response in rat monocytes, neutrophils, and lymphocytes

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    hsa-miR-3163
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    Inhib. RNA
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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:0008009chemokine activity IDA11415443


    CKLF for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for CKLF:
     Decreased circadian period len 


    (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



    Interactions:

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

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008283cell proliferation IDA11415443
    GO:0030593neutrophil chemotaxis IDA11415443
    GO:0032940secretion by cell IDA11415443
    GO:0048246macrophage chemotaxis IDA11415443
    GO:0048247lymphocyte chemotaxis IDA11415443


    CKLF 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

    CKLF for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CKLF
    1 Novoseek chemical compound relationship for CKLF gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tarc 77.4 5 16137713 (2)

    Search CenterWatch for drugs/clinical trials and news about CKLF 

    (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 CKLF gene (6 alternative transcripts): 
    NM_001040138.2  NM_016326.3  NM_016951.3  NM_181640.2  NM_181641.2  NM_001040139.1  

    Unigene Cluster for CKLF:

    Chemokine-like factor
    Hs.15159  [show with all ESTs]
    Unigene Representative Sequence: AK126041
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000534692 ENST00000264001(uc002eow.3 uc002eou.3 uc002eot.3 uc002eov.3)
    ENST00000351137 ENST00000345436 ENST00000362093 ENST00000526149 ENST00000417030(uc002eox.2)
    ENST00000532838 ENST00000563092

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate CKLF:
    hsa-miR-3163
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    Inhib. RNA
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    Clone
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    Additional cDNA sequence: 

    AF057306.1 AF096895.2 AF135380.2 AF135381.2 AF145216.2 AF151058.1 AK126041.1 AK290307.1 
    AK301240.1 AY358999.1 BC004380.1 BC028676.1 BC091478.1 

    16 DOTS entries:

    DT.100866960  DT.100025938  DT.415915  DT.100754363  DT.97839329  DT.120724950  DT.91914577  DT.120725002 
    DT.75119879  DT.120725027  DT.120724958  DT.120724970  DT.120725032  DT.120725010  DT.75197958  DT.95260932 

    24/231 AceView cDNA sequences (see all 231):

    AI206661 BQ631073 AA876539 BF475590 BQ130559 AI540221 NM_181293 AF135381 
    BU599247 AF145216 NM_181283 NM_181301 NM_181285 AY358999 AJ712987 BC004380 
    BU753845 BU782576 BU782607 AA911088 AK126041 BQ130813 AA516431 BU077917 

    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

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

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

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

    SOURCE GeneReport for Unigene cluster: Hs.15159

    UniProtKB/Swiss-Prot: CKLF_HUMAN, Q9UBR5
    Tissue specificity: Isoform 1, isoform 2, isoform 3 and isoform 4 have highest expression levels in adult spleen, lung,
    testis, ovary, peripheral blood leukocyte, placenta, pancreas, and in fetal brain, skeletal muscle, thymus and heart.
    Lower expression levels in adult skeletal muscle, liver, thymus colon, prostate and fetal spleen and liver

        SABiosciences Expression via Pathway-Focused PCR Arrays including CKLF: 
              Inflammatory Response & Autoimmunity 384HT in human mouse rat
              Chemokines & Receptors in human mouse rat

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    In Situ
    Assay Products:
     

     
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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 chordates.

    Orthologs for CKLF gene from 1/6 species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves --
    --
    Uncharacterized protein
    36(a)
    36(a)
    many ↔ many
    many ↔ many
    11(12309899-12312498)
    11(12321662-12324317)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CKLF gene
    CMTM12  CKLF-CMTM12  
    2 SIMAP similar genes for CKLF using alignment to 4 protein entries:     CKLF_HUMAN (see all proteins):
    CKLF-CMTM1    CMTM1

    CKLF for paralogs           About GeneDecksing



    (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

    10/166 NCBI SNPs in CKLF are shown (see all 166    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1393465261,2
    --66586352(+) TGCCCA/CGCTCT 8 -- us2k10--------
    rs1500440231,2
    --66586371(+) TAATGC/TGCTAC 8 -- us2k10--------
    rs1836349191,2
    --66586432(+) TTGGGC/GCGCAT 8 -- us2k10--------
    rs22327241,2
    C,F,H,--66586609(+) GGGTCT/GGCAGA 8 -- ut516Minor allele frequency- G:0.00NS NA 560
    rs2005063861,2
    --66586741(+) GCTGGG/TGGGCG 8 -- int10--------
    rs22327251,2
    C,F,A,H,--66586759(+) TGGGTG/ATGAAG 8 -- int128Minor allele frequency- A:0.15EA NS NA CSA WA 4252
    rs1513349701,2
    --66586840(+) TTGGG-/GAAGAAGG 8 -- int10--------
    rs1877943411,2
    --66586858(+) GATACA/GGCACT 8 -- int10--------
    rs1923120971,2
    --66586870(+) TCCTCA/CCCTTA 8 -- int10--------
    rs1136922121,2
    C,--66587064(+) CTTTAAAAACA  
     AAAAC
    /-
    AAAAC
    8 -- int11Minor allele frequency- -:0.50CSA 2

    HapMap Linkage Disequilibrium report for CKLF (66586466 - 66600331 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for CKLF: --

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

    CKLF for disorders           About GeneDecksing

    8 diseases for CKLF:    About MalaCards
    myocardial infarction    acute myocardial infarction    ovarian cystadenoma    myopathy
    cystadenoma    hepatitis b    hepatitis    prostatitis

    1 disease from the University of Copenhagen DISEASES database for CKLF:
    Ovarian cystadenoma

    2 Novoseek disease relationships for CKLF gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    inflammation 0 2 14672409 (1), 11415443 (1)
    tumors 0 2 16303766 (1)

    Human Genome Epidemiology (HuGE) Navigator: CKLF (9 documents)

    Export disorders for CKLF 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)
    About This Section

    PubMed articles for CKLF gene, integrated from 9 sources (see all 34):
    (articles sorted by number of sources associating them with CKLF)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and characterization of chemokine-like factor 1 (CKLF1), a novel human cytokine with unique structure and potential chemotactic activity. (PubMed id 11415443)1, 2, 3, 9 Han W.... Ma D. (2001)
    2. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PubMed id 11042152)1, 2, 3 Zhang Q.-H.... Chen Z. (2000)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (2003)
    5. Chemokine-like factor expression in the idiopathic inflammatory myopathies. (PubMed id 18294340)1, 9 Chowdhury M.H....Yamaguchi S. (2008)
    6. Effects of novel human chemokine-like factor 1 (CKLF1) on bone marrow hematopoietic stem cell/progenitor cell in vitro. (PubMed id 12411060)1, 9 Ke X....Di C. (2002)
    7. [The expression of chemokine-like factor 1 in human a therosclerotic plaques.] (PubMed id 20137403)1, 9 Jiao Y....Zhang X.M. (2009)
    8. Two C-terminal peptides of human CKLF1 interact with the chemokine receptor CCR4. (PubMed id 18069042)1, 9 Wang Y....Ma D. (2008)
    9. Last intron of the chemokine-like factor gene contains a putative promoter for the downstream CKLF super family member 1 gene. (PubMed id 14672709)1, 9 Xu M....Ma D. (2004)
    10. Overexpression of chemokine-like factor 2 promotes the proliferation and survival of C2C12 skeletal muscle cells. (PubMed id 12183067)1, 9 Xia D....Ma D. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 51192 HGNC: 13253 AceView: CKLFandCKLFSF1 Ensembl:ENSG00000217555 euGenes: HUgn51192
    ECgene: CKLF H-InvDB: CKLF

    (According to HUGE)
    About This Section
      --

    (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 CKLF Pharmacogenomics, SNPs, Pathways
    SeattleSNPshttp://pga.gs.washington.edu/data/cklf/

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

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
    In Situ Hybridization Assays from
    Advanced Cell Diagnostics
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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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