Human Gene RPN2 (uc002xgp.3)
  Description: Homo sapiens ribophorin II (RPN2), transcript variant 1, mRNA.
RefSeq Summary (NM_002951): This gene encodes a type I integral membrane protein found only in the rough endoplasmic reticulum. The encoded protein is part of an N-oligosaccharyl transferase complex that links high mannose oligosaccharides to asparagine residues found in the Asn-X-Ser/Thr consensus motif of nascent polypeptide chains. This protein is similar in sequence to the yeast oligosaccharyl transferase subunit SWP1. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008].
Transcript (Including UTRs)
   Position: hg19 chr20:35,807,456-35,870,025 Size: 62,570 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr20:35,807,760-35,869,718 Size: 61,959 Coding Exon Count: 17 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:35,807,456-35,870,025)mRNA (may differ from genome)Protein (631 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RPN2_HUMAN
DESCRIPTION: RecName: Full=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2; EC=2.4.1.119; AltName: Full=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunit; AltName: Full=RIBIIR; AltName: Full=Ribophorin II; Short=RPN-II; AltName: Full=Ribophorin-2; Flags: Precursor;
FUNCTION: Essential subunit of N-oligosaccharyl transferase enzyme which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains.
CATALYTIC ACTIVITY: Dolichyl diphosphooligosaccharide + protein L- asparagine = dolichyl diphosphate + a glycoprotein with the oligosaccharide chain attached by N-glycosyl linkage to protein L- asparagine.
SUBUNIT: Component of the oligosaccharyltransferase (OST) complex. OST seems to exist in different forms which contain at least RPN1, RPN2, OST48, DAD1, OSTC, KRTCAP2 and either STT3A or STT3B. OST can form stable complexes with the Sec61 complex or with both the Sec61 and TRAP complexes (By similarity).
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein (Potential).
TISSUE SPECIFICITY: Expressed in all tissues tested.
SIMILARITY: Belongs to the SWP1 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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RPN2
CDC HuGE Published Literature: RPN2
Positive Disease Associations: hippocampal atrophy , Hippocampus
Related Studies:
  1. hippocampal atrophy
    Potkin ,et al. 2009, Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease, PloS one 2010 4- 8 : e6501. [PubMed 19668339]
  2. Hippocampus
    Steven G Potkin et al. PloS one 2010, Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease., PloS one. [PubMed 19668339]
    Using hippocampal atrophy as a quantitative phenotype in a genome-wide scan, we have identified candidate risk genes for sporadic Alzheimers disease that merit further investigation.

-  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: 116.16 RPKM in Cells - Cultured fibroblasts
Total median expression: 3159.60 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 -151.50304-0.498 Picture PostScript Text
3' UTR -61.49307-0.200 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
IPR008814 - Ribophorin_II

Pfam Domains:
PF05817 - Oligosaccharyltransferase subunit Ribophorin II

ModBase Predicted Comparative 3D Structure on P04844
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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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0043022 ribosome binding
GO:0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity

Biological Process:
GO:0006464 cellular protein modification process
GO:0006486 protein glycosylation
GO:0006487 protein N-linked glycosylation
GO:0007568 aging
GO:0018279 protein N-linked glycosylation via asparagine
GO:0042493 response to drug

Cellular Component:
GO:0000421 autophagosome membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005791 rough endoplasmic reticulum
GO:0008250 oligosaccharyltransferase complex
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  Y00282 - Human mRNA for ribophorin II.
AK096243 - Homo sapiens cDNA FLJ38924 fis, clone NT2NE2011896, highly similar to Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunit precursor (EC 2.4.1.119).
BC020222 - Homo sapiens ribophorin II, mRNA (cDNA clone MGC:31916 IMAGE:3640766), complete cds.
JD408624 - Sequence 389648 from Patent EP1572962.
AK315801 - Homo sapiens cDNA, FLJ96923, highly similar to Homo sapiens ribophorin II (RPN2), mRNA.
BC003560 - Homo sapiens ribophorin II, mRNA (cDNA clone MGC:1817 IMAGE:3546673), complete cds.
JD395120 - Sequence 376144 from Patent EP1572962.
JD407382 - Sequence 388406 from Patent EP1572962.
JD400196 - Sequence 381220 from Patent EP1572962.
AK308683 - Homo sapiens cDNA, FLJ98724.
CR456899 - Homo sapiens full open reading frame cDNA clone RZPDo834H0314D for gene RPN2, ribophorin II; complete cds, incl. stopcodon.
DQ895552 - Synthetic construct Homo sapiens clone IMAGE:100010012; FLH187269.01L; RZPDo839F0762D ribophorin II (RPN2) gene, encodes complete protein.
DQ892347 - Synthetic construct clone IMAGE:100004977; FLH187273.01X; RZPDo839F0772D ribophorin II (RPN2) gene, encodes complete protein.
CU678504 - Synthetic construct Homo sapiens gateway clone IMAGE:100020343 5' read RPN2 mRNA.
KJ897495 - Synthetic construct Homo sapiens clone ccsbBroadEn_06889 RPN2 gene, encodes complete protein.
AK296126 - Homo sapiens cDNA FLJ60278 complete cds, highly similar to Dolichyl-diphosphooligosaccharide--proteinglycosyltransferase 63 kDa subunit precursor (EC 2.4.1.119).
BC002380 - Homo sapiens ribophorin II, mRNA (cDNA clone IMAGE:2961244), partial cds.
DJ434623 - use of RPN2 gene expression inhibitor.
DJ434598 - use of RPN2 gene expression inhibitor.
BC013028 - Homo sapiens ribophorin II, mRNA (cDNA clone IMAGE:3532152), partial cds.
AK123690 - Homo sapiens cDNA FLJ41696 fis, clone HCHON2001853.
JD113202 - Sequence 94226 from Patent EP1572962.
JD554015 - Sequence 535039 from Patent EP1572962.
JD044525 - Sequence 25549 from Patent EP1572962.
JD050495 - Sequence 31519 from Patent EP1572962.
JD467194 - Sequence 448218 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00510 - N-Glycan biosynthesis
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein P04844 (Reactome details) participates in the following event(s):

R-HSA-1799326 Signal-containing nascent peptide translocates to endoplasmic reticulum
R-HSA-1799329 Signal peptidase hydrolyzes signal peptide from ribosome-associated nascent protein
R-HSA-446209 Transfer of N-glycan to the protein
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane
R-HSA-72766 Translation
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-392499 Metabolism of proteins
R-HSA-597592 Post-translational protein modification

-  Other Names for This Gene
  Alternate Gene Symbols: NM_002951, NP_002942, P04844, Q5JYR6, Q6IBA5, Q96E21, Q9BUQ3, Q9UBE1, RPN2_HUMAN
UCSC ID: uc002xgp.3
RefSeq Accession: NM_002951
Protein: P04844 (aka RPN2_HUMAN)
CCDS: CCDS13291.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002951.3
exon count: 17CDS single in 3' UTR: no RNA size: 2538
ORF size: 1896CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3992.00frame shift in genome: no % Coverage: 98.78
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.