Human Gene JAM2 (uc031rvc.1)
  Description: Homo sapiens junctional adhesion molecule 2 (JAM2), transcript variant 3, mRNA.
RefSeq Summary (NM_001270408): This gene belongs to the immunoglobulin superfamily, and the junctional adhesion molecule (JAM) family. The protein encoded by this gene is a type I membrane protein that is localized at the tight junctions of both epithelial and endothelial cells. It acts as an adhesive ligand for interacting with a variety of immune cell types, and may play a role in lymphocyte homing to secondary lymphoid organs. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2012].
Transcript (Including UTRs)
   Position: hg19 chr21:27,011,594-27,086,885 Size: 75,292 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr21:27,012,134-27,086,617 Size: 74,484 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:27,011,594-27,086,885)mRNA (may differ from genome)Protein (312 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: JAM2_HUMAN
DESCRIPTION: RecName: Full=Junctional adhesion molecule B; Short=JAM-B; AltName: Full=Junctional adhesion molecule 2; Short=JAM-2; AltName: Full=Vascular endothelial junction-associated molecule; Short=VE-JAM; AltName: CD_antigen=CD322; Flags: Precursor;
FUNCTION: May play a role in the processes of lymphocyte homing to secondary lymphoid organs.
SUBUNIT: Interacts with JAM3.
INTERACTION: Q9BX67:JAM3; NbExp=2; IntAct=EBI-3918416, EBI-4314733;
SUBCELLULAR LOCATION: Cell junction, tight junction (By similarity). Cell membrane; Single-pass type I membrane protein (By similarity). Note=Localized at tight junctions of both epithelial and endothelial cells (By similarity).
TISSUE SPECIFICITY: Highest expression in the heart, placenta, lung, foreskin and lymph node. Prominently expressed on high endothelial venules, also present on the endothelia of other vessels. Localized to the intercellular boundaries of high endothelial cells.
SIMILARITY: Belongs to the immunoglobulin superfamily.
SIMILARITY: Contains 1 Ig-like C2-type (immunoglobulin-like) domain.
SIMILARITY: Contains 1 Ig-like V-type (immunoglobulin-like) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): JAM2
CDC HuGE Published Literature: JAM2
Positive Disease Associations: Blood Pressure , Cognitive performance , Hip , Respiratory Function Tests
Related Studies:
  1. Blood Pressure
    Daniel Levy et al. BMC medical genetics 2007, Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness., BMC medical genetics. [PubMed 17903302]
    These results of genome-wide association testing for blood pressure and arterial stiffness phenotypes in an unselected community-based sample of adults may aid in the identification of the genetic basis of hypertension and arterial disease, help identify high risk individuals, and guide novel therapies for hypertension. Additional studies are needed to replicate any associations identified in these analyses.
  2. Cognitive performance
    Need ,et al. 2009, A Genome-wide Study of Common SNPs and CNVs in Cognitive Performance in the CANTAB battery, Human molecular genetics 2009 18- 23 : 4650-61. [PubMed 19734545]
  3. Hip
    Douglas P Kiel et al. BMC medical genetics 2007, Genome-wide association with bone mass and geometry in the Framingham Heart Study., BMC medical genetics. [PubMed 17903296]
    The FHS 100K SNP project offers an unbiased genome-wide strategy to identify new candidate loci and to replicate previously suggested candidate genes for osteoporosis.
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 18.29 RPKM in Testis
Total median expression: 373.05 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -222.30540-0.412 Picture PostScript Text
3' UTR -72.80268-0.272 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
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR013098 - Ig_I-set
IPR003599 - Ig_sub
IPR003598 - Ig_sub2
IPR013106 - Ig_V-set

Pfam Domains:
PF00047 - Immunoglobulin domain
PF07679 - Immunoglobulin I-set domain
PF07686 - Immunoglobulin V-set domain
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin

ModBase Predicted Comparative 3D Structure on P57087
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0007162 negative regulation of cell adhesion
GO:0030198 extracellular matrix organization
GO:0050900 leukocyte migration
GO:0098609 cell-cell adhesion

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005923 bicellular tight junction
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction


-  Descriptions from all associated GenBank mRNAs
  JD105447 - Sequence 86471 from Patent EP1572962.
JD104543 - Sequence 85567 from Patent EP1572962.
JD335816 - Sequence 316840 from Patent EP1572962.
JD129191 - Sequence 110215 from Patent EP1572962.
JD140854 - Sequence 121878 from Patent EP1572962.
AK312708 - Homo sapiens cDNA, FLJ93108, Homo sapiens junctional adhesion molecule 2 (JAM2), mRNA.
AY077698 - Homo sapiens clone tf15b10 C21ORF43 (C21orf43) mRNA, complete cds.
JD494175 - Sequence 475199 from Patent EP1572962.
AY016009 - Homo sapiens junctional adhesion molecule 2 (JAM2) mRNA, complete cds.
AX772824 - Sequence 21 from Patent WO03046180.
AK294769 - Homo sapiens cDNA FLJ50148 complete cds, highly similar to Junctional adhesion molecule B precursor.
JD540751 - Sequence 521775 from Patent EP1572962.
AF255910 - Homo sapiens vascular endothelial junction-associated molecule mRNA, complete cds.
JD396523 - Sequence 377547 from Patent EP1572962.
JD133405 - Sequence 114429 from Patent EP1572962.
JD397729 - Sequence 378753 from Patent EP1572962.
AY358361 - Homo sapiens clone DNA35638 JAM-IT/VE-JAM (UNQ219) mRNA, complete cds.
BC017779 - Homo sapiens junctional adhesion molecule 2, mRNA (cDNA clone MGC:22264 IMAGE:4616238), complete cds.
AX810711 - Sequence 35 from Patent EP1333092.
JD395331 - Sequence 376355 from Patent EP1572962.
JD150267 - Sequence 131291 from Patent EP1572962.
CU676060 - Synthetic construct Homo sapiens gateway clone IMAGE:100022175 5' read JAM2 mRNA.
AB463809 - Synthetic construct DNA, clone: pF1KB8367, Homo sapiens JAM2 gene for junctional adhesion molecule 2, without stop codon, in Flexi system.
AM392801 - Synthetic construct Homo sapiens clone IMAGE:100002958 for hypothetical protein (JAM2 gene).
AM392870 - Synthetic construct Homo sapiens clone IMAGE:100002711 for hypothetical protein (JAM2 gene).
AM393811 - Synthetic construct Homo sapiens clone IMAGE:100002710 for hypothetical protein (JAM2 gene).
KJ894469 - Synthetic construct Homo sapiens clone ccsbBroadEn_03863 JAM2 gene, encodes complete protein.
JD446395 - Sequence 427419 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04514 - Cell adhesion molecules (CAMs)
hsa04530 - Tight junction
hsa04670 - Leukocyte transendothelial migration
hsa05120 - Epithelial cell signaling in Helicobacter pylori infection

Reactome (by CSHL, EBI, and GO)

Protein P57087 (Reactome details) participates in the following event(s):

R-HSA-202709 JAM2 dimerises
R-HSA-202721 JAM2 binds JAM3
R-HSA-202706 Integrin alpha4beta1 binds JAM2:JAM3
R-HSA-202733 Cell surface interactions at the vascular wall
R-HSA-216083 Integrin cell surface interactions
R-HSA-109582 Hemostasis
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: B2R6T9, C21orf43, JAM2_HUMAN, NM_001270408, NP_001257337, P57087, Q6UXG6, Q6YNC1, uc011ace.1, UNQ219/PRO245, VEJAM
UCSC ID: uc031rvc.1
RefSeq Accession: NM_001270408
Protein: P57087 (aka JAM2_HUMAN)
CCDS: CCDS58787.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001270408.1
exon count: 10CDS single in 3' UTR: no RNA size: 1747
ORF size: 939CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1938.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.