Human Gene ERGIC2 (uc001riv.3) Description and Page Index
  Description: Homo sapiens ERGIC and golgi 2 (ERGIC2), mRNA.
RefSeq Summary (NM_016570): ERGIC2, or PTX1, is a ubiquitously expressed nuclear protein that is downregulated in prostate carcinoma (Kwok et al., 2001 [PubMed 11445006]).[supplied by OMIM, Aug 2008]. ##Evidence-Data-START## Transcript exon combination :: SRR1803617.452088.1, AL834128.2 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000360150.9/ ENSP00000353270.4 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr12:29,493,579-29,534,143 Size: 40,565 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr12:29,494,089-29,524,566 Size: 30,478 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:29,493,579-29,534,143)mRNA (may differ from genome)Protein (377 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: ERGI2_HUMAN
DESCRIPTION: RecName: Full=Endoplasmic reticulum-Golgi intermediate compartment protein 2;
FUNCTION: Possible role in transport between endoplasmic reticulum and Golgi (By similarity).
SUBUNIT: May interact with EEF1A1.
SUBCELLULAR LOCATION: Endoplasmic reticulum-Golgi intermediate compartment membrane; Multi-pass membrane protein. Golgi apparatus, cis-Golgi network membrane; Multi-pass membrane protein. Endoplasmic reticulum membrane; Multi-pass membrane protein. Cytoplasm. Nucleus. Note=Cycles between the endoplasmic reticulum and the Golgi. PubMed:11445006 states that it localizes to the nucleus; PubMed:17980171 shows a partial localization in the nucleus.
TISSUE SPECIFICITY: Ubiquitously expressed.
SIMILARITY: Belongs to the ERGIC family.
SEQUENCE CAUTION: Sequence=AAF61208.1; Type=Frameshift; Positions=202, 209, 212;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 16.18 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 385.51 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 -45.10133-0.339 Picture PostScript Text
3' UTR -92.51510-0.181 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
IPR012936 - DUF1692

Pfam Domains:
PF07970 - Endoplasmic reticulum vesicle transporter
PF13850 - Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)

ModBase Predicted Comparative 3D Structure on Q96RQ1
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 BrowserGenome BrowserGenome BrowserNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsemblFlyBase SGD
 Protein SequenceProtein SequenceProtein Sequence Protein Sequence
 AlignmentAlignmentAlignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER
GO:0016192 vesicle-mediated transport

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0033116 endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  KJ893872 - Synthetic construct Homo sapiens clone ccsbBroadEn_03266 ERGIC2 gene, encodes complete protein.
KJ902576 - Synthetic construct Homo sapiens clone ccsbBroadEn_11970 ERGIC2 gene, encodes complete protein.
AL834128 - Homo sapiens mRNA; cDNA DKFZp451J152 (from clone DKFZp451J152); complete cds.
AK074520 - Homo sapiens cDNA FLJ90039 fis, clone HEMBA1002163.
BC064522 - Homo sapiens ERGIC and golgi 2, mRNA (cDNA clone IMAGE:5587750), containing frame-shift errors.
AF183410 - Homo sapiens cd002 protein mRNA, complete cds.
AF216751 - Homo sapiens CDA14 (CDA14) mRNA, complete cds.
BC000887 - Homo sapiens ERGIC and golgi 2, mRNA (cDNA clone MGC:4913 IMAGE:3462408), complete cds.
AF302767 - Homo sapiens PTX1 protein mRNA, complete cds.
BC107794 - Homo sapiens ERGIC and golgi 2, mRNA (cDNA clone MGC:111152 IMAGE:30319807), complete cds.
AK222799 - Homo sapiens mRNA for CDA14 variant, clone: HEP03420.
EU446804 - Synthetic construct Homo sapiens clone IMAGE:100070053; IMAGE:100012013; FLH258313.01L ERGIC and golgi 2 (ERGIC2) gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NHH6, CDA14, ERGI2_HUMAN, ERV41, NM_016570, NP_057654, PTX1, Q53GY2, Q8N2Q9, Q96RQ1, Q9BVV9, Q9NZA3
UCSC ID: uc001riv.3
RefSeq Accession: NM_016570
Protein: Q96RQ1 (aka ERGI2_HUMAN)
CCDS: CCDS41765.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016570.2
exon count: 14CDS single in 3' UTR: no RNA size: 1781
ORF size: 1134CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2367.00frame shift in genome: no % Coverage: 99.78
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.