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CMTM1 CKLF like MARVEL transmembrane domain containing 1 [ Homo sapiens (human) ]

Gene ID: 113540, updated on 2-May-2024

Summary

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Official Symbol
CMTM1provided by HGNC
Official Full Name
CKLF like MARVEL transmembrane domain containing 1provided by HGNC
Primary source
HGNC:HGNC:19172
See related
Ensembl:ENSG00000089505 MIM:607884; AllianceGenome:HGNC:19172
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
CKLFH; CKLFH1; CKLFSF1
Summary
This gene belongs to the chemokine-like factor gene superfamily, a novel family that is similar to the chemokine and the transmembrane 4 superfamilies of signaling molecules. The protein encoded by this gene may play an important role in testicular development. Alternatively spliced transcript variants encoding different isoforms have been identified. Naturally occurring read-through transcription occurs between this locus and the neighboring locus CKLF (chemokine-like factor).[provided by RefSeq, Feb 2011]
Expression
Biased expression in testis (RPKM 16.1), spleen (RPKM 1.5) and 1 other tissue See more
Orthologs
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Genomic context

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Location:
16q21
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (66566439..66579135)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72360734..72373430)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (66600342..66613038)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes 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 chemokine like factor Neighboring gene CKLF like MARVEL transmembrane domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7561 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7562 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66642903-66643714 Neighboring gene CKLF like MARVEL transmembrane domain containing 4 Neighboring gene CKLF like MARVEL transmembrane domain containing 3

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. CMTM1_v17 is associated with chemotherapy resistance and poor prognosis in non-small cell lung cancer. Si J, et al. World J Surg Oncol, 2017 Jan 28. PMID 28129775, Free PMC Article
  2. CMTM1_v17 is a novel potential therapeutic target in breast cancer. Wang J, et al. Oncol Rep, 2014 Nov. PMID 25175386
  3. Molecular cloning and characterization of chemokine-like factor super family member 1 (CKLFSF1), a novel human gene with at least 23 alternative splicing isoforms in testis tissue. Wang L, et al. Int J Biochem Cell Biol, 2004 Aug. PMID 15147728
  4. Systematic investigation of CMTM family genes suggests relevance to glioblastoma pathogenesis and CMTM1 and CMTM3 as priority targets. Delic S, et al. Genes Chromosomes Cancer, 2015 Jul. PMID 25931111
  5. A functional promoter region of the CKLFSF2 gene is located in the last intron/exon region of the upstream CKLFSF1 gene. Xu M, et al. Int J Biochem Cell Biol, 2005 Jun. PMID 15778092

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. High CMTM1_v17 expression was associated with chemotherapy resistance in lung cancer.
    Title: CMTM1_v17 is associated with chemotherapy resistance and poor prognosis in non-small cell lung cancer.
  2. CMTM1 and 3 are priority targets in glioblastomas. First insights into signalling of these two genes that might be conveyed by growth factor receptor, Src family kinase and WNT activation was presented.
    Title: Systematic investigation of CMTM family genes suggests relevance to glioblastoma pathogenesis and CMTM1 and CMTM3 as priority targets.
  3. Study shows that CMTM1_v17 is highly expressed in human testis and many human tumor tissues and cell lines and seems to enhance cell proliferation and resistance to tumor necrosis factor-alpha (TNF-alpha)-induced apoptosis in MDA-MB-231 breast cancer cells.
    Title: CMTM1_v17 is a novel potential therapeutic target in breast cancer.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: New genetic associations detected in a host response study to hepatitis B vaccine.
  5. gene structure, mapping to chromsome 16, identification of altenative transcription start sites, expression in spermatocyte and testes
    Title: Molecular cloning and characterization of chemokine-like factor super family member 1 (CKLFSF1), a novel human gene with at least 23 alternative splicing isoforms in testis tissue.
  6. Bioinformatics based on CKLF2 cDNA and protein sequences in combination with experimental validation identified CKLFSF1-8 gene clusters, between the SCY and the TM4SF gene families. The 8 family members were cloned and characterized.
    Title: Identification of eight genes encoding chemokine-like factor superfamily members 1-8 (CKLFSF1-8) by in silico cloning and experimental validation.
  7. novel evidence that the final intron/exon region of the CKLFSF1 gene contains a novel eukaryotic promoter capable of directing expression of the downstream gene, CKLFSF2
    Title: A functional promoter region of the CKLFSF2 gene is located in the last intron/exon region of the upstream CKLFSF1 gene.
Submit: New GeneRIF Correction

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)

Genotypes

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: CKLF

Homology

Clone Names

  • MGC71870

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cytokine activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chemotaxis IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
CKLF-like MARVEL transmembrane domain-containing protein 1
Names
chemokine-like factor super family 1
chemokine-like factor superfamily 1
chemokine-like factor superfamily member 1
chemokine-like factor-like protein CKLFH1

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_052999.4 → NP_443725.3  CKLF-like MARVEL transmembrane domain-containing protein 1 isoform 13

    See identical proteins and their annotated locations for NP_443725.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (17) encodes the longest isoform (13).
    Source sequence(s)
    AC010542, AY174119, BC057852, DN992496
    Consensus CDS
    CCDS10812.2
    UniProtKB/TrEMBL
    E9PIL3
    Related
    ENSP00000368814.2, ENST00000379500.7
    Conserved Domains (1) summary
    cl04571
    Location:131 → 216
    MARVEL; Membrane-associating domain

  2. NM_181268.3 → NP_851785.2  CKLF-like MARVEL transmembrane domain-containing protein 1 isoform 14

    Status: REVIEWED

    Description
    Transcript Variant: This variant (18) lacks an exon segment, compared to variant 17, which results in a translational frameshift in the last coding exon. The encoded isoform (14) is shorter and contains a distinct C-terminus, compared to the protein (isoform 13) encoded by variant 17.
    Source sequence(s)
    AC010542, AY174119, BC057852, DN992496
    Consensus CDS
    CCDS45504.1
    UniProtKB/TrEMBL
    E9PAX0
    Related
    ENSP00000330061.6, ENST00000328020.10
    Conserved Domains (1) summary
    cl04571
    Location:131 → 216
    MARVEL; Membrane-associating domain

  3. NM_181269.3 → NP_851786.1  CKLF-like MARVEL transmembrane domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_851786.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame segment of the first coding exon, compared to variant 17. The encoded isoform (1) is shorter than the protein (isoform 13) encoded by variant 17.
    Source sequence(s)
    AY174118, DN992496
    Consensus CDS
    CCDS45503.1
    UniProtKB/Swiss-Prot
    Q2PPY5, Q6PEV5, Q8IU76, Q8IU83, Q8IU86, Q8IU93, Q8IZ87, Q8IZ88, Q8IZ89, Q8IZ90, Q8IZ91, Q8IZ92, Q8IZ93, Q8IZ94, Q8IZ95, Q8IZ96, Q96JC2, Q96JC3
    Related
    ENSP00000405729.2, ENST00000457188.6
    Conserved Domains (1) summary
    cl14876
    Location:2 → 98
    Zinc_peptidase_like; Zinc peptidases M18, M20, M28, and M42

  4. NM_181270.3 → NP_851787.1  CKLF-like MARVEL transmembrane domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_851787.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has multiple differences in the coding region, compared to variant 17, one of which results in a translational frameshift in the last coding exon. The encoded isoform (2) is shorter and contains a distinct C-terminus, compared to the protein (isoform 13) encoded by variant 17.
    Source sequence(s)
    AY174119, DN992496
    Consensus CDS
    CCDS54019.1
    UniProtKB/Swiss-Prot
    Q8IZ96
    Related
    ENSP00000432398.1, ENST00000528324.5
    Conserved Domains (1) summary
    cl14876
    Location:2 → 98
    Zinc_peptidase_like; Zinc peptidases M18, M20, M28, and M42

  5. NM_181271.3 → NP_851788.1  CKLF-like MARVEL transmembrane domain-containing protein 1 isoform 3

    See identical proteins and their annotated locations for NP_851788.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences in the coding region but maintains the reading frame, compared to variant 17. The encoded isoform (3) is shorter than the protein (isoform 13) encoded by variant 17.
    Source sequence(s)
    AY174120, DN992496
    Consensus CDS
    CCDS10810.1
    UniProtKB/Swiss-Prot
    Q8IZ96
    Related
    ENSP00000331428.7, ENST00000332695.11

  6. NM_181272.3 → NP_851789.1  CKLF-like MARVEL transmembrane domain-containing protein 1 isoform 4

    See identical proteins and their annotated locations for NP_851789.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple differences in the 5' coding region, compared to variant 17. The encoded isoform (4) is shorter than the protein (isoform 13) encoded by variant 17.
    Source sequence(s)
    AY174121, DN992496
    Consensus CDS
    CCDS10811.1
    UniProtKB/Swiss-Prot
    Q8IZ96
    Related
    ENSP00000337119.6, ENST00000336328.10

  7. NM_181283.3 → NP_851800.1  CKLF-like MARVEL transmembrane domain-containing protein 1 isoform 5

    See identical proteins and their annotated locations for NP_851800.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has multiple differences in the coding region, compared to variant 17, one of which results in a translational frameshift in the last coding exon. The encoded isoform (5) is shorter and contains a distinct C-terminus, compared to the protein (isoform 13) encoded by variant 17.
    Source sequence(s)
    AY174122, DN992496
    Consensus CDS
    CCDS54020.1
    UniProtKB/Swiss-Prot
    Q8IZ96
    Related
    ENSP00000432687.1, ENST00000531885.5

  8. NM_181296.3 → NP_851813.1  CKLF-like MARVEL transmembrane domain-containing protein 1 isoform 12

    See identical proteins and their annotated locations for NP_851813.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (16) has multiple differences in the coding region, compared to variant 17, one of which results in a translational frameshift in the last coding exon. The encoded isoform (12) is shorter and contains a distinct C-terminus, compared to the protein (isoform 13) encoded by variant 17.
    Source sequence(s)
    AY174133, DN992496
    Consensus CDS
    CCDS54021.1
    UniProtKB/Swiss-Prot
    Q8IZ96
    Related
    ENSP00000435020.1, ENST00000533666.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    66566439..66579135
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    72360734..72373430
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_181285.1: Suppressed sequence

    Description
    NM_181285.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  2. NM_181286.1: Suppressed sequence

    Description
    NM_181286.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  3. NM_181287.1: Suppressed sequence

    Description
    NM_181287.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  4. NM_181288.1: Suppressed sequence

    Description
    NM_181288.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  5. NM_181289.2: Suppressed sequence

    Description
    NM_181289.2: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.

  6. NM_181290.1: Suppressed sequence

    Description
    NM_181290.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  7. NM_181292.1: Suppressed sequence

    Description
    NM_181292.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  8. NM_181293.1: Suppressed sequence

    Description
    NM_181293.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  9. NM_181294.1: Suppressed sequence

    Description
    NM_181294.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  10. NM_181295.1: Suppressed sequence

    Description
    NM_181295.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  11. NM_181297.1: Suppressed sequence

    Description
    NM_181297.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  12. NM_181298.1: Suppressed sequence

    Description
    NM_181298.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  13. NM_181299.1: Suppressed sequence

    Description
    NM_181299.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  14. NM_181300.1: Suppressed sequence

    Description
    NM_181300.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  15. NM_181301.1: Suppressed sequence

    Description
    NM_181301.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IZ96.1 GenPept UniProtKB/Swiss-Prot:Q8IZ96

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