Human Gene F11R (ENST00000368026.11_7) from GENCODE V47lift37
  Description: F11 receptor, transcript variant 1 (from RefSeq NM_016946.6)
Gencode Transcript: ENST00000368026.11_7
Gencode Gene: ENSG00000158769.19_11
Transcript (Including UTRs)
   Position: hg19 chr1:160,965,001-160,990,942 Size: 25,942 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr1:160,968,661-160,990,863 Size: 22,203 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:160,965,001-160,990,942)mRNA (may differ from genome)Protein (299 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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-  Comments and Description Text from UniProtKB
  ID: JAM1_HUMAN
DESCRIPTION: RecName: Full=Junctional adhesion molecule A; Short=JAM-A; AltName: Full=Junctional adhesion molecule 1; Short=JAM-1; AltName: Full=Platelet F11 receptor; AltName: Full=Platelet adhesion molecule 1; Short=PAM-1; AltName: CD_antigen=CD321; Flags: Precursor;
FUNCTION: Seems to play a role in epithelial tight junction formation. Appears early in primordial forms of cell junctions and recruits PARD3. The association of the PARD6-PARD3 complex may prevent the interaction of PARD3 with JAM1, thereby preventing tight junction assembly (By similarity). Plays a role in regulating monocyte transmigration involved in integrity of epithelial barrier. Involved in platelet activation. In case of orthoreovirus infection, serves as receptor for the virus.
SUBUNIT: Interacts with the ninth PDZ domain of MPDZ. Interacts with the first PDZ domain of PARD3. The association between PARD3 and PARD6B probably disrupts this interaction. Interacts with the orthoreovirus sigma-1 capsid protein (By similarity).
SUBCELLULAR LOCATION: Cell junction, tight junction. Cell membrane; Single-pass type I membrane protein. Note=Localized at tight junctions of both epithelial and endothelial cells.
PTM: N-glycosylated.
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


-  MalaCards Disease Associations
  MalaCards Gene Search: F11R
Diseases sorted by gene-association score: mednik syndrome (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 0.36 RPKM in Testis
Total median expression: 0.36 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 -27.6079-0.349 Picture PostScript Text
3' UTR -1285.103660-0.351 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
IPR003598 - Ig_sub2
IPR013106 - Ig_V-set
IPR003596 - Ig_V-set_subgr

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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1NBQ - X-ray MuPIT 3EOY - X-ray MuPIT 3TSZ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9Y624
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001618 virus receptor activity
GO:0005515 protein binding
GO:0030165 PDZ domain binding
GO:0045296 cadherin binding

Biological Process:
GO:0001817 regulation of cytokine production
GO:0006954 inflammatory response
GO:0007155 cell adhesion
GO:0007179 transforming growth factor beta receptor signaling pathway
GO:0009314 response to radiation
GO:0016032 viral process
GO:0030154 cell differentiation
GO:0030198 extracellular matrix organization
GO:0030855 epithelial cell differentiation
GO:0031032 actomyosin structure organization
GO:0034260 negative regulation of GTPase activity
GO:0043547 positive regulation of GTPase activity
GO:0045777 positive regulation of blood pressure
GO:0046718 viral entry into host cell
GO:0050892 intestinal absorption
GO:0050900 leukocyte migration
GO:0070830 bicellular tight junction assembly
GO:0072659 protein localization to plasma membrane
GO:0090557 establishment of endothelial intestinal barrier
GO:0090559 regulation of membrane permeability
GO:2000249 regulation of actin cytoskeleton reorganization

Cellular Component:
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005923 bicellular tight junction
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0031410 cytoplasmic vesicle
GO:0036057 slit diaphragm
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  JD346544 - Sequence 327568 from Patent EP1572962.
JD346543 - Sequence 327567 from Patent EP1572962.
JD312050 - Sequence 293074 from Patent EP1572962.
JD346545 - Sequence 327569 from Patent EP1572962.
JD312051 - Sequence 293075 from Patent EP1572962.
AF172398 - Homo sapiens junctional adhesion molecule-1 mRNA, complete cds.
AL136649 - Homo sapiens mRNA; cDNA DKFZp564H1562 (from clone DKFZp564H1562).
JD424637 - Sequence 405661 from Patent EP1572962.
JD268290 - Sequence 249314 from Patent EP1572962.
JD221711 - Sequence 202735 from Patent EP1572962.
JD546851 - Sequence 527875 from Patent EP1572962.
JD500952 - Sequence 481976 from Patent EP1572962.
JD550900 - Sequence 531924 from Patent EP1572962.
JD369607 - Sequence 350631 from Patent EP1572962.
JD317159 - Sequence 298183 from Patent EP1572962.
JD379584 - Sequence 360608 from Patent EP1572962.
JD560670 - Sequence 541694 from Patent EP1572962.
JD264764 - Sequence 245788 from Patent EP1572962.
JD408661 - Sequence 389685 from Patent EP1572962.
JD119918 - Sequence 100942 from Patent EP1572962.
JD240429 - Sequence 221453 from Patent EP1572962.
JD072395 - Sequence 53419 from Patent EP1572962.
JD225419 - Sequence 206443 from Patent EP1572962.
JD525908 - Sequence 506932 from Patent EP1572962.
JD080273 - Sequence 61297 from Patent EP1572962.
JD541332 - Sequence 522356 from Patent EP1572962.
JD119366 - Sequence 100390 from Patent EP1572962.
JD513600 - Sequence 494624 from Patent EP1572962.
AL365518 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 147447.
JD550968 - Sequence 531992 from Patent EP1572962.
JD124294 - Sequence 105318 from Patent EP1572962.
JD092567 - Sequence 73591 from Patent EP1572962.
JD159930 - Sequence 140954 from Patent EP1572962.
JD539544 - Sequence 520568 from Patent EP1572962.
JD473287 - Sequence 454311 from Patent EP1572962.
JD160492 - Sequence 141516 from Patent EP1572962.
JD241073 - Sequence 222097 from Patent EP1572962.
JD560812 - Sequence 541836 from Patent EP1572962.
JD437124 - Sequence 418148 from Patent EP1572962.
DQ595178 - Homo sapiens piRNA piR-61290, complete sequence.
JD133512 - Sequence 114536 from Patent EP1572962.
JD113333 - Sequence 94357 from Patent EP1572962.
JD194550 - Sequence 175574 from Patent EP1572962.
JD554574 - Sequence 535598 from Patent EP1572962.
JD500378 - Sequence 481402 from Patent EP1572962.
BC001533 - Homo sapiens F11 receptor, mRNA (cDNA clone MGC:651 IMAGE:2990019), complete cds.
AK026665 - Homo sapiens cDNA: FLJ23012 fis, clone LNG00655, highly similar to AF172398 Homo sapiens platelet adhesion molecule PAM-1 mRNA.
AK075152 - Homo sapiens cDNA FLJ90671 fis, clone PLACE1005544, highly similar to Junctional adhesion molecule 1 precursor.
AF191495 - Homo sapiens F11 receptor protein mRNA, complete cds.
JD279115 - Sequence 260139 from Patent EP1572962.
AF207907 - Homo sapiens platelet F11 receptor mRNA, complete cds.
AY358896 - Homo sapiens clone DNA40628 JAM (UNQ264) mRNA, complete cds.
AF111713 - Homo sapiens junctional adhesion molecule (JAM1) mRNA, complete cds.
JD135917 - Sequence 116941 from Patent EP1572962.
JD118734 - Sequence 99758 from Patent EP1572962.
JD411972 - Sequence 392996 from Patent EP1572962.
JD130425 - Sequence 111449 from Patent EP1572962.
JD411973 - Sequence 392997 from Patent EP1572962.
JD130426 - Sequence 111450 from Patent EP1572962.
JD036913 - Sequence 17937 from Patent EP1572962.
JD105294 - Sequence 86318 from Patent EP1572962.
AF154005 - Homo sapiens junction adhesion molecule mRNA, complete cds.
JD037481 - Sequence 18505 from Patent EP1572962.
JD496585 - Sequence 477609 from Patent EP1572962.
JD353337 - Sequence 334361 from Patent EP1572962.
JD152764 - Sequence 133788 from Patent EP1572962.
JD437892 - Sequence 418916 from Patent EP1572962.
DQ578709 - Homo sapiens piRNA piR-46821, complete sequence.
AK304412 - Homo sapiens cDNA FLJ59609 complete cds, highly similar to Junctional adhesion molecule A precursor.
JD486737 - Sequence 467761 from Patent EP1572962.
JD358718 - Sequence 339742 from Patent EP1572962.
JD422223 - Sequence 403247 from Patent EP1572962.
JD166894 - Sequence 147918 from Patent EP1572962.
AK299487 - Homo sapiens cDNA FLJ54854 complete cds, highly similar to Junctional adhesion molecule A precursor.
JD402145 - Sequence 383169 from Patent EP1572962.
JD521442 - Sequence 502466 from Patent EP1572962.
CR533512 - Homo sapiens full open reading frame cDNA clone RZPDo834D0919D for gene F11R, F11 receptor; complete cds, incl. stopcodon.
JD513066 - Sequence 494090 from Patent EP1572962.
JD129217 - Sequence 110241 from Patent EP1572962.
KJ893762 - Synthetic construct Homo sapiens clone ccsbBroadEn_03156 F11R gene, encodes complete protein.
BT020103 - Homo sapiens F11 receptor mRNA, complete cds.
DQ892228 - Synthetic construct clone IMAGE:100004858; FLH184311.01X; RZPDo839E06144D F11 receptor (F11R) gene, encodes complete protein.
DQ895428 - Synthetic construct Homo sapiens clone IMAGE:100009888; FLH184307.01L; RZPDo839E06143D F11 receptor (F11R) gene, encodes complete protein.
EU831648 - Synthetic construct Homo sapiens clone HAIB:100066677; DKFZo007F1119 F11 receptor protein (F11R) gene, encodes complete protein.
EU831732 - Synthetic construct Homo sapiens clone HAIB:100066761; DKFZo003F1120 F11 receptor protein (F11R) gene, encodes complete protein.
AB528601 - Synthetic construct DNA, clone: pF1KB4155, Homo sapiens F11R gene for F11 receptor, without stop codon, in Flexi system.
DQ599232 - Homo sapiens piRNA piR-37298, complete sequence.
DQ585870 - Homo sapiens piRNA piR-52982, complete sequence.
CS123438 - Sequence 9 from Patent WO2005058362.
JD283824 - Sequence 264848 from Patent EP1572962.
JD390668 - Sequence 371692 from Patent EP1572962.

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

Protein Q9Y624 (Reactome details) participates in the following event(s):

R-HSA-202718 Integrin alphaLbeta2 (LFA-1) binds F11R (JAM-A)
R-HSA-202726 F11R dimerises
R-HSA-419981 Recruitment of PAR-3:PAR-6:aPKC complex to tight junctions
R-HSA-2134506 TGFBR1 is recruited to tight junctions by PARD6A
R-NUL-2161147 TGFBR1 is recruited to tight junction by binding Pard6a
R-HSA-2134519 TGFBR2 is recruited to tight junctions after TGF-beta stimulation
R-HSA-2134532 TGFBR2 phosphorylates TGFBR1 and PARD6A
R-HSA-2160932 SMURF1 binds phosphorylated PARD6A
R-NUL-2161165 TGFBR2 phosphorylates Pard6a
R-NUL-2161160 TGFBR2 is recruited to tight junctions-associated, Pard6a-bound, TGFBR1 after TGF-beta stimulation
R-HSA-2160935 SMURF1 ubiquitinates RHOA
R-HSA-202733 Cell surface interactions at the vascular wall
R-HSA-216083 Integrin cell surface interactions
R-HSA-420029 Tight junction interactions
R-HSA-109582 Hemostasis
R-HSA-1474244 Extracellular matrix organization
R-HSA-421270 Cell-cell junction organization
R-HSA-2173791 TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition)
R-HSA-446728 Cell junction organization
R-HSA-170834 Signaling by TGF-beta Receptor Complex
R-HSA-1500931 Cell-Cell communication
R-HSA-9006936 Signaling by TGF-beta family members
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z941, ENST00000368026.1, ENST00000368026.10, ENST00000368026.2, ENST00000368026.3, ENST00000368026.4, ENST00000368026.5, ENST00000368026.6, ENST00000368026.7, ENST00000368026.8, ENST00000368026.9, JAM1, JAM1_HUMAN, JCAM, NM_016946, Q9Y624, uc318gki.1, uc318gki.2, UNQ264/PRO301
UCSC ID: ENST00000368026.11_7
RefSeq Accession: NM_016946.6
Protein: Q9Y624 (aka JAM1_HUMAN)

-  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.