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CKLF chemokine like factor [ Homo sapiens (human) ]

Gene ID: 51192, updated on 27-Nov-2024

Summary

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Official Symbol
CKLFprovided by HGNC
Official Full Name
chemokine like factorprovided by HGNC
Primary source
HGNC:HGNC:13253
See related
Ensembl:ENSG00000217555 MIM:616074; AllianceGenome:HGNC:13253
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
C32; CKLF1; CKLF2; CKLF3; CKLF4; UCK-1; HSPC224
Summary
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]
Expression
Ubiquitous expression in appendix (RPKM 18.6), testis (RPKM 17.1) and 24 other tissues See more
Orthologs
all
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Genomic context

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See CKLF in Genome Data Viewer
Location:
16q21
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (66552563..66566287)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72346858..72360582)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (66586466..66600190)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene brain expressed associated with NEDD4 1 Neighboring gene uncharacterized LOC124903698 Neighboring gene BEAN1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7558 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66510981-66511522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66512063-66512603 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66513685-66514224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66518060-66519040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66521703-66522203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66543229-66544204 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66545181-66546156 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66546157-66547132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66553931-66554431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10940 Neighboring gene thymidine kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10941 Neighboring gene CKLF-CMTM1 readthrough Neighboring gene CKLF like MARVEL transmembrane domain containing 1 Neighboring gene CKLF like MARVEL transmembrane domain containing 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Research insights into the chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing family (CMTM): their roles in various tumors. Duan SL, et al. PeerJ, 2024. PMID 38223763, Free PMC Article
  2. Effects of novel human chemokine-like factor 1 (CKLF1) on bone marrow hematopoietic stem cell/progenitor cell in vitro. Ke X, et al. Zhonghua Xue Ye Xue Za Zhi, 2002 Jun. PMID 12411060
  3. Last intron of the chemokine-like factor gene contains a putative promoter for the downstream CKLF super family member 1 gene. Xu M, et al. Biochem Biophys Res Commun, 2004 Jan 2. PMID 14672709
  4. Two C-terminal peptides of human CKLF1 interact with the chemokine receptor CCR4. Wang Y, et al. Int J Biochem Cell Biol, 2008. PMID 18069042
  5. Chemokine-like factor expression in the idiopathic inflammatory myopathies. Chowdhury MH, et al. Acta Neurol Scand, 2008 Aug. PMID 18294340

See all (34) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CKLF instigates a "cold" microenvironment to promote MYCN-mediated tumor aggressiveness.
    Title: CKLF instigates a "cold" microenvironment to promote MYCN-mediated tumor aggressiveness.
  2. Research insights into the chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing family (CMTM): their roles in various tumors.
    Title: Research insights into the chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing family (CMTM): their roles in various tumors.
  3. Neuronal chemokine-like-factor 1 (CKLF1) up-regulation promotes M1 polarization of microglia in rat brain after stroke.
    Title: Neuronal chemokine-like-factor 1 (CKLF1) up-regulation promotes M1 polarization of microglia in rat brain after stroke.
  4. Chemokine-like factor 1 (CKLF1) aggravates neointimal hyperplasia through activating the NF-kappaB /VCAM-1 pathway.
    Title: Chemokine-like factor 1 (CKLF1) aggravates neointimal hyperplasia through activating the NF-κB /VCAM-1 pathway.
  5. CKLF and IL1B transcript levels at diagnosis are predictive of relapse in children with pre-B-cell acute lymphoblastic leukaemia.
    Title: CKLF and IL1B transcript levels at diagnosis are predictive of relapse in children with pre-B-cell acute lymphoblastic leukaemia.
  6. Kanglaite enhances the efficacy of cisplatin in suppression of hepatocellular carcinoma via inhibiting CKLF1 mediated NF-kappaB pathway and regulating transporter mediated drug efflux.
    Title: Kanglaite enhances the efficacy of cisplatin in suppression of hepatocellular carcinoma via inhibiting CKLF1 mediated NF-κB pathway and regulating transporter mediated drug efflux.
  7. Data indicate that leukocyte-infiltrate derived chemokine-like factor (CKLF) expression is a candidate biomarker of favorable prognosis.
    Title: Stratified analysis reveals chemokine-like factor (CKLF) as a potential prognostic marker in the MSI-immune consensus molecular subtype CMS1 of colorectal cancer.
  8. CKLF1 expression was up-regulated in synovim from rheumatoid arthritis and ankylosing spondylitis patients.
    Title: Distinct expression of chemokine-like factor 1 in synovium of osteoarthritis, rheumatoid arthritis and ankylosing spondylitis.
  9. expression elevated in the skin of keloid patients
    Title: Chemokine-Like Factor 1 (CKLF-1) is Overexpressed in Keloid Patients: A Potential Indicating Factor for Keloid-Predisposed Individuals.
  10. role in the pathogenesis of psoriasis by promoting the proliferation of microvascular endothelial cells
    Title: Chemokine-like factor 1-derived C-terminal peptides induce the proliferation of dermal microvascular endothelial cells in psoriasis.
Submit: New GeneRIF Correction See all GeneRIFs (18)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of chemokine-like factor (CKLF; HSPC224) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed
Knockdown of chemokine-like factor (CKLF) by siRNA has both activating and inhibiting activities on HIV-1 replication in HeLa P4/R5 cells, suggesting a regulatory role in HIV replication PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Readthrough CKLF-CMTM1

Readthrough gene: CKLF-CMTM1, Included gene: CMTM1

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chemokine activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in lymphocyte chemotaxis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in macrophage chemotaxis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in neutrophil chemotaxis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in secretion by cell IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in extracellular region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
  
located_in membrane HDA PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
chemokine-like factor
Names
chemokine-like factor 1
chemokine-like factor 2
chemokine-like factor 3
chemokine-like factor 4
transmembrane proteolipid

NCBI Reference Sequences (RefSeq)

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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_001040138.3 → NP_001035228.1  chemokine-like factor isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the coding region and 3' UTR, compared to variant 1. The encoded isoform (e) is shorter and contains a unique C-terminus, compared to isoform a.
    Source sequence(s)
    BU189908, DA113473, DA804889
    Consensus CDS
    CCDS45502.1
    UniProtKB/TrEMBL
    I7GPS8
    Related
    ENSP00000416678.2, ENST00000417030.2

  2. NM_016326.3 → NP_057410.1  chemokine-like factor isoform c

    See identical proteins and their annotated locations for NP_057410.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two an in-frame exons in the coding region, compared to variant 1. It encodes a shorter isoform (c), also known as an isoform CKL3.
    Source sequence(s)
    AF135381, BU189908, DA113473
    Consensus CDS
    CCDS10806.1
    UniProtKB/Swiss-Prot
    Q9UBR5
    Related
    ENSP00000355417.4, ENST00000362093.4

  3. NM_016951.4 → NP_058647.1  chemokine-like factor isoform a

    See identical proteins and their annotated locations for NP_058647.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript, and encodes the longest isoform (a), also known as an isoform CKLF2.
    Source sequence(s)
    AF135380
    Consensus CDS
    CCDS10807.1
    UniProtKB/Swiss-Prot
    C9JE38, Q9UBR5, Q9UHM7, Q9UHN8, Q9UI41
    UniProtKB/TrEMBL
    I7GPS8
    Related
    ENSP00000264001.5, ENST00000264001.9
    Conserved Domains (1) summary
    pfam01284
    Location:26 → 98
    MARVEL; Membrane-associating domain

  4. NM_181640.2 → NP_857591.1  chemokine-like factor isoform b

    See identical proteins and their annotated locations for NP_857591.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (b), also known as an isoform CKLF1.
    Source sequence(s)
    AF096895, BU189908, DA113473
    Consensus CDS
    CCDS10808.1
    UniProtKB/TrEMBL
    Q5BJH6
    Related
    ENSP00000264003.4, ENST00000351137.8

  5. NM_181641.2 → NP_857592.1  chemokine-like factor isoform d

    See identical proteins and their annotated locations for NP_857592.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (d), also known as an isoform CKLF4.
    Source sequence(s)
    AF145216, BU189908, DA113473
    Consensus CDS
    CCDS10809.1
    UniProtKB/Swiss-Prot
    Q9UBR5
    Related
    ENSP00000290771.4, ENST00000345436.8

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    66552563..66566287
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    72346858..72360582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001040139.1: Suppressed sequence

    Description
    NM_001040139.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UBR5.1 GenPept UniProtKB/Swiss-Prot:Q9UBR5

Gene LinkOut

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