Human Gene TFF1 (ENST00000291527.3) from GENCODE V44
  Description: Homo sapiens trefoil factor 1 (TFF1), mRNA. (from RefSeq NM_003225)
RefSeq Summary (NM_003225): Members of the trefoil family are characterized by having at least one copy of the trefoil motif, a 40-amino acid domain that contains three conserved disulfides. They are stable secretory proteins expressed in gastrointestinal mucosa. Their functions are not defined, but they may protect the mucosa from insults, stabilize the mucus layer, and affect healing of the epithelium. This gene, which is expressed in the gastric mucosa, has also been studied because of its expression in human tumors. This gene and two other related trefoil family member genes are found in a cluster on chromosome 21. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000291527.3
Gencode Gene: ENSG00000160182.3
Transcript (Including UTRs)
   Position: hg38 chr21:42,362,282-42,366,535 Size: 4,254 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg38 chr21:42,362,479-42,366,495 Size: 4,017 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:42,362,282-42,366,535)mRNA (may differ from genome)Protein (84 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TFF1_HUMAN
DESCRIPTION: RecName: Full=Trefoil factor 1; AltName: Full=Breast cancer estrogen-inducible protein; AltName: Full=PNR-2; AltName: Full=Polypeptide P1.A; Short=hP1.A; AltName: Full=Protein pS2; Flags: Precursor;
FUNCTION: Stabilizer of the mucous gel overlying the gastrointestinal mucosa that provides a physical barrier against various noxious agents. May inhibit the growth of calcium oxalate crystals in urine.
SUBUNIT: Heterodimer with GKN2; disulfide linked.
INTERACTION: O00481:BTN3A1; NbExp=3; IntAct=EBI-743871, EBI-2809309; Q6UX41:BTNL8; NbExp=3; IntAct=EBI-743871, EBI-4314379; Q6UXZ3:CD300LD; NbExp=3; IntAct=EBI-743871, EBI-4314468; Q96PJ5:FCRL4; NbExp=3; IntAct=EBI-743871, EBI-4314687; Q9NYZ4:SIGLEC8; NbExp=3; IntAct=EBI-743871, EBI-4314991;
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Found in stomach, with highest levels in the upper gastric mucosal cells (at protein level). Detected in goblet cells of the small and large intestine and rectum, small submucosal glands in the esophagus, mucous acini of the sublingual gland, submucosal glands of the trachea, and epithelial cells lining the exocrine pancreatic ducts but not in the remainder of the pancreas (at protein level). Scattered expression is detected in the epithelial cells of the gallbladder and submucosal glands of the vagina, and weak expression is observed in the bronchial goblet cells of the pseudostratified epithelia in the respiratory system (at protein level). Detected in urine (at protein level). Strongly expressed in breast cancer but at low levels in normal mammary tissue. It is regulated by estrogen in MCF-7 cells. Strong expression found in normal gastric mucosa and in the regenerative tissues surrounding ulcerous lesions of gastrointestinal tract, but lower expression found in gastric cancer (at protein level).
SIMILARITY: Contains 1 P-type (trefoil) domain.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/TFF1ID201.html";

-  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: TFF1
Diseases sorted by gene-association score: breast cancer (17), gastric ulcer (16), gastrointestinal adenoma (15), bile reflux (15), breast ductal carcinoma (9), gastric adenocarcinoma (9), autosomal recessive nonsyndromic deafness (8), autosomal recessive nonsyndromic deafness 8 (6), stomach cancer (3), nonsyndromic deafness (2), corneal disease (1), gastric cancer, somatic (1)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 769.25 RPKM in Stomach
Total median expression: 807.31 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 -12.4040-0.310 Picture PostScript Text
3' UTR -47.20197-0.240 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
IPR000519 - P_trefoil
IPR017994 - P_trefoil_chordata
IPR017957 - P_trefoil_CS

Pfam Domains:
PF00088 - Trefoil (P-type) domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1HI7 - NMR MuPIT 1PS2 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P04155
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008083 growth factor activity

Biological Process:
GO:0005975 carbohydrate metabolic process
GO:0007586 digestion
GO:0008285 negative regulation of cell proliferation
GO:0010039 response to iron ion
GO:0010469 regulation of receptor activity
GO:0030154 cell differentiation
GO:0030277 maintenance of gastrointestinal epithelium
GO:0035902 response to immobilization stress
GO:0042060 wound healing
GO:0043434 response to peptide hormone

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space


-  Descriptions from all associated GenBank mRNAs
  KJ897658 - Synthetic construct Homo sapiens clone ccsbBroadEn_07052 TFF1 gene, encodes complete protein.
JD560624 - Sequence 541648 from Patent EP1572962.
BC032811 - Homo sapiens trefoil factor 1, mRNA (cDNA clone MGC:45303 IMAGE:5186922), complete cds.
X00474 - Human pS2 mRNA induced by estrogen from human breast cancer cell line MCF-7.
M12075 - Human estrogen receptor mRNA, partial cds.
E02904 - DNA encoding polypeptide secreted from tumor cell.
X52003 - H.sapiens pS2 protein gene.
JD412612 - Sequence 393636 from Patent EP1572962.
JD152396 - Sequence 133420 from Patent EP1572962.
JD243133 - Sequence 224157 from Patent EP1572962.
JD173632 - Sequence 154656 from Patent EP1572962.
E03953 - DNA sequence encoding human pS2 protein.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_tffPathway - Trefoil Factors Initiate Mucosal Healing

Reactome (by CSHL, EBI, and GO)

Protein P04155 (Reactome details) participates in the following event(s):

R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-8939211 ESR-mediated signaling
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: BCEI, ENST00000291527.1, ENST00000291527.2, NM_003225, P04155, PS2, TFF1_HUMAN, uc002zax.1, uc002zax.2, uc002zax.3
UCSC ID: ENST00000291527.3
RefSeq Accession: NM_003225
Protein: P04155 (aka TFF1_HUMAN)
CCDS: CCDS13685.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.