Mouse Gene Jaml (ENSMUST00000050020.7) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus junction adhesion molecule like (Jaml), mRNA. (from RefSeq NM_001005421)
Gencode Transcript: ENSMUST00000050020.7
Gencode Gene: ENSMUSG00000048534.7
Transcript (Including UTRs)
   Position: mm10 chr9:45,079,183-45,108,534 Size: 29,352 Total Exon Count: 11 Strand: +
Coding Region
   Position: mm10 chr9:45,084,064-45,107,444 Size: 23,381 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:45,079,183-45,108,534)mRNA (may differ from genome)Protein (379 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeSOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: JAML1_MOUSE
DESCRIPTION: RecName: Full=Junctional adhesion molecule-like; AltName: Full=Dendritic cell-specific protein CREA7; Short=mCrea7; Flags: Precursor;
FUNCTION: May function in transmigration of leukocytes through epithelial and endothelial tissues. Expressed at the plasma membrane of polymorphonuclear leukocytes, it mediates adhesive interactions with CXADR, a protein of the junctional complex of epithelial cells. Enhances myeloid leukemia cell adhesion to endothelial cells (By similarity).
SUBUNIT: Interacts with CXADR.
SUBCELLULAR LOCATION: Cell junction (By similarity). Cell membrane; Single-pass type I membrane protein (By similarity). Note=Localized at the plasma membrane in areas of cell-cell contacts and at the cell surface of PMN (By similarity).
DOMAIN: The Ig-like V-type domain 2 mediates interaction with CXADR (By similarity).
SIMILARITY: Belongs to the immunoglobulin superfamily.
SIMILARITY: Contains 2 Ig-like V-type (immunoglobulin-like) domains.

-  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


-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -78.00231-0.338 Picture PostScript Text
3' UTR -342.501090-0.314 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
IPR003599 - Ig_sub
IPR013106 - Ig_V-set

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

SCOP Domains:
48726 - Immunoglobulin

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3MJ6 - X-ray 3MJ7 - X-ray 3MJ9 - X-ray


ModBase Predicted Comparative 3D Structure on Q80UL9
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.
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:0005178 integrin binding
GO:0042803 protein homodimerization activity
GO:0050839 cell adhesion molecule binding

Biological Process:
GO:0002376 immune system process
GO:0007155 cell adhesion
GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0030593 neutrophil chemotaxis
GO:0035696 monocyte extravasation
GO:0046629 gamma-delta T cell activation
GO:0050900 leukocyte migration
GO:0060054 positive regulation of epithelial cell proliferation involved in wound healing
GO:0072672 neutrophil extravasation

Cellular Component:
GO:0005886 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
  AY093688 - Mus musculus dendritic-cell specific protein Crea7 (Crea7) mRNA, complete cds.
BC050133 - Mus musculus adhesion molecule, interacts with CXADR antigen 1, mRNA (cDNA clone MGC:61025 IMAGE:30023491), complete cds.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q80UL9 (Reactome details) participates in the following event(s):

R-MMU-199093 CXADR binds to AMICA1
R-MMU-202733 Cell surface interactions at the vascular wall
R-MMU-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-MMU-109582 Hemostasis
R-MMU-1280218 Adaptive Immune System
R-MMU-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: Amica1, E9QNV7, Gm638, JAML1_MOUSE, NM_001005421, Q5DTC4, Q80UL9, uc009pfd.1, uc009pfd.2, uc009pfd.3
UCSC ID: uc009pfd.3
RefSeq Accession: NM_001005421
Protein: Q80UL9 (aka JAML1_MOUSE)
CCDS: CCDS23128.1

-  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.