Mouse Gene Cadm1 (ENSMUST00000114547.7) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus cell adhesion molecule 1 (Cadm1), transcript variant 3, mRNA. (from RefSeq NM_018770)
Gencode Transcript: ENSMUST00000114547.7
Gencode Gene: ENSMUSG00000032076.19
Transcript (Including UTRs)
   Position: mm10 chr9:47,530,257-47,853,380 Size: 323,124 Total Exon Count: 10 Strand: +
Coding Region
   Position: mm10 chr9:47,530,373-47,850,390 Size: 320,018 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:47,530,257-47,853,380)mRNA (may differ from genome)Protein (445 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CADM1_MOUSE
DESCRIPTION: RecName: Full=Cell adhesion molecule 1; AltName: Full=Immunoglobulin superfamily member 4; Short=IgSF4; AltName: Full=Nectin-like protein 2; Short=NECL-2; AltName: Full=Spermatogenic immunoglobulin superfamily; Short=SgIgSF; AltName: Full=Synaptic cell adhesion molecule; Short=SynCAM; AltName: Full=Tumor suppressor in lung cancer 1; Short=TSLC-1; Flags: Precursor;
FUNCTION: Mediates homophilic cell-cell adhesion in a Ca(2+)- independent manner. Also mediates heterophilic cell-cell adhesion with CADM3 and PVRL3 in a Ca(2+)-independent manner. Acts as a tumor suppressor in non-small-cell lung cancer (NSCLC) cells. Interaction with CRTAM promotes natural killer (NK) cell cytotoxicity and interferon-gamma (IFN-gamma) secretion by CD8+ cells in vitro as well as NK cell-mediated rejection of tumors expressing CADM3 in vivo. May contribute to the less invasive phenotypes of lepidic growth tumor cells. In mast cells, may mediate attachment to and promote communication with nerves. CADM1, together with MITF, is essential for development and survival of mast cells in vivo. May act as a synaptic cell adhesion molecule that drives synapse assembly. May be involved in neuronal migration, axon growth, pathfinding, and fasciculation on the axons of differentiating neurons. May play diverse roles in the spermatogenesis including in the adhesion of spermatocytes and spermatids to Sertoli cells and for their normal differentiation into mature spermatozoa.
SUBUNIT: Homodimer. Interacts with CRTAM and EPB41L3/DAL1. The interaction with EPB41L3/DAL1 may act to anchor CADM1 to the actin cytoskeleton. Interacts via its C-terminus with the PDZ domain of MPP3 and the PDZ domain of MPP6.
INTERACTION: P16144:ITGB4 (xeno); NbExp=3; IntAct=EBI-5651941, EBI-948678;
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein. Cell junction, synapse. Note=Associates with perinuclear and plasma membranes in vivo. Localized to the basolateral plasma membrane of epithelial cells in gall bladder.
TISSUE SPECIFICITY: Expressed in brain, lung, kidney, testis, heart, spleen and liver, but not expressed in skeletal muscle. In brain, enriched in the synaptic plasma membrane. Expressed dominantly in epithelial cells but not expressed in fibroblast cells (at protein level).
DEVELOPMENTAL STAGE: Expressed in spermatogenic cells during early spermatogenesis. Expression increases in intermediate spermatogonia through to zygotene spermatocytes but becomes diminished in the steps from early pachytene spermatocytes through to round spermatids. After meiosis, expression reappears in spermatids and is present in elongating spermatids until spermiation. Not detected in Sertoli cells.
DOMAIN: The cytoplasmic domain appears to play a critical role in proapoptosis and tumor suppressor activity in NSCLC (By similarity).
PTM: N-glycosylated.
PTM: Glycosylation at Asn-70 and Asn-104 promotes adhesive binding and synapse induction (By similarity).
DISRUPTION PHENOTYPE: Male mice are infertile, due to a defect at the spermatid stage of spermatogenesis, and show oligoasthenoteratozoospermia with almost no mature motile spermatozoa in the epididymis. Heterozygous males and females and homozygous null females are fertile and have no overt developmental defects.
SIMILARITY: Belongs to the nectin family.
SIMILARITY: Contains 2 Ig-like C2-type (immunoglobulin-like) domains.
SIMILARITY: Contains 1 Ig-like V-type (immunoglobulin-like) domain.
SEQUENCE CAUTION: Sequence=AAC67243.1; Type=Frameshift; Positions=65;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

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Click here to open Exonprimer with this transcript

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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D001564 Benzo(a)pyrene
  • D011794 Quercetin
  • D013749 Tetrachlorodibenzodioxin
  • C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene
  • C016403 2,4-dinitrotoluene
  • C573693 2-(4-((4-(6-methoxy-3-pyridinyl)-5-(4-(trifluoromethoxy)phenyl)-2-thiazolyl)methoxy)-2-methylphenoxy)acetic acid
  • D015073 2-Acetylaminofluorene
  • C009505 4,4'-diaminodiphenylmethane
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • C547126 AZM551248
          more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -35.40116-0.305 Picture PostScript Text
3' UTR -773.602990-0.259 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013162 - CD80_C2-set
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub
IPR003598 - Ig_sub2
IPR013106 - Ig_V-set
IPR003585 - Neurexin-like

Pfam Domains:
PF00047 - Immunoglobulin domain
PF07679 - Immunoglobulin I-set domain
PF07686 - Immunoglobulin V-set domain
PF08205 - CD80-like C2-set immunoglobulin domain
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin

ModBase Predicted Comparative 3D Structure on Q8R5M8
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005515 protein binding
GO:0030165 PDZ domain binding
GO:0042803 protein homodimerization activity
GO:0050839 cell adhesion molecule binding

Biological Process:
GO:0001889 liver development
GO:0002376 immune system process
GO:0006915 apoptotic process
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0007275 multicellular organism development
GO:0007283 spermatogenesis
GO:0007416 synapse assembly
GO:0008037 cell recognition
GO:0009826 unidimensional cell growth
GO:0016338 calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules
GO:0030154 cell differentiation
GO:0042271 susceptibility to natural killer cell mediated cytotoxicity
GO:0045954 positive regulation of natural killer cell mediated cytotoxicity
GO:0050715 positive regulation of cytokine secretion
GO:0051606 detection of stimulus
GO:0060348 bone development

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005911 cell-cell junction
GO:0005913 cell-cell adherens junction
GO:0008021 synaptic vesicle
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016323 basolateral plasma membrane
GO:0030054 cell junction
GO:0030424 axon
GO:0030425 dendrite
GO:0043005 neuron projection
GO:0043196 varicosity
GO:0045202 synapse
GO:0070852 cell body fiber


-  Descriptions from all associated GenBank mRNAs
  LF197577 - JP 2014500723-A/5080: Polycomb-Associated Non-Coding RNAs.
BC090970 - Mus musculus cell adhesion molecule 1, mRNA (cDNA clone MGC:107101 IMAGE:6703838), complete cds.
AK013911 - Mus musculus 13 days embryo head cDNA, RIKEN full-length enriched library, clone:3100001I08 product:immunoglobulin superfamily, member 4, full insert sequence.
AF434663 - Mus musculus tumor suprressor in lung cancer 1 mRNA, complete cds.
LF204933 - JP 2014500723-A/12436: Polycomb-Associated Non-Coding RNAs.
AK172628 - Mus musculus activated spleen cDNA, RIKEN full-length enriched library, clone:F830221K06 product:immunoglobulin superfamily, member 4A, full insert sequence.
AK053839 - Mus musculus 0 day neonate eyeball cDNA, RIKEN full-length enriched library, clone:E130314H03 product:immunoglobulin superfamily, member 4, full insert sequence.
AB377192 - Mus musculus Cadm1 mRNA for immunoglobulin superfamily member 4A isoform e, complete cds.
AB052293 - Mus musculus sgigsf mRNA for spermatogenic immunoglobulin superfamily protein, complete cds.
AF539424 - Mus musculus synaptic cell adhesion molecule 1 mRNA, complete cds.
BC095986 - Mus musculus cell adhesion molecule 1, mRNA (cDNA clone MGC:106033 IMAGE:5372277), complete cds.
BC069937 - Mus musculus immunoglobulin superfamily, member 4A, mRNA (cDNA clone IMAGE:5008124).
BC057125 - Mus musculus cell adhesion molecule 1, mRNA (cDNA clone MGC:73503 IMAGE:6414884), complete cds.
AK013775 - Mus musculus adult male hippocampus cDNA, RIKEN full-length enriched library, clone:2900073G06 product:immunoglobulin superfamily, member 4A, full insert sequence.
AB183402 - Mus musculus RA175 mRNA for RA175 isoform e, complete cds.
AB092414 - Mus musculus mRNA for a secretion form of SgIGSF/TSLC1, complete cds.
DQ279856 - Mus musculus strain C57BL/6J nectin-like 2 mRNA, partial cds.
AB183399 - Mus musculus RA175 mRNA for RA175 isoform c, complete cds.
AB183400 - Mus musculus RA175 mRNA for RA175 isoform b, complete cds.
AB183401 - Mus musculus RA175 mRNA for RA175 isoform d, complete cds.
AY351388 - Mus musculus nectin-like molecule 2 mRNA, complete cds; alternatively spliced.
JQ782219 - Mus musculus cell adhesion molecule 1 transcript variant 8abc (Cadm1) mRNA, complete cds, alternatively spliced.
AB064265 - Mus musculus mRNA for RA175, complete cds.
AF061260 - Mus musculus nectin-like protein 2 (Necl2) mRNA, complete cds.
BC094661 - Mus musculus cell adhesion molecule 1, mRNA (cDNA clone IMAGE:5705843), partial cds.
AB021964 - Mus musculus mRNA for adhesion protein RA175A, complete cds.
AB021965 - Mus musculus mRNA for adhesion protein RA175B, complete cds.
AB021966 - Mus musculus mRNA for adhesion protein RA175C, complete cds.
AB021967 - Mus musculus mRNA for adhesion protein RA175N, complete cds.
EU541474 - Mus musculus RA175 isoform f mRNA, partial cds.
EU541475 - Mus musculus RA175 isoform g mRNA, partial cds.
EU541476 - Mus musculus RA175 isoform h mRNA, partial cds.
EU541477 - Mus musculus RA175 isoform i mRNA, partial cds.
EU541478 - Mus musculus RA175 isoform j mRNA, partial cds.
AK207220 - Mus musculus cDNA, clone:Y2G0107F04, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000034581, based on BLAT search.
AK210200 - Mus musculus cDNA, clone:Y2G0117K07, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000034581, based on BLAT search.
AK215363 - Mus musculus cDNA, clone:Y2G0134M15, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000034581, based on BLAT search.
MA433154 - JP 2018138019-A/5080: Polycomb-Associated Non-Coding RNAs.
MA440510 - JP 2018138019-A/12436: Polycomb-Associated Non-Coding RNAs.
AK205040 - Mus musculus cDNA, clone:Y1G0150H04, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000034581, based on BLAT search.
LF306713 - JP 2014500723-A/114216: Polycomb-Associated Non-Coding RNAs.
LF306714 - JP 2014500723-A/114217: Polycomb-Associated Non-Coding RNAs.
AK164133 - Mus musculus 12 days embryo spinal cord cDNA, RIKEN full-length enriched library, clone:C530046D19 product:immunoglobulin superfamily, member 4A, full insert sequence.
LF306716 - JP 2014500723-A/114219: Polycomb-Associated Non-Coding RNAs.
AK161604 - Mus musculus 6 days neonate head cDNA, RIKEN full-length enriched library, clone:5430428G21 product:immunoglobulin superfamily, member 4A, full insert sequence.
LF306717 - JP 2014500723-A/114220: Polycomb-Associated Non-Coding RNAs.
MA542290 - JP 2018138019-A/114216: Polycomb-Associated Non-Coding RNAs.
MA542291 - JP 2018138019-A/114217: Polycomb-Associated Non-Coding RNAs.
MA542293 - JP 2018138019-A/114219: Polycomb-Associated Non-Coding RNAs.
MA542294 - JP 2018138019-A/114220: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu04514 - Cell adhesion molecules (CAMs)

Reactome (by CSHL, EBI, and GO)

Protein Q8R5M8 (Reactome details) participates in the following event(s):

R-MMU-420586 Necl-1:Necl-2 trans heterodimer interaction
R-MMU-420595 Necl-2:Nectin 3 trans heterodimer interaction
R-MMU-420592 Transhomodimerization of Nectin-like (Necl) proteins
R-MMU-420597 Nectin/Necl trans heterodimerization
R-MMU-418990 Adherens junctions interactions
R-MMU-421270 Cell-cell junction organization
R-MMU-446728 Cell junction organization
R-MMU-1500931 Cell-Cell communication

-  Other Names for This Gene
  Alternate Gene Symbols: CADM1_MOUSE, Igsf4, Necl2, NM_018770, Q6F3J3, Q7TNL1, Q80VG4, Q8K3T6, Q8R4L1, Q8R5M8, Q9QYL5, Q9QYL6, Q9Z2H8, Ra175, Syncam, SynCam1, Tslc1, uc009phs.1, uc009phs.2, uc009phs.3
UCSC ID: uc009phs.3
RefSeq Accession: NM_001310841
Protein: Q8R5M8 (aka CADM1_MOUSE)
CCDS: CCDS23148.1, CCDS23149.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.