Human Gene TF (ENST00000402696.9_5) from GENCODE V47lift37
  Description: transferrin, transcript variant 3 (from RefSeq NM_001354704.2)
Gencode Transcript: ENST00000402696.9_5
Gencode Gene: ENSG00000091513.16_12
Transcript (Including UTRs)
   Position: hg19 chr3:133,465,237-133,515,485 Size: 50,249 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr3:133,465,285-133,497,464 Size: 32,180 Coding Exon Count: 17 

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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 (chr3:133,465,237-133,515,485)mRNA (may differ from genome)Protein (698 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
ReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TRFE_HUMAN
DESCRIPTION: RecName: Full=Serotransferrin; Short=Transferrin; AltName: Full=Beta-1 metal-binding globulin; AltName: Full=Siderophilin; Flags: Precursor;
FUNCTION: Transferrins are iron binding transport proteins which can bind two Fe(3+) ions in association with the binding of an anion, usually bicarbonate. It is responsible for the transport of iron from sites of absorption and heme degradation to those of storage and utilization. Serum transferrin may also have a further role in stimulating cell proliferation.
SUBUNIT: Monomer.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Expressed by the liver and secreted in plasma.
POLYMORPHISM: Different polymorphic variants of transferrin are known. The sequence shown is the predominant electrophoretic variant (C1 or TF*C1).
DISEASE: Defects in TF are the cause of atransferrinemia (ATRAF) [MIM:209300]. Atransferrinemia is rare autosomal recessive disorder characterized by iron overload and hypochromic anemia.
SIMILARITY: Belongs to the transferrin family.
SIMILARITY: Contains 2 transferrin-like domains.
SEQUENCE CAUTION: Sequence=AAF22007.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
WEB RESOURCE: Name=Wikipedia; Note=Transferrin entry; URL="http://en.wikipedia.org/wiki/Transferrin";
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/tf/";

-  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: TF
Diseases sorted by gene-association score: atransferrinemia* (1703), iron metabolism disease (37), hemosiderosis (35), nutritional deficiency disease (31), iron deficiency anemia (27), iron overload in africa (27), deficiency anemia (25), alcohol abuse (24), siderosis (23), dysentery (22), microcytic anemia (20), protein-energy malnutrition (19), substance abuse (18), hemochromatosis (17), congenital hemolytic anemia (16), interstitial lung disease (15), chronic kidney failure (15), marasmus (15), hyperferritinemia-cataract syndrome (15), liver cirrhosis (14), congenital disorder of glycosylation, type in (14), melancholia (12), adult respiratory distress syndrome (12), hypochromic microcytic anemia (12), thalassemia major (12), porphyria cutanea tarda (11), metal metabolism disorder (11), testicular yolk sac tumor (11), congenital disorder of glycosylation, type ia (11), superficial siderosis of the central nervous system (11), vitamin b12 deficiency (11), angular cheilitis (11), histoplasmosis (10), alcoholic liver cirrhosis (10), epstein-barr virus hepatitis (10), galactosemia (10), thalassemia (9), haemophilus influenzae (9), superficial siderosis (9), pure red-cell aplasia (9), radiation proctitis (9), thalassemia intermedia (9), wilson disease (8), cardiomyopathy, familial hypertrophic, 9 (8), multiple congenital anomalies-hypotonia-seizures syndrome 3 (8), porphyria (8), cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome (8), analbuminemia (7), uremia (7), eales disease (7), end stage renal failure (7), prion disease (7), kwashiorkor (6), thalassemia, hispanic gamma-delta-beta (6), inherited metabolic disorder (6), epileptic encephalopathy, early infantile, 36 (6), trypanosomiasis (6), lipoid nephrosis (6), hemoglobinopathy (6), sleeping sickness (6), scrapie (6), fructose intolerance, hereditary (6), median rhomboid glossitis (5), yellow nail syndrome (5), factitious disorder (5), orbital cyst (5), liver disease (5), folic acid deficiency anemia (5), retinitis pigmentosa 7 and digenic (4), immune system disease (4), senile angioma (4), kidney disease (4), peripheral retinal degeneration (4), ancylostomiasis (4), progressive bulbar palsy (4), congenital disorder of glycosylation, type ii (4), vernal conjunctivitis (4), ariboflavinosis (4), keratomalacia (4), angiomatous meningioma (4), cerebellar ataxia (2), diabetes mellitus, insulin-dependent (1), urinary system disease (1)
* = Manually curated disease association

-  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: 977.89 RPKM in Liver
Total median expression: 2791.60 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 -14.2048-0.296 Picture PostScript Text
3' UTR -5347.2718021-0.297 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
IPR016357 - Transferrin
IPR001156 - Transferrin_fam
IPR018195 - Transferrin_Fe_BS

Pfam Domains:
PF00405 - Transferrin

SCOP Domains:
53850 - Periplasmic binding protein-like II

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1A8E - X-ray MuPIT 1A8F - X-ray MuPIT 1B3E - X-ray MuPIT 1BP5 - X-ray MuPIT 1BTJ - X-ray MuPIT 1D3K - X-ray MuPIT 1D4N - X-ray MuPIT 1DTG - X-ray MuPIT 1FQE - X-ray MuPIT 1FQF - X-ray MuPIT 1JQF - X-ray MuPIT 1N7W - X-ray MuPIT 1N7X - X-ray MuPIT 1N84 - X-ray MuPIT 1OQG - X-ray MuPIT 1OQH - X-ray MuPIT 1RYO - X-ray MuPIT 1SUV - EM MuPIT 2HAU - X-ray MuPIT 2HAV - X-ray 2O7U - X-ray MuPIT 2O84 - X-ray MuPIT 3FGS - X-ray MuPIT 3QYT - X-ray 3S9L - X-ray MuPIT 3S9M - X-ray MuPIT 3S9N - X-ray MuPIT 3SKP - X-ray MuPIT 3V83 - X-ray 3V89 - X-ray MuPIT 3V8X - X-ray MuPIT 3VE1 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P02787
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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    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008198 ferrous iron binding
GO:0008199 ferric iron binding
GO:0015091 ferric iron transmembrane transporter activity
GO:0034986 iron chaperone activity
GO:0046872 metal ion binding
GO:1990459 transferrin receptor binding

Biological Process:
GO:0001895 retina homeostasis
GO:0002576 platelet degranulation
GO:0006811 ion transport
GO:0006826 iron ion transport
GO:0006879 cellular iron ion homeostasis
GO:0031647 regulation of protein stability
GO:0033572 transferrin transport
GO:0043687 post-translational protein modification
GO:0044267 cellular protein metabolic process
GO:0048260 positive regulation of receptor-mediated endocytosis
GO:0055072 iron ion homeostasis
GO:0061024 membrane organization
GO:0071281 cellular response to iron ion
GO:1900390 regulation of iron ion import

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005769 early endosome
GO:0005770 late endosome
GO:0005788 endoplasmic reticulum lumen
GO:0005905 clathrin-coated pit
GO:0009925 basal plasma membrane
GO:0009986 cell surface
GO:0010008 endosome membrane
GO:0016324 apical plasma membrane
GO:0030139 endocytic vesicle
GO:0030665 clathrin-coated vesicle membrane
GO:0031232 extrinsic component of external side of plasma membrane
GO:0031410 cytoplasmic vesicle
GO:0031982 vesicle
GO:0034774 secretory granule lumen
GO:0045178 basal part of cell
GO:0048471 perinuclear region of cytoplasm
GO:0055037 recycling endosome
GO:0070062 extracellular exosome
GO:0072562 blood microparticle
GO:1990712 HFE-transferrin receptor complex


-  Descriptions from all associated GenBank mRNAs
  CR936810 - Homo sapiens mRNA; cDNA DKFZp781D0156 (from clone DKFZp781D0156).
AJ252279 - Homo sapiens partial mRNA for transferrin (TF gene), alternatively spliced transcript.
BC045772 - Homo sapiens cDNA clone IMAGE:5265104, containing frame-shift errors.
AK293842 - Homo sapiens cDNA FLJ56687 complete cds, highly similar to Serotransferrin precursor.
AK295334 - Homo sapiens cDNA FLJ54029 complete cds, highly similar to Serotransferrin precursor.
AK222755 - Homo sapiens mRNA for transferrin variant, clone: HEP00268.
AK295419 - Homo sapiens cDNA FLJ54111 complete cds, highly similar to Serotransferrin precursor.
AK303753 - Homo sapiens cDNA FLJ53691 complete cds, highly similar to Serotransferrin precursor.
BX648533 - Homo sapiens mRNA; cDNA DKFZp686O0685 (from clone DKFZp686O0685).
BC059367 - Homo sapiens transferrin, mRNA (cDNA clone MGC:71545 IMAGE:5264299), complete cds.
GQ472199 - Homo sapiens epididymis secretory sperm binding protein Li 71p (HEL-S-71p) mRNA, complete cds.
S95936 - transferrin [human, liver, mRNA, 2347 nt].
DQ923758 - Homo sapiens transferrin (TF) mRNA, complete cds.
JD137928 - Sequence 118952 from Patent EP1572962.
M12530 - Human transferrin mRNA, complete cds.
JD024586 - Sequence 5610 from Patent EP1572962.
JD029398 - Sequence 10422 from Patent EP1572962.
AB590492 - Synthetic construct DNA, clone: pFN21AE2058, Homo sapiens TF gene for transferrin, without stop codon, in Flexi system.
KJ897654 - Synthetic construct Homo sapiens clone ccsbBroadEn_07048 TF gene, encodes complete protein.
AF118063 - Homo sapiens PRO1400 mRNA, complete cds.
BC020671 - Homo sapiens transferrin, mRNA (cDNA clone IMAGE:4722434), partial cds.
JD024897 - Sequence 5921 from Patent EP1572962.
JD028223 - Sequence 9247 from Patent EP1572962.
M12525 - Human transferrin mRNA, 3' end.
AK126941 - Homo sapiens cDNA FLJ44994 fis, clone BRAWH3010560.
BC022262 - Homo sapiens transferrin, mRNA (cDNA clone IMAGE:4734580), with apparent retained intron.
BX537660 - Homo sapiens mRNA; cDNA DKFZp686L1398 (from clone DKFZp686L1398).
U88581 - Human transferrin mRNA, C2 allele, partial cds.
M26641 - Human transferrin.
JD454187 - Sequence 435211 from Patent EP1572962.
JD376900 - Sequence 357924 from Patent EP1572962.
JD430451 - Sequence 411475 from Patent EP1572962.
JD529661 - Sequence 510685 from Patent EP1572962.
JD170172 - Sequence 151196 from Patent EP1572962.
JD307037 - Sequence 288061 from Patent EP1572962.
JD322915 - Sequence 303939 from Patent EP1572962.
JD401574 - Sequence 382598 from Patent EP1572962.
JD201511 - Sequence 182535 from Patent EP1572962.
JD291428 - Sequence 272452 from Patent EP1572962.
JD431121 - Sequence 412145 from Patent EP1572962.
JD532486 - Sequence 513510 from Patent EP1572962.
JD443761 - Sequence 424785 from Patent EP1572962.
JD194377 - Sequence 175401 from Patent EP1572962.
JD401776 - Sequence 382800 from Patent EP1572962.
JD165429 - Sequence 146453 from Patent EP1572962.
DQ594916 - Homo sapiens piRNA piR-61028, complete sequence.
DQ581620 - Homo sapiens piRNA piR-49732, complete sequence.
DQ578550 - Homo sapiens piRNA piR-46662, complete sequence.
DQ591787 - Homo sapiens piRNA piR-58899, complete sequence.
DQ591044 - Homo sapiens piRNA piR-58156, complete sequence.
DQ571320 - Homo sapiens piRNA piR-31432, complete sequence.
JD549343 - Sequence 530367 from Patent EP1572962.
JD549344 - Sequence 530368 from Patent EP1572962.
BC041815 - Homo sapiens cDNA clone IMAGE:5266959.
JD153097 - Sequence 134121 from Patent EP1572962.
JD153100 - Sequence 134124 from Patent EP1572962.
JD198381 - Sequence 179405 from Patent EP1572962.
JD272029 - Sequence 253053 from Patent EP1572962.
JD153098 - Sequence 134122 from Patent EP1572962.
JD153099 - Sequence 134123 from Patent EP1572962.
JD198380 - Sequence 179404 from Patent EP1572962.
JD272028 - Sequence 253052 from Patent EP1572962.
JD479277 - Sequence 460301 from Patent EP1572962.
JD113647 - Sequence 94671 from Patent EP1572962.
JD291161 - Sequence 272185 from Patent EP1572962.
JD358548 - Sequence 339572 from Patent EP1572962.
JD527560 - Sequence 508584 from Patent EP1572962.
JD527562 - Sequence 508586 from Patent EP1572962.
JD160966 - Sequence 141990 from Patent EP1572962.
JD160960 - Sequence 141984 from Patent EP1572962.
JD546540 - Sequence 527564 from Patent EP1572962.
JD546541 - Sequence 527565 from Patent EP1572962.
JD081606 - Sequence 62630 from Patent EP1572962.
JD433483 - Sequence 414507 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_eea1Pathway - The role of FYVE-finger proteins in vesicle transport

Reactome (by CSHL, EBI, and GO)

Protein P02787 (Reactome details) participates in the following event(s):

R-HSA-917888 apoTF binds 2Fe3+ to form holoTF
R-HSA-917839 apo-Transferrin dissociates from the receptor complex
R-HSA-482770 Release of platelet secretory granule components
R-HSA-917814 apoTF:TFRC dimer translocates from endosome membrane to plasma membrane
R-HSA-917987 TFRC dimer binds 2xholoTF
R-HSA-5691150 TFR2 dimer binds 2xholoTF
R-HSA-917835 Fe3+ dissociates from holoTF:TFRC dimer
R-HSA-8952289 FAM20C phosphorylates FAM20C substrates
R-HSA-8866277 AP-2 directly binds some endocytic cargo
R-HSA-8867756 CLASP proteins and cargo are recruited to the nascent clathrin-coated pit
R-HSA-8868071 Clathrin recruits PIK3C2A
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8867754 F- and N- BAR domain proteins bind the clathrin-coated pit
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-8868072 Clathrin-associated PIK3C2A phosphorylates PI(4)P to PI(3,4)P2
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-917937 Iron uptake and transport
R-HSA-917977 Transferrin endocytosis and recycling
R-HSA-114608 Platelet degranulation
R-HSA-382551 Transport of small molecules
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-381426 Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
R-HSA-8957275 Post-translational protein phosphorylation
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-392499 Metabolism of proteins
R-HSA-597592 Post-translational protein modification
R-HSA-109582 Hemostasis
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000402696.1, ENST00000402696.2, ENST00000402696.3, ENST00000402696.4, ENST00000402696.5, ENST00000402696.6, ENST00000402696.7, ENST00000402696.8, NM_001354704, O43890, P02787, PRO1400, Q1HBA5, Q9NQB8, Q9UHV0, TF , TRFE_HUMAN, uc319bxv.1, uc319bxv.2
UCSC ID: ENST00000402696.9_5
RefSeq Accession: NM_001063.4
Protein: P02787 (aka TRFE_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.