Human Gene SMAGP (uc001rye.1) Description and Page Index
  Description: Homo sapiens small cell adhesion glycoprotein (SMAGP), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr12:51,639,133-51,664,202 Size: 25,070 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr12:51,639,725-51,663,062 Size: 23,338 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:51,639,133-51,664,202)mRNA (may differ from genome)Protein (97 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
PubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Small cell adhesion glycoprotein; AltName: Full=Small transmembrane and glycosylated protein;
FUNCTION: May play a role in epithelial cell-cell contacts. May play a role in tumor invasiveness and metastasis formation.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type III membrane protein. Cytoplasmic vesicle membrane; Single-pass type III membrane protein. Note=Predominantly on lateral parts of the membrane, at cell-cell epithelial junctions. Detected on cytoplasmic membranes in undifferentiated tumors.
TISSUE SPECIFICITY: Detected in breast, endometrium, colon and biliary tract. Detected in polarized epithelial structures characterized by cell-cell adhesion (at protein level).
PTM: O-glycosylated. The O-glycan is modified with sialic acid residues.
SIMILARITY: Belongs to the SMAGP family.

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.25 RPKM in Esophagus - Mucosa
Total median expression: 102.53 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -78.50201-0.391 Picture PostScript Text
3' UTR -181.54592-0.307 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
  ModBase Predicted Comparative 3D Structure on Q0VAQ4
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 Details    
 Gene Sorter    
 Protein Sequence    

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

Biological Process:
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0008037 cell recognition

Cellular Component:
GO:0005654 nucleoplasm
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005913 cell-cell adherens junction
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle

-  Descriptions from all associated GenBank mRNAs
  BC045658 - Homo sapiens small trans-membrane and glycosylated protein, mRNA (cDNA clone IMAGE:5270771).
LF385082 - JP 2014500723-A/192585: Polycomb-Associated Non-Coding RNAs.
BC001400 - Homo sapiens small trans-membrane and glycosylated protein, mRNA (cDNA clone IMAGE:3051495).
AK001839 - Homo sapiens cDNA FLJ10977 fis, clone PLACE1001412.
BC008712 - Homo sapiens small trans-membrane and glycosylated protein, mRNA (cDNA clone MGC:16004 IMAGE:3546069), complete cds.
BC120965 - Homo sapiens small trans-membrane and glycosylated protein, mRNA (cDNA clone MGC:149453 IMAGE:40115343), complete cds.
BC120966 - Homo sapiens small trans-membrane and glycosylated protein, mRNA (cDNA clone MGC:149454 IMAGE:40115344), complete cds.
KJ894416 - Synthetic construct Homo sapiens clone ccsbBroadEn_03810 SMAGP gene, encodes complete protein.
MA620659 - JP 2018138019-A/192585: Polycomb-Associated Non-Coding RNAs.
AF091087 - Homo sapiens clone 643 unknown mRNA, complete sequence.
BC003379 - Homo sapiens small trans-membrane and glycosylated protein, mRNA (cDNA clone IMAGE:2984805), partial cds.
JD556145 - Sequence 537169 from Patent EP1572962.
JD078839 - Sequence 59863 from Patent EP1572962.
JD487335 - Sequence 468359 from Patent EP1572962.
JD237432 - Sequence 218456 from Patent EP1572962.
JD343076 - Sequence 324100 from Patent EP1572962.
JD457963 - Sequence 438987 from Patent EP1572962.
JD436839 - Sequence 417863 from Patent EP1572962.
JD553253 - Sequence 534277 from Patent EP1572962.
KJ902945 - Synthetic construct Homo sapiens clone ccsbBroadEn_12339 SMAGP gene, encodes complete protein.
CR456943 - Homo sapiens full open reading frame cDNA clone RZPDo834C068D for gene LOC57228, hypothetical protein from clone 643; complete cds, incl. stopcodon.
JD131124 - Sequence 112148 from Patent EP1572962.
JD449684 - Sequence 430708 from Patent EP1572962.
JD309102 - Sequence 290126 from Patent EP1572962.
JD161247 - Sequence 142271 from Patent EP1572962.
JD317446 - Sequence 298470 from Patent EP1572962.
JD261485 - Sequence 242509 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NIL5, NM_001031628, NP_001029045, Q0VAQ4, SMAGP_HUMAN
UCSC ID: uc001rye.1
RefSeq Accession: NM_001031628
Protein: Q0VAQ4 (aka SMAGP_HUMAN)
CCDS: CCDS44889.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001031628.1
exon count: 4CDS single in 3' UTR: no RNA size: 1087
ORF size: 294CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 785.00frame 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.