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

    Gene ID: 113540, updated on 27-Nov-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
    mouse all
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    Genomic context

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    See CMTM1 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 (66566439..66579135)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72360734..72373430)
    RS_2024_09 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)

    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_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
      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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