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

CMTM1 Gene

protein-coding   GIFtS: 43
GCID: GC16P066600

CKLF-Like MARVEL Transmembrane Domain Containing 1

(Previous names: chemokine-like factor super family 1, chemokine-like factor...)
(Previous symbol: CKLFSF1)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
CKLF-Like MARVEL Transmembrane Domain Containing 11 2     CKLFH2
CKLFSF11 2 3     CKLFH12
Chemokine-Like Factor Super Family 11 2     Chemokine-Like Factor-Like Protein CKLFH12
Chemokine-Like Factor Superfamily 11 2     CKLF-Like MARVEL Transmembrane Domain-Containing Protein 12
Chemokine-Like Factor Superfamily Member 12 3     

External Ids:    HGNC: 191721   Entrez Gene: 1135402   Ensembl: ENSG000000895057   OMIM: 6078845   UniProtKB: Q8IZ963   

Export aliases for CMTM1 gene to outside databases

Previous GC identifers: GC16P065157 GC16P052476


(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 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. Diseases associated with CMTM1 include hepatitis b, and hepatitis. GO annotations related to this gene include cytokine activity. An important paralog of this gene is 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000016.9  NT_010498.15  NC_018927.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CMTM1 gene promoter:
         MyoD   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): CMTM1 promoter sequence
   Search SABiosciences Chromatin IP Primers for CMTM1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CMTM1


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

CMTM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CMTM1 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P066600:  view genomic region     (about GC identifiers)

Start:
66,600,294 bp from pter      End:
66,613,040 bp from pter
Size:
12,747 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CKLF1_HUMAN, Q8IZ96 (See protein sequence)
Recommended Name: CKLF-like MARVEL transmembrane domain-containing protein 1  
Size: 169 amino acids; 18576 Da
Subcellular location: Membrane; Multi-pass membrane protein
Secondary accessions: Q2PPY5 Q6PEV5 Q8IU76 Q8IU83 Q8IU86 Q8IU93 Q8IZ87 Q8IZ88 Q8IZ89 Q8IZ90
Q8IZ91 Q8IZ92 Q8IZ93 Q8IZ94 Q8IZ95 Q96JC2 Q96JC3
Alternative splicing: 17 isoforms:  Q8IZ96-1   Q8IZ96-2   Q8IZ96-3   Q8IZ96-4   Q8IZ96-5   Q8IZ96-6   Q8IZ96-7   Q8IZ96-8   
Q8IZ96-9   Q8IZ96-10   Q8IZ96-11   Q8IZ96-12   Q8IZ96-13   Q8IZ96-14   Q8IZ96-15   Q8IZ96-16   
Q8IZ96-17   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CMTM1: NX_Q8IZ96

Explore proteomics data for CMTM1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8IZ96

  • CMTM1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CMTM1 Protein Expression
    REFSEQ proteins (8 alternative transcripts): 
    NP_443725.3  NP_851785.2  NP_851786.1  NP_851787.1  NP_851788.1  NP_851789.1  NP_851800.1  NP_851813.1  

    ENSEMBL proteins: 
     ENSP00000331428   ENSP00000337119   ENSP00000432398   ENSP00000431303   ENSP00000437079  
     ENSP00000432687   ENSP00000435755   ENSP00000331494   ENSP00000434434   ENSP00000432387  
     ENSP00000405729   ENSP00000435020   ENSP00000435786   ENSP00000368814   ENSP00000330061  
     ENSP00000431135   ENSP00000435485   ENSP00000431609   ENSP00000435208   ENSP00000433160  
     ENSP00000443374  

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    Cloud-Clone Corp. Proteins for CMTM1 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615extracellular space IEA--
    GO:0016020membrane ----
    GO:0016021integral to membrane IEA--

    CMTM1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR008253 Marvel

    Graphical View of Domain Structure for InterPro Entry Q8IZ96

    ProtoNet protein and cluster: Q8IZ96

    UniProtKB/Swiss-Prot: CKLF1_HUMAN, Q8IZ96
    Similarity: Belongs to the chemokine-like factor family
    Similarity: Contains 1 MARVEL domain


    CMTM1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005125cytokine activity IEA--
         
    CMTM1 for ontologies           About GeneDecksing


    Animal Models:
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, 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 Oct 2013 via Entrez Gene).
    About This Section




    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CMTM1

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006935chemotaxis IEA--

    CMTM1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CMTM1 (CKLF1)

    Search CenterWatch for drugs/clinical trials and news about CMTM1 / CKLF1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CMTM1 gene (23 alternative transcripts): 
    NM_052999.3  NM_181268.2  NM_181269.2  NM_181270.2  NM_181271.2  NM_181272.2  NM_181283.2  NM_181296.2  
    NM_181285.1  NM_181286.1  NM_181287.1  NM_181288.1  NM_181289.2  NM_181290.1  NM_181292.1  NM_181293.1  
    NM_181294.1  NM_181295.1  NM_181297.1  NM_181298.1  NM_181299.1  NM_181300.1  NM_181301.1  

    Unigene Clusters for CMTM1:

    CKLF-like MARVEL transmembrane domain containing 1
    Hs.698621  [show with all ESTs], Hs.722591
    Unigene Representative Sequences: BU588362, NM_181296
    18/21 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 21):
    ENST00000332695(uc002epl.4) ENST00000336328(uc002epk.4) ENST00000528324(uc002eph.4)
    ENST00000529386(uc002epd.4) ENST00000528484(uc002epe.4) ENST00000531885(uc002epj.4)
    ENST00000533915(uc002epc.4 uc002eps.3) ENST00000333001(uc002epb.4)
    ENST00000529506(uc002epg.4) ENST00000533078(uc002epf.4) ENST00000457188(uc002epi.4)
    ENST00000533666(uc002epa.4) ENST00000533953 ENST00000379500(uc002epm.4 uc002epo.4 uc010cds.3 uc002epn.4 uc002epr.4)
    ENST00000328020 ENST00000465057 ENST00000479381(uc002epp.4) ENST00000534143

    miRNA
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    Inhib. RNA
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    23 DOTS entries:

    DT.95260932  DT.100025067  DT.100025059  DT.75155006  DT.100025065  DT.120724968  DT.100025061  DT.100025064 
    DT.100797384  DT.100797385  DT.120724942  DT.100025054  DT.100025938  DT.97839329  DT.100025058  DT.100025062 
    DT.100642508  DT.100754363  DT.100866960  DT.120724939  DT.120725010  DT.75197958  DT.91914577 

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

    NM_181269 NM_016326 AY174138 NM_181288 NM_181292 NM_181290 BM768745 AY174134 
    NM_181295 AJ712987 AI265924 BQ613826 AA778301 AI968172 BQ130559 BQ130813 
    AA338760 BM929895 BU782576 BC004380 AL042424 NM_181270 AI631831 AI206661 

    GeneLoc Exon Structure

    5/18 Alternative Splicing Database (ASD) splice patterns (SP) for CMTM1 (see all 18)    About this scheme

    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:                          -     -           -                                                                                       


    ECgene alternative splicing isoforms for CMTM1

    (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

    CMTM1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGTCACCCA
    CMTM1 Expression
    About this image


    See CMTM1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CMTM1

    SOURCE GeneReport for Unigene clusters: Hs.698621 Hs.722591

    UniProtKB/Swiss-Prot: CKLF1_HUMAN, Q8IZ96
    Tissue specificity: Highly expressed in testis

        SABiosciences Expression via Pathway-Focused PCR Arrays including CMTM1: 
              Inflammatory Response & Autoimmunity 384HT in human mouse rat
              Chemokines & Receptors in human mouse rat

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    In Situ
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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 CMTM1 gene from 3/7 species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cmtm11 , 5 CKLF-like MARVEL transmembrane domain containing 11, 5 49.59(n)1
    34.15(a)1
      8 (53.04 cM)5
    1005041641  NM_181990.21  NP_871790.21 
     1042813475 
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    32(a)
    1 → many
    11(10903706-10906364)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    26(a)
    1 → many
    GL343295.1(60779-70851)


    ENSEMBL Gene Tree for CMTM1 (if available)
    TreeFam Gene Tree for CMTM1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CMTM1 gene
    CKLF2  CKLF-CMTM12  
    2 SIMAP similar genes for CMTM1 using alignment to 5 protein entries:     CKLF1_HUMAN (see all proteins):
    CKLF-CMTM1    CKLF

    CMTM1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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

    1 SNPs in CMTM1 are shown    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0530394
    ----see VAR_0530392 S T mis40--------

    HapMap Linkage Disequilibrium report for CMTM1 (66600294 - 66613040 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for CMTM1:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv906785CNV Loss21882294
    nsv906786CNV Loss21882294
    nsv906787CNV Gain21882294

    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for CMTM1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 607884    OMIM disorders: --

    2 diseases for CMTM1:    About MalaCards
    hepatitis b    hepatitis


    CMTM1 for disorders           About GeneDecksing

    Human Genome Epidemiology (HuGE) Navigator: CMTM1 (2 documents)

    Export disorders for CMTM1 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 CMTM1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with CMTM1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of eight genes encoding chemokine-like factor superfamily members 1-8 (CKLFSF1-8) by in silico cloning and experimental validation. (PubMed id 12782130)1, 2, 3 Han W.... Ma D. (2003)
    2. 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. (PubMed id 15147728)1, 2, 9 Wang L....Ma D. (2004)
    3. A functional promoter region of the CKLFSF2 gene is located in the last intron/exon region of the upstream CKLFSF1 gene. (PubMed id 15778092)1, 9 Xu M....Ma D. (2005)
    4. Bcl2-associated Athanogene 3 Interactome Analysis Reve als a New Role in Modulating Proteasome Activity. (PubMed id 23824909)1 Chen Y....Ge F. (2013)
    5. New genetic associations detected in a host response study to hepatitis B vaccine. (PubMed id 20237496)1 Davila S....Seielstad M. (2010)
    6. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)2 Martin J.... Pennacchio L.A. (2004)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    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)9 Xu M....Ma D. (2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 113540 HGNC: 19172 AceView: CKLFandCKLFSF1 Ensembl:ENSG00000089505 euGenes: HUgn113540
    ECgene: CMTM1 H-InvDB: CMTM1

    (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 CMTM1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CMTM1 gene:
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