Human Gene TPBG (ENST00000369750.4_4) from GENCODE V47lift37
  Description: trophoblast glycoprotein, transcript variant 3 (from RefSeq NM_001376922.1)
Gencode Transcript: ENST00000369750.4_4
Gencode Gene: ENSG00000146242.9_5
Transcript (Including UTRs)
   Position: hg19 chr6:83,073,534-83,077,137 Size: 3,604 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr6:83,074,679-83,075,941 Size: 1,263 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:83,073,534-83,077,137)mRNA (may differ from genome)Protein (420 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TPBG_HUMAN
DESCRIPTION: RecName: Full=Trophoblast glycoprotein; AltName: Full=5T4 oncofetal antigen; AltName: Full=5T4 oncofetal trophoblast glycoprotein; Short=5T4 oncotrophoblast glycoprotein; AltName: Full=M6P1; Flags: Precursor;
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (Potential).
TISSUE SPECIFICITY: Expressed by all types of trophoblasts as early as 9 weeks of development. Specific for trophoblastic cells except for amniotic epithelium. In adult tissues, the expression is limited to a few epithelial cell types but is found on a variety of carcinoma.
MISCELLANEOUS: Antigen 5T4 is overexpressed by a wide spectrum of cancers, including colorectal, ovarian and gastric, but with a limited normal tissue expression. Could be used for tumor immunotherapy.
SIMILARITY: Contains 6 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 LRRCT domain.
SIMILARITY: Contains 1 LRRNT 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


-  MalaCards Disease Associations
  MalaCards Gene Search: TPBG
Diseases sorted by gene-association score: vaccinia (4), renal cell carcinoma (2)

-  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: 31.04 RPKM in Esophagus - Muscularis
Total median expression: 253.94 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -207.50431-0.481 Picture PostScript Text
3' UTR -270.201196-0.226 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
IPR000483 - Cys-rich_flank_reg_C
IPR001611 - Leu-rich_rpt
IPR003591 - Leu-rich_rpt_typical-subtyp
IPR000372 - LRR-contain_N

Pfam Domains:
PF00560 - Leucine Rich Repeat
PF01462 - Leucine rich repeat N-terminal domain
PF01463 - Leucine rich repeat C-terminal domain
PF13516 - Leucine Rich repeat
PF13855 - Leucine rich repeat

SCOP Domains:
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1

ModBase Predicted Comparative 3D Structure on Q13641
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007155 cell adhesion
GO:0051965 positive regulation of synapse assembly

Cellular Component:
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  LF212298 - JP 2014500723-A/19801: Polycomb-Associated Non-Coding RNAs.
AK291170 - Homo sapiens cDNA FLJ78281 complete cds, highly similar to Homo sapiens trophoblast glycoprotein (TPBG), mRNA.
LF208569 - JP 2014500723-A/16072: Polycomb-Associated Non-Coding RNAs.
BC037161 - Homo sapiens trophoblast glycoprotein, mRNA (cDNA clone MGC:15317 IMAGE:4138906), complete cds.
AK074786 - Homo sapiens cDNA FLJ90305 fis, clone NT2RP2000694, highly similar to Homo sapiens 5T4 oncofetal trophoblast glycoprotein gene.
AK074790 - Homo sapiens cDNA FLJ90309 fis, clone NT2RP2000903, highly similar to Trophoblast glycoprotein precursor.
JD462447 - Sequence 443471 from Patent EP1572962.
JD073730 - Sequence 54754 from Patent EP1572962.
Z29083 - Homo sapiens 5T4 gene for 5T4 oncofoetal antigen.
JD021568 - Sequence 2592 from Patent EP1572962.
JD031510 - Sequence 12534 from Patent EP1572962.
KJ897695 - Synthetic construct Homo sapiens clone ccsbBroadEn_07089 TPBG gene, encodes complete protein.
JD020626 - Sequence 1650 from Patent EP1572962.
LF377997 - JP 2014500723-A/185500: Polycomb-Associated Non-Coding RNAs.
LF377998 - JP 2014500723-A/185501: Polycomb-Associated Non-Coding RNAs.
LF377999 - JP 2014500723-A/185502: Polycomb-Associated Non-Coding RNAs.
LF378001 - JP 2014500723-A/185504: Polycomb-Associated Non-Coding RNAs.
LF378002 - JP 2014500723-A/185505: Polycomb-Associated Non-Coding RNAs.
LF378005 - JP 2014500723-A/185508: Polycomb-Associated Non-Coding RNAs.
LF378006 - JP 2014500723-A/185509: Polycomb-Associated Non-Coding RNAs.
JD258927 - Sequence 239951 from Patent EP1572962.
JD549226 - Sequence 530250 from Patent EP1572962.
JD392355 - Sequence 373379 from Patent EP1572962.
JD288132 - Sequence 269156 from Patent EP1572962.
JD235467 - Sequence 216491 from Patent EP1572962.
JD287777 - Sequence 268801 from Patent EP1572962.
LF378007 - JP 2014500723-A/185510: Polycomb-Associated Non-Coding RNAs.
JD046060 - Sequence 27084 from Patent EP1572962.
JD331588 - Sequence 312612 from Patent EP1572962.
LF378008 - JP 2014500723-A/185511: Polycomb-Associated Non-Coding RNAs.
JD205437 - Sequence 186461 from Patent EP1572962.
LF378009 - JP 2014500723-A/185512: Polycomb-Associated Non-Coding RNAs.
MA447875 - JP 2018138019-A/19801: Polycomb-Associated Non-Coding RNAs.
MA444146 - JP 2018138019-A/16072: Polycomb-Associated Non-Coding RNAs.
MA613574 - JP 2018138019-A/185500: Polycomb-Associated Non-Coding RNAs.
MA613575 - JP 2018138019-A/185501: Polycomb-Associated Non-Coding RNAs.
MA613576 - JP 2018138019-A/185502: Polycomb-Associated Non-Coding RNAs.
MA613578 - JP 2018138019-A/185504: Polycomb-Associated Non-Coding RNAs.
MA613579 - JP 2018138019-A/185505: Polycomb-Associated Non-Coding RNAs.
MA613582 - JP 2018138019-A/185508: Polycomb-Associated Non-Coding RNAs.
MA613583 - JP 2018138019-A/185509: Polycomb-Associated Non-Coding RNAs.
MA613584 - JP 2018138019-A/185510: Polycomb-Associated Non-Coding RNAs.
MA613585 - JP 2018138019-A/185511: Polycomb-Associated Non-Coding RNAs.
MA613586 - JP 2018138019-A/185512: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: 5T4, A8K555, ENST00000369750.1, ENST00000369750.2, ENST00000369750.3, NM_001376922, Q13641, TPBG_HUMAN, uc318hva.1, uc318hva.2
UCSC ID: ENST00000369750.4_4
RefSeq Accession: NM_001376922.1
Protein: Q13641 (aka TPBG_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.