Human Gene TCN1 (ENST00000257264.4) from GENCODE V44
  Description: Homo sapiens transcobalamin 1 (TCN1), mRNA. (from RefSeq NM_001062)
RefSeq Summary (NM_001062): This gene encodes a member of the vitamin B12-binding protein family. This family of proteins, alternatively referred to as R binders, is expressed in various tissues and secretions. This protein is a major constituent of secondary granules in neutrophils and facilitates the transport of cobalamin into cells. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000257264.4
Gencode Gene: ENSG00000134827.8
Transcript (Including UTRs)
   Position: hg38 chr11:59,852,808-59,866,487 Size: 13,680 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg38 chr11:59,852,975-59,866,470 Size: 13,496 Coding Exon Count: 9 

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 (chr11:59,852,808-59,866,487)mRNA (may differ from genome)Protein (433 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TCO1_HUMAN
DESCRIPTION: RecName: Full=Transcobalamin-1; Short=TC-1; AltName: Full=Transcobalamin I; Short=TC I; Short=TCI; Flags: Precursor;
FUNCTION: Vitamin B12-binding protein. Transports cobalamin into cells.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Neutrophil granule protein.
PTM: Contains about 30% carbohydrates.
SIMILARITY: Belongs to the eukaryotic cobalamin transport proteins family.

-  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: TCN1
Diseases sorted by gene-association score: transcobalamin i deficiency (18), transcobalamin ii deficiency (10), vitamin b12 deficiency (10), vitamin metabolic disorder (9), megaloblastic anemia (6), pernicious anemia (5), autoimmune lymphoproliferative syndrome (5)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 464.14 RPKM in Minor Salivary Gland
Total median expression: 506.32 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 0.00170.000 Picture PostScript Text
3' UTR -30.20167-0.181 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
IPR002157 - Cbl-bd_transpt_euk

Pfam Domains:
PF01122 - Eukaryotic cobalamin-binding protein

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2CKV - Model


ModBase Predicted Comparative 3D Structure on P20061
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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0031419 cobalamin binding

Biological Process:
GO:0006811 ion transport
GO:0006824 cobalt ion transport
GO:0009235 cobalamin metabolic process
GO:0015889 cobalamin transport
GO:0043312 neutrophil degranulation

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0035580 specific granule lumen
GO:1904724 tertiary granule lumen


-  Descriptions from all associated GenBank mRNAs
  BC018632 - Homo sapiens transcobalamin I (vitamin B12 binding protein, R binder family), mRNA (cDNA clone IMAGE:4132206).
J05068 - human transcobalamin I mRNA, complete cds.
JD053033 - Sequence 34057 from Patent EP1572962.
JD239297 - Sequence 220321 from Patent EP1572962.
JD253742 - Sequence 234766 from Patent EP1572962.
AK292990 - Homo sapiens cDNA FLJ77232 complete cds, highly similar to Homo sapiens transcobalamin I (vitamin B12 binding protein, R binder family) (TCN1), mRNA.
JD284884 - Sequence 265908 from Patent EP1572962.
JD537621 - Sequence 518645 from Patent EP1572962.
JD323917 - Sequence 304941 from Patent EP1572962.
BC156607 - Synthetic construct Homo sapiens clone IMAGE:100062024, MGC:190144 transcobalamin I (vitamin B12 binding protein, R binder family) (TCN1) mRNA, encodes complete protein.
DQ892807 - Synthetic construct clone IMAGE:100005437; FLH189919.01X; RZPDo839C0775D transcobalamin I (vitamin B12 binding protein, R binder family) (TCN1) gene, encodes complete protein.
DQ896054 - Synthetic construct Homo sapiens clone IMAGE:100010514; FLH189915.01L; RZPDo839C0765D transcobalamin I (vitamin B12 binding protein, R binder family) (TCN1) gene, encodes complete protein.
KJ901784 - Synthetic construct Homo sapiens clone ccsbBroadEn_11178 TCN1 gene, encodes complete protein.

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

Protein P20061 (Reactome details) participates in the following event(s):

R-HSA-3132759 TCN1 binds Cbl
R-HSA-3245898 TCN1 binds Cbl in the circulation
R-HSA-6798749 Exocytosis of specific granule lumen proteins
R-HSA-6798745 Exocytosis of tertiary granule lumen proteins
R-HSA-196741 Cobalamin (Cbl, vitamin B12) transport and metabolism
R-HSA-6798695 Neutrophil degranulation
R-HSA-196849 Metabolism of water-soluble vitamins and cofactors
R-HSA-168249 Innate Immune System
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-168256 Immune System
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A8KAC5, ENST00000257264.1, ENST00000257264.2, ENST00000257264.3, NM_001062, P20061, Q8WV77, TC1, TCO1_HUMAN, uc001noj.1, uc001noj.2, uc001noj.3, uc001noj.4
UCSC ID: ENST00000257264.4
RefSeq Accession: NM_001062
Protein: P20061 (aka TCO1_HUMAN)
CCDS: CCDS7978.1

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