Human Gene GIF (uc001noi.3) Description and Page Index
  Description: Homo sapiens gastric intrinsic factor (vitamin B synthesis) (GIF), mRNA.
RefSeq Summary (NM_005142): This gene is a member of the cobalamin transport protein family. It encodes a glycoprotein secreted by parietal cells of the gastric mucosa and is required for adequate absorption of vitamin B12. Vitamin B12 is necessary for erythrocyte maturation and mutations in this gene may lead to congenital pernicious anemia. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC037958.1, X76562.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2157511 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000257248.3/ ENSP00000257248.2 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:59,596,746-59,612,974 Size: 16,229 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr11:59,596,957-59,612,926 Size: 15,970 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:59,596,746-59,612,974)mRNA (may differ from genome)Protein (417 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: IF_HUMAN
DESCRIPTION: RecName: Full=Gastric intrinsic factor; AltName: Full=Intrinsic factor; Short=IF; Short=INF; Flags: Precursor;
FUNCTION: Promotes absorption of the essential vitamin cobalamin (Cbl) in the ileum. After interaction with CUBN, the GIF-cobalamin complex is internalized via receptor-mediated endocytosis.
SUBUNIT: Interacts with CUBN (via CUB domains).
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Gastric mucosa.
DISEASE: Defects in GIF are the cause of hereditary intrinsic factor deficiency (IFD) [MIM:261000]; also known as congenital pernicious anemia. IFD is an autosomal recessive disorder characterized by megaloblastic anemia.
SIMILARITY: Belongs to the eukaryotic cobalamin transport proteins family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/GIF";
WEB RESOURCE: Name=Wikipedia; Note=Intrinsic factor entry; URL="http://en.wikipedia.org/wiki/Intrinsic_factor";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GIF
CDC HuGE Published Literature: GIF

-  MalaCards Disease Associations
  MalaCards Gene Search: GIF
Diseases sorted by gene-association score: intrinsic factor deficiency* (1374), congenital intrinsic factor deficiency* (775), pernicious anemia (49), megaloblastic anemia (29), vitamin metabolic disorder (19), transcobalamin ii deficiency (17), blind loop syndrome (16), granulomatous gastritis (15), vitamin b12 deficiency (14), folic acid deficiency anemia (10), tropical sprue (9), gastroduodenal crohn's disease (9), diphyllobothriasis (8), nutritional deficiency disease (8), gamma heavy chain disease (6), stomach disease (6), small intestine lymphoma (5), galactosemia (5), pancreatic steatorrhea (5)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 838.83 RPKM in Stomach
Total median expression: 840.35 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 -7.7048-0.160 Picture PostScript Text
3' UTR -41.90211-0.199 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
PF14478 - Domain of unknown function (DUF4430)

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

2CKT
- Model

2PMV
- X-ray MuPIT

3KQ4
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P27352
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  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

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005768 endosome
GO:0005902 microvillus
GO:0016324 apical plasma membrane
GO:0043202 lysosomal lumen


-  Descriptions from all associated GenBank mRNAs
  BC037958 - Homo sapiens gastric intrinsic factor (vitamin B synthesis), mRNA (cDNA clone MGC:46168 IMAGE:5759934), complete cds.
M63154 - Human intrinsic factor mRNA, complete cds.
AK301295 - Homo sapiens cDNA FLJ53880 complete cds, highly similar to Gastric intrinsic factor precursor.
X76562 - H.sapiens IFMH mRNA.
JD512995 - Sequence 494019 from Patent EP1572962.
AK314275 - Homo sapiens cDNA, FLJ95029, highly similar to Homo sapiens gastric intrinsic factor (vitamin B synthesis) (GIF), mRNA.
DQ892469 - Synthetic construct clone IMAGE:100005099; FLH186605.01X; RZPDo839G0471D gastric intrinsic factor (vitamin B synthesis) (GIF) gene, encodes complete protein.
KJ891243 - Synthetic construct Homo sapiens clone ccsbBroadEn_00637 GIF gene, encodes complete protein.
KR710908 - Synthetic construct Homo sapiens clone CCSBHm_00018114 GIF (GIF) mRNA, encodes complete protein.
KR710909 - Synthetic construct Homo sapiens clone CCSBHm_00018115 GIF (GIF) mRNA, encodes complete protein.
DQ895682 - Synthetic construct Homo sapiens clone IMAGE:100010142; FLH186601.01L; RZPDo839G0461D gastric intrinsic factor (vitamin B synthesis) (GIF) gene, encodes complete protein.
E04240 - DNA encoding human intrinsic factor.
CU691524 - Synthetic construct Homo sapiens gateway clone IMAGE:100019302 5' read GIF mRNA.
E04349 - cDNA encoding Vitamin12 binding protein.
AK301290 - Homo sapiens cDNA FLJ57091 complete cds, highly similar to Gastric intrinsic factor precursor.
JD333081 - Sequence 314105 from Patent EP1572962.
JD480743 - Sequence 461767 from Patent EP1572962.

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

Protein P27352 (Reactome details) participates in the following event(s):

R-HSA-3000120 GIF binds Cbl
R-HSA-3000103 CUBN:AMN binds GIF:Cbl
R-HSA-3000137 CUBN:AMN transports extracellular GIF:Cbl to endosome
R-HSA-196741 Cobalamin (Cbl, vitamin B12) transport and metabolism
R-HSA-3359457 Defective GIF causes intrinsic factor deficiency
R-HSA-3359463 Defective CUBN causes hereditary megaloblastic anemia 1
R-HSA-3359462 Defective AMN causes hereditary megaloblastic anemia 1
R-HSA-196849 Metabolism of water-soluble vitamins and cofactors
R-HSA-3296469 Defects in cobalamin (B12) metabolism
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-3296482 Defects in vitamin and cofactor metabolism
R-HSA-1430728 Metabolism
R-HSA-5668914 Diseases of metabolism
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: B2RAN8, B4DVZ1, IFMH, IF_HUMAN, NM_005142, NP_005133, P27352
UCSC ID: uc001noi.3
RefSeq Accession: NM_005142
Protein: P27352 (aka IF_HUMAN)
CCDS: CCDS7977.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005142.2
exon count: 9CDS single in 3' UTR: no RNA size: 1536
ORF size: 1254CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2695.00frame shift in genome: no % Coverage: 98.50
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.