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

CMTM3 Gene

protein-coding   GIFtS: 51
GCID: GC16P066637

CKLF-Like MARVEL Transmembrane Domain Containing 3

(Previous name: chemokine-like factor superfamily 3)
(Previous symbol: CKLFSF3)
  Search for CMTM3
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

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
CKLF-Like MARVEL Transmembrane Domain Containing 31 2
CKLFSF31 2 3
Chemokine-Like Factor Superfamily Member 32 3
Chemokine-Like Factor Superfamily 31
BNAS22
CKLF-Like MARVEL Transmembrane Domain-Containing Protein 32

External Ids:    HGNC: 191741   Entrez Gene: 1239202   Ensembl: ENSG000001409317   OMIM: 6078865   UniProtKB: Q96MX03   
ORGUL members:         
NONCODE14:n410469 n410473      

Export aliases for CMTM3 gene to outside databases

Previous GC identifers: GC16P065196 GC16P052514


(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 CMTM3 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. This gene is one of several chemokine-like factor
genes located in a cluster on chromosome 16. Alternatively spliced transcript variants containing different 5'
UTRs, but encoding the same protein, have been identified. (provided by RefSeq, Jul 2008)

GeneCards Summary for CMTM3 Gene: 
CMTM3 (CKLF-like MARVEL transmembrane domain containing 3) is a protein-coding gene, and is affiliated with the lncRNA class. GO annotations related to this gene include cytokine activity. An important paralog of this gene is CMTM5.




(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  NC_018927.2  NT_010498.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CMTM3 gene promoter:
         NF-kappaB1   NF-kappaB   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCMTM3 promoter sequence
   Search SABiosciences Chromatin IP Primers for CMTM3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CMTM3


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-q22.3

CMTM3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CMTM3 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P066637:  view genomic region     (about GC identifiers)

Start:
66,637,777 bp from pter      End:
66,647,795 bp from pter
Size:
10,019 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for CMTM3

(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: CKLF3_HUMAN, Q96MX0 (See protein sequence)
Recommended Name: CKLF-like MARVEL transmembrane domain-containing protein 3  
Size: 182 amino acids; 19714 Da
Subcellular location: Membrane; Multi-pass membrane protein
Secondary accessions: A6NCL9 Q8IUU8 Q8IWQ6 Q8IYE2 Q8IZ39 Q8IZ59
Alternative splicing: 2 isoforms:  Q96MX0-1   Q96MX0-2   

Explore the universe of human proteins at neXtProt for CMTM3: NX_Q96MX0

Explore proteomics data for CMTM3 at MOPED 

CMTM3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

CMTM3 Protein Expression

REFSEQ proteins (2 alternative transcripts): 
NP_653202.1  NP_853531.1  

ENSEMBL proteins: 
 ENSP00000457451   ENSP00000400482   ENSP00000454628   ENSP00000455758   ENSP00000354579  
 ENSP00000461758   ENSP00000462554   ENSP00000455851   ENSP00000457589   ENSP00000456426  
 ENSP00000462613   ENSP00000460330   ENSP00000461654   ENSP00000457923   ENSP00000353199  

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Cloud-Clone Corp. Proteins for CMTM3 

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--

CMTM3 for ontologies           About GeneDecksing



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Cloud-Clone Corp. CLIAs for CMTM3


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
2 InterPro protein domains:
 IPR021128 MARVEL-like_dom
 IPR008253 Marvel

Graphical View of Domain Structure for InterPro Entry Q96MX0

ProtoNet protein and cluster: Q96MX0

1 Blocks protein domain: IPB008253 Marvel

UniProtKB/Swiss-Prot: CKLF3_HUMAN, Q96MX0
Similarity: Belongs to the chemokine-like factor family
Similarity: Contains 1 MARVEL domain


CMTM3 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--
     
CMTM3 for ontologies           About GeneDecksing


Animal Models:
   inGenious Targeting Laboratory - Custom generated mouse model solutions for CMTM3 
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   genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CMTM3 
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miRNA
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hsa-miR-3163 hsa-miR-3140-3p hsa-miR-622 hsa-miR-3175 hsa-miR-105 hsa-miR-4287 hsa-miR-135b hsa-miR-629*
SwitchGear 3'UTR luciferase reporter plasmidCMTM3 3' UTR sequence
Inhib. RNA
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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

SuperPaths for CMTM3 About                                                                                                See pathways by source

SuperPathContained pathways About
1B Cell Receptor Signaling Pathway
B Cell Receptor Signaling Pathway


1 BioSystems Pathway for CMTM3
    B Cell Receptor Signaling Pathway


Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CMTM3

STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

5 Interacting proteins for CMTM3 (Q96MX02, 3 ENSP000003531994) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
MESTQ5EB522, 3, ENSP000002232154MINT-8263027 I2D: score=2 STRING: ENSP00000223215
RABAC1Q9UI142, 3, ENSP000002220084MINT-8267764 I2D: score=2 STRING: ENSP00000222008
BTKQ061873, ENSP000003081764I2D: score=2 STRING: ENSP00000308176
MAPK1P284823, ENSP000002158324I2D: score=2 STRING: ENSP00000215832
BLNKQ8WV283, ENSP000002243374I2D: score=3 STRING: ENSP00000224337
About this table

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

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

CMTM3 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 CMTM3 (CKLF3)

Search CenterWatch for drugs/clinical trials and news about CMTM3 / CKLF3

(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 CMTM3 gene (5 alternative transcripts): 
NM_144601.3  NM_181553.2  NM_001048251.1  NM_181554.1  NM_181555.1  

Unigene Cluster for CMTM3:

CKLF-like MARVEL transmembrane domain containing 3
Hs.298198  [show with all ESTs]
Unigene Representative Sequence: NR_037613
16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000563672 ENST00000424011(uc002epu.3) ENST00000562357 ENST00000562707
ENST00000361909(uc002epv.3) ENST00000460097 ENST00000565666 ENST00000567572(uc002epx.3)
ENST00000564060 ENST00000565922 ENST00000566756(uc002epy.3) ENST00000565003
ENST00000568477 ENST00000566121 ENST00000564247 ENST00000360086
miRNA
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hsa-miR-3163 hsa-miR-3140-3p hsa-miR-622 hsa-miR-3175 hsa-miR-105 hsa-miR-4287 hsa-miR-135b hsa-miR-629*
SwitchGear 3'UTR luciferase reporter plasmidCMTM3 3' UTR sequence
Inhib. RNA
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Additional mRNA sequence: 

AF479813.1 AK056324.1 AK075075.1 AY166714.1 BC023509.1 BC023591.2 BC036042.1 BC040227.1 
BC047701.1 NR_037613.1 NR_037619.1 

14 DOTS entries:

DT.100030736  DT.419471  DT.100887815  DT.95076933  DT.100887837  DT.97855400  DT.100887822  DT.100887814 
DT.100887832  DT.100887808  DT.100887831  DT.120659287  DT.40305308  DT.95076876 

24/400 AceView cDNA sequences (see all 400):

CR597108 CR613081 BG231643 CR616563 BG055808 BG323663 CA308811 CR618108 
BQ446404 AI597911 T39692 AI637864 Z46193 AA351880 AW196460 BQ004224 
AI969469 BC023591 AK056324 BG231815 AI492163 BP367481 AW327573 CB123487 

GeneLoc Exon Structure

5/9 Alternative Splicing Database (ASD) splice patterns (SP) for CMTM3 (see all 9)    About this scheme

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b · 8c · 8d · 8e · 8f ^ 9
SP1:              -     -     -     -     -     -                 -                                                         
SP2:                                      -     -                 -                                                         
SP3:                                      -     -                                                                           
SP4:                                      -     -                 -                                                         
SP5:                                                              -                                                         


ECgene alternative splicing isoforms for CMTM3

(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

CMTM3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TTTGGAGCAT
CMTM3 Expression
About this image


See CMTM3 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for CMTM3

SOURCE GeneReport for Unigene cluster: Hs.298198

UniProtKB/Swiss-Prot: CKLF3_HUMAN, Q96MX0
Tissue specificity: Expressed in the leukocytes, placenta and testis

    SABiosciences Expression via Pathway-Focused PCR Array including CMTM3: 
          Chemokines & Receptors in human mouse rat

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CMTM3

(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 CMTM3 gene from 5/11 species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Cmtm31 , 5 CKLF-like MARVEL transmembrane domain containing 31, 5 85.71(n)1
88.46(a)1
  8 (53.04 cM)5
681191  NM_024217.31  NP_077179.11 
 1043405945 
chicken
(Gallus gallus)
Aves CMTM31 CKLF-like MARVEL transmembrane domain containing 3 68.26(n)
69.46(a)
  414829  NM_001001778.2  NP_001001778.2 
lizard
(Anolis carolinensis)
Reptilia CMTM36
CKLF-like MARVEL transmembrane domain containing 3...
55(a)
1 ↔ 1
GL343295.1(75632-97970)
African clawed frog
(Xenopus laevis)
Amphibia Xl.98112 Xenopus laevis transcribed sequence with weak similarity more 71.34(n)    48051914 
zebrafish
(Danio rerio)
Actinopterygii cmtm31 CKLF-like MARVEL transmembrane domain containing 3 65.8(n)
57.79(a)
  445074  NM_001003468.2  NP_001003468.1 


ENSEMBL Gene Tree for CMTM3 (if available)
TreeFam Gene Tree for CMTM3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for CMTM3 gene
CMTM52  PLP22  
2 SIMAP similar genes for CMTM3 using alignment to 8 protein entries:     CKLF3_HUMAN (see all proteins):
CMTM5    CMTM4

CMTM3 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

10/227 SNPs in CMTM3 are shown (see all 227)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 16 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs285218071,2
C,F--66636017(+) AGGTCC/TGGCCA 1 -- us2k11Minor allele frequency- T:0.00CSA 1
rs1387769301,2
--66636071(+) GAGGCA/GGGAAG 1 -- us2k10--------
rs1456683191,2
C--66636384(+) AGGGT-/AAAAAA 2 -- us2k10--------
rs1153148081,2
F--66636430(+) TTGCTT/GCTTCT 2 -- us2k11Minor allele frequency- G:0.01WA 118
rs1166940671,2
F--66636444(+) TCTTCT/GTCTTT 2 -- us2k11Minor allele frequency- G:0.03WA 118
rs1827676451,2
--66636449(+) TTCTTC/TTTTCT 2 -- us2k10--------
rs1865221081,2
--66636532(+) GCAACC/TTCTGC 2 -- us2k10--------
rs1917423991,2
--66636560(+) TTCTCA/CTGCCT 2 -- us2k10--------
rs1412533421,2
--66636606(+) CACCAC/TGCCCA 3 -- us2k10--------
rs1503622031,2
C--66636681(+) CTGACC/TTCAGG 4 -- us2k10--------

HapMap Linkage Disequilibrium report for CMTM3 (66637777 - 66647795 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for CMTM3:    About this table     
Variant IDTypeSubtypePubMed ID
nsv906786CNV Loss21882294

SABiosciences Cancer Mutation PCR Assays
SeqTarget long-range PCR primers for resequencing CMTM3
DNA2.0 Custom Variant and Variant Library Synthesis for CMTM3

(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

CMTM3 for disorders           About MalaCards
OMIM gene information: 607886    OMIM disorders: --


CMTM3 for disorders           About GeneDecksing

Human Genome Epidemiology (HuGE) Navigator: CMTM3 (1 document)

Export disorders for CMTM3 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 CMTM3 gene, integrated from 9 sources (see all 12):
(articles sorted by number of sources associating them with CMTM3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Identification and characterization of a novel BASH N terminus-associated protein, BNAS2. (PubMed id 15087455)1, 3 Imamura Y....Kitamura D. (2004)
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
  4. 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 Han W.... Ma D. (2003)
  5. CMTM3, located at the critical tumor suppressor locus 16q22.1, is silenced by CpG methylation in carcinomas and inhibits tumor cell growth through inducing apoptosis. (PubMed id 19509237)1, 9 Wang Y....Han W. (2009)
  6. A yeast two-hybrid screen reveals that osteopontin ass ociates with MAP1A and MAP1B in addition to other proteins linked to microtubule stability, apoptosis and protein degradation in the human brain. (PubMed id 22779921)1 Long P....Rose S. (2012)
  7. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
  8. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)
  9. CMTM3 can affect the transcription activity of androgen receptor and inhibit the expression level of PSA in LNCaP cells. (PubMed id 18402773)1 Wang Y....Han W. (2008)
  10. Characterization and expression profile of CMTM3/CKLFSF3. (PubMed id 17002874)1 Zhong J....Han W. (2006)

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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 123920 HGNC: 19174 AceView: CKLFSF3 Ensembl:ENSG00000140931 euGenes: HUgn123920
ECgene: CMTM3 H-InvDB: CMTM3

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for CMTM3 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
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