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Aliases for CMTM1 Gene

Aliases for CMTM1 Gene

  • CKLF Like MARVEL Transmembrane Domain Containing 1 2 3 5
  • Chemokine-Like Factor Superfamily Member 1 3 4
  • Chemokine-Like Factor Super Family 1 2 3
  • Chemokine-Like Factor Superfamily 1 2 3
  • CKLFSF1 3 4
  • CKLF-Like MARVEL Transmembrane Domain-Containing Protein 1 3
  • CKLF-Like MARVEL Transmembrane Domain Containing 1 2
  • Chemokine-Like Factor-Like Protein CKLFH1 3
  • CKLFH1 3
  • CKLFH 3

External Ids for CMTM1 Gene

Previous HGNC Symbols for CMTM1 Gene


Previous GeneCards Identifiers for CMTM1 Gene

  • GC16P065157
  • GC16P066600
  • GC16P052476

Summaries for CMTM1 Gene

Entrez Gene Summary for CMTM1 Gene

  • 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]

GeneCards Summary for CMTM1 Gene

CMTM1 (CKLF Like MARVEL Transmembrane Domain Containing 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include cytokine activity. An important paralog of this gene is CKLF-CMTM1.

Additional gene information for CMTM1 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CMTM1 Gene

Genomics for CMTM1 Gene

GeneHancer (GH) Regulatory Elements for CMTM1 Gene

Promoters and enhancers for CMTM1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J066566 Promoter 0.6 EPDnew 650.7 0.0 -2 0.1 SUZ12 ENSG00000277978 CMTM1 CKLF-CMTM1
GH16J066567 Promoter 0.6 EPDnew 650.7 +0.3 271 0.1 SUZ12 ENSG00000277978 CMTM1 CMTM2 CKLF-CMTM1
GH16J066564 Enhancer 0.4 ENCODE dbSUPER 650.7 -1.5 -1498 0.2 ENSG00000277978 CMTM1 BEAN1 CKLF GC16M066555 PIR36312 CKLF-CMTM1
GH16J066515 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 1.3 -45.2 -45167 12.4 MLX DMAP1 IRF4 YY1 SLC30A9 ZNF143 SP3 NFYC SSRP1 GLIS1 TK2 CKLF ENSG00000260465 ZDHHC1 NAE1 BEAN1 CKLF-CMTM1 E2F4 CMTM2 PLEKHG4
GH16J066161 Enhancer 0.4 FANTOM5 2.3 -404.3 -404260 0.4 SREBF1 ZBTB11 CMTM1 CMTM2 LOC105371316 GC16M066229
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CMTM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CMTM1 gene promoter:

Genomic Locations for CMTM1 Gene

Genomic Locations for CMTM1 Gene
12,747 bases
Plus strand

Genomic View for CMTM1 Gene

Genes around CMTM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CMTM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CMTM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CMTM1 Gene

Proteins for CMTM1 Gene

neXtProt entry for CMTM1 Gene

Post-translational modifications for CMTM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CMTM1 Gene

Domains & Families for CMTM1 Gene

Gene Families for CMTM1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for CMTM1 Gene


Suggested Antigen Peptide Sequences for CMTM1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the chemokine-like factor family.
  • Belongs to the chemokine-like factor family.
genes like me logo Genes that share domains with CMTM1: view

Function for CMTM1 Gene

Gene Ontology (GO) - Molecular Function for CMTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005125 cytokine activity IEA --
genes like me logo Genes that share ontologies with CMTM1: view
genes like me logo Genes that share phenotypes with CMTM1: view

Animal Model Products

CRISPR Products

miRNA for CMTM1 Gene

miRTarBase miRNAs that target CMTM1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CMTM1

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CMTM1 Gene

Localization for CMTM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CMTM1 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CMTM1 gene
Compartment Confidence
plasma membrane 3
extracellular 3
nucleus 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CMTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,IBA --
genes like me logo Genes that share ontologies with CMTM1: view

Pathways & Interactions for CMTM1 Gene

SuperPathways for CMTM1 Gene

No Data Available

Interacting Proteins for CMTM1 Gene

Gene Ontology (GO) - Biological Process for CMTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006935 chemotaxis IEA --
GO:0010469 regulation of signaling receptor activity IEA --
genes like me logo Genes that share ontologies with CMTM1: view

No data available for Pathways by source and SIGNOR curated interactions for CMTM1 Gene

Drugs & Compounds for CMTM1 Gene

No Compound Related Data Available

Transcripts for CMTM1 Gene

mRNA/cDNA for CMTM1 Gene

Unigene Clusters for CMTM1 Gene

CKLF-like MARVEL transmembrane domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CMTM1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CMTM1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b · 8c ^ 9 ^ 10a · 10b ^ 11a · 11b
SP1: - - - - -
SP2: - - -
SP3: - - - -
SP4: - -
SP5: - - -
SP6: - -
SP7: - - - -
SP8: - - - - -
SP9: -
SP10: - - -
SP11: - - -
SP12: - - -
SP13: - - - - - - -
SP14: - - - - - - - -
SP15: - - - - - - - - - -
SP16: - - - - - -
SP18: - - - - - - - - - - - - - - -

Relevant External Links for CMTM1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CMTM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CMTM1 Gene

mRNA differential expression in normal tissues according to GTEx for CMTM1 Gene

This gene is overexpressed in Testis (x28.0) and Whole Blood (x7.1).

NURSA nuclear receptor signaling pathways regulating expression of CMTM1 Gene:


SOURCE GeneReport for Unigene cluster for CMTM1 Gene:


mRNA Expression by UniProt/SwissProt for CMTM1 Gene:

Tissue specificity: Highly expressed in testis.

Evidence on tissue expression from TISSUES for CMTM1 Gene

  • Lung(3.7)
  • Muscle(2.8)
  • Liver(2.7)
  • Nervous system(2.5)
  • Heart(2.4)
genes like me logo Genes that share expression patterns with CMTM1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CMTM1 Gene

Orthologs for CMTM1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for CMTM1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC100610567 33
  • 99.18 (n)
-- 34
  • 99 (a)
(Bos Taurus)
Mammalia LOC525286 33
  • 74.26 (n)
(Canis familiaris)
Mammalia CMTM1 34 33
  • 68.45 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 39 (a)
(Mus musculus)
Mammalia Cmtm1 34
  • 23 (a)
Species where no ortholog for CMTM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for CMTM1 Gene

Gene Tree for CMTM1 (if available)
Gene Tree for CMTM1 (if available)
Evolutionary constrained regions (ECRs) for CMTM1: view image

Paralogs for CMTM1 Gene

Paralogs for CMTM1 Gene

(2) SIMAP similar genes for CMTM1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with CMTM1: view

Variants for CMTM1 Gene

Sequence variations from dbSNP and Humsavar for CMTM1 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000154538 -- 66,574,882(+) C/G/T intron_variant
rs1000211221 -- 66,567,241(+) G/A intron_variant
rs1000214068 -- 66,573,258(+) T/A intron_variant
rs1000334257 -- 66,575,868(+) C/ intron_variant
rs1000418669 -- 66,574,576(+) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CMTM1 Gene

Variant ID Type Subtype PubMed ID
dgv123n111 CNV duplication 26073780
esv3638871 CNV gain 21293372
nsv472890 CNV novel sequence insertion 20440878

Variation tolerance for CMTM1 Gene

Residual Variation Intolerance Score: 46.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.95; 19.56% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CMTM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CMTM1 Gene

Disorders for CMTM1 Gene

Additional Disease Information for CMTM1

No disorders were found for CMTM1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CMTM1 Gene

Publications for CMTM1 Gene

  1. 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. (PMID: 15147728) Wang L … Ma D (The international journal of biochemistry & cell biology 2004) 3 4 22 58
  2. Identification of eight genes encoding chemokine-like factor superfamily members 1-8 (CKLFSF1-8) by in silico cloning and experimental validation. (PMID: 12782130) Han W … Ma D (Genomics 2003) 2 3 4 58
  3. A functional promoter region of the CKLFSF2 gene is located in the last intron/exon region of the upstream CKLFSF1 gene. (PMID: 15778092) Xu M … Ma D (The international journal of biochemistry & cell biology 2005) 3 22 58
  4. CMTM1_v17 is associated with chemotherapy resistance and poor prognosis in non-small cell lung cancer. (PMID: 28129775) Si J … Yang Y (World journal of surgical oncology 2017) 3 58
  5. Systematic investigation of CMTM family genes suggests relevance to glioblastoma pathogenesis and CMTM1 and CMTM3 as priority targets. (PMID: 25931111) Delic S … Riemenschneider MJ (Genes, chromosomes & cancer 2015) 3 58

Products for CMTM1 Gene

Sources for CMTM1 Gene

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