Human Gene RFT1 (uc003dgj.3) Description and Page Index
  Description: Homo sapiens RFT1 homolog (S. cerevisiae) (RFT1), mRNA.
RefSeq Summary (NM_052859): This gene encodes an enzyme which catalyzes the translocation of the Man(5)GlcNAc (2)-PP-Dol intermediate from the cytoplasmic to the luminal side of the endoplasmic reticulum membrane in the pathway for the N-glycosylation of proteins. Mutations in this gene are associated with congenital disorder of glycosylation type In.[provided by RefSeq, Dec 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 :: KY814482.1, SRR1803614.119714.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000296292.8/ ENSP00000296292.3 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr3:53,122,501-53,164,470 Size: 41,970 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr3:53,125,919-53,164,416 Size: 38,498 Coding Exon Count: 13 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:53,122,501-53,164,470)mRNA (may differ from genome)Protein (541 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: RFT1_HUMAN
DESCRIPTION: RecName: Full=Protein RFT1 homolog;
FUNCTION: May be involved in N-linked oligosaccharide assembly. May participate in the translocation of oligosaccharide from the cytoplasmic side to the lumenal side of the endoplasmic reticulum membrane.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
DISEASE: Defects in RFT1 are the cause of congenital disorder of glycosylation type 1N (CDG1N) [MIM:612015]. CDGs are a genetically heterogeneous group of autosomal recessive disorders caused by enzymatic defects in the synthesis and processing of asparagine (N)-linked glycans or oligosaccharides on glycoproteins. CDGs present with a wide variety of clinical features, such as disorders of the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. Type 1 CDGs comprise defects in the assembly of the dolichol lipid-linked oligosaccharide chain and its transfer to the nascent protein. These disorders can be identified by a characteristic abnormal isoelectric focusing profile of plasma transferrin.
SIMILARITY: Belongs to the RFT1 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RFT1
CDC HuGE Published Literature: RFT1

-  MalaCards Disease Associations
  MalaCards Gene Search: RFT1
Diseases sorted by gene-association score: congenital disorder of glycosylation, type in* (1569)
* = 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: 6.28 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 159.37 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 -13.6054-0.252 Picture PostScript Text
3' UTR -1265.013418-0.370 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
IPR007594 - RFT1

Pfam Domains:
PF04506 - Rft protein

ModBase Predicted Comparative 3D Structure on Q96AA3
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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 orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005319 lipid transporter activity

Biological Process:
GO:0006869 lipid transport
GO:0008643 carbohydrate transport
GO:0034203 glycolipid translocation

Cellular Component:
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AL713685 - Homo sapiens mRNA; cDNA DKFZp667J092 (from clone DKFZp667J092).
KY814482 - Homo sapiens protein RFT1 homolog (RFT1) mRNA, complete cds.
AK098811 - Homo sapiens cDNA FLJ25945 fis, clone JTH12731.
JD513963 - Sequence 494987 from Patent EP1572962.
JD524555 - Sequence 505579 from Patent EP1572962.
JD352398 - Sequence 333422 from Patent EP1572962.
JD223872 - Sequence 204896 from Patent EP1572962.
JD150810 - Sequence 131834 from Patent EP1572962.
JD541341 - Sequence 522365 from Patent EP1572962.
JD119383 - Sequence 100407 from Patent EP1572962.
JD150593 - Sequence 131617 from Patent EP1572962.
JD525856 - Sequence 506880 from Patent EP1572962.
JD413621 - Sequence 394645 from Patent EP1572962.
JD107573 - Sequence 88597 from Patent EP1572962.
JD505851 - Sequence 486875 from Patent EP1572962.
JD356387 - Sequence 337411 from Patent EP1572962.
JD505852 - Sequence 486876 from Patent EP1572962.
JD398813 - Sequence 379837 from Patent EP1572962.
JD070580 - Sequence 51604 from Patent EP1572962.
JD422137 - Sequence 403161 from Patent EP1572962.
JD463317 - Sequence 444341 from Patent EP1572962.
JD213415 - Sequence 194439 from Patent EP1572962.
JD407686 - Sequence 388710 from Patent EP1572962.
JD152370 - Sequence 133394 from Patent EP1572962.
JD258846 - Sequence 239870 from Patent EP1572962.
JD353127 - Sequence 334151 from Patent EP1572962.
JD513566 - Sequence 494590 from Patent EP1572962.
JD523038 - Sequence 504062 from Patent EP1572962.
JD361302 - Sequence 342326 from Patent EP1572962.
JD157618 - Sequence 138642 from Patent EP1572962.
JD524906 - Sequence 505930 from Patent EP1572962.
JD420684 - Sequence 401708 from Patent EP1572962.
JD199197 - Sequence 180221 from Patent EP1572962.
JD257901 - Sequence 238925 from Patent EP1572962.
JD090561 - Sequence 71585 from Patent EP1572962.
JD239288 - Sequence 220312 from Patent EP1572962.
JD536311 - Sequence 517335 from Patent EP1572962.
JD459928 - Sequence 440952 from Patent EP1572962.
JD410293 - Sequence 391317 from Patent EP1572962.
JD232043 - Sequence 213067 from Patent EP1572962.
JD370690 - Sequence 351714 from Patent EP1572962.
JD422367 - Sequence 403391 from Patent EP1572962.
JD399682 - Sequence 380706 from Patent EP1572962.
JD392799 - Sequence 373823 from Patent EP1572962.
BC101247 - Homo sapiens hypothetical locus LOC285398, mRNA (cDNA clone IMAGE:40023165).
BC101248 - Homo sapiens hypothetical locus LOC285398, mRNA (cDNA clone IMAGE:40023166).
BC101250 - Homo sapiens hypothetical locus LOC285398, mRNA (cDNA clone IMAGE:40023168).
BC101249 - Homo sapiens hypothetical locus LOC285398, mRNA (cDNA clone IMAGE:40023167).
BC113058 - Homo sapiens hypothetical locus LOC285398, mRNA (cDNA clone IMAGE:40023169).
BC113059 - Homo sapiens hypothetical locus LOC285398, mRNA (cDNA clone IMAGE:40023170).
JD043033 - Sequence 24057 from Patent EP1572962.
JD161092 - Sequence 142116 from Patent EP1572962.
JD324962 - Sequence 305986 from Patent EP1572962.
JD500787 - Sequence 481811 from Patent EP1572962.
JD051741 - Sequence 32765 from Patent EP1572962.
JD197889 - Sequence 178913 from Patent EP1572962.
KJ903577 - Synthetic construct Homo sapiens clone ccsbBroadEn_12971 RFT1 gene, encodes complete protein.
JD482829 - Sequence 463853 from Patent EP1572962.
JD345258 - Sequence 326282 from Patent EP1572962.
JD064141 - Sequence 45165 from Patent EP1572962.
JD291269 - Sequence 272293 from Patent EP1572962.
JD102514 - Sequence 83538 from Patent EP1572962.
BC043595 - Homo sapiens RFT1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:50674 IMAGE:5769824), complete cds.
JD384731 - Sequence 365755 from Patent EP1572962.
JD457683 - Sequence 438707 from Patent EP1572962.
JD324836 - Sequence 305860 from Patent EP1572962.
JD315205 - Sequence 296229 from Patent EP1572962.
JD363833 - Sequence 344857 from Patent EP1572962.
JD301940 - Sequence 282964 from Patent EP1572962.
JD174226 - Sequence 155250 from Patent EP1572962.
JD231469 - Sequence 212493 from Patent EP1572962.
JD344926 - Sequence 325950 from Patent EP1572962.
JD042463 - Sequence 23487 from Patent EP1572962.
JD095878 - Sequence 76902 from Patent EP1572962.
JD328667 - Sequence 309691 from Patent EP1572962.
JD501666 - Sequence 482690 from Patent EP1572962.
JD115285 - Sequence 96309 from Patent EP1572962.
JD171400 - Sequence 152424 from Patent EP1572962.
JD526770 - Sequence 507794 from Patent EP1572962.
BC006846 - Homo sapiens RFT1 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3450968), partial cds.
AJ318099 - Homo sapiens mRNA for putative endoplasmic reticulum multispan transmembrane protein (RFT1 gene).
JD180976 - Sequence 162000 from Patent EP1572962.
JD185108 - Sequence 166132 from Patent EP1572962.
JD180841 - Sequence 161865 from Patent EP1572962.
JD452090 - Sequence 433114 from Patent EP1572962.
JD462305 - Sequence 443329 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00510 - N-Glycan biosynthesis

Reactome (by CSHL, EBI, and GO)

Protein Q96AA3 (Reactome details) participates in the following event(s):

R-HSA-446212 Flipping of the N-glycan precursor to inside the ER
R-HSA-446193 Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: NM_052859, NP_443091, Q96AA3, Q96J03, RFT1_HUMAN
UCSC ID: uc003dgj.3
RefSeq Accession: NM_052859
Protein: Q96AA3 (aka RFT1_HUMAN)
CCDS: CCDS2869.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene RFT1:
cdg (Congenital Disorders of N-Linked Glycosylation and Multiple Pathway Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_052859.3
exon count: 13CDS single in 3' UTR: no RNA size: 5112
ORF size: 1626CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3452.00frame shift in genome: no % Coverage: 99.73
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
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.