Human Gene ERGIC3 (uc002xcs.3)
  Description: Homo sapiens ERGIC and golgi 3 (ERGIC3), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr20:34,129,778-34,145,405 Size: 15,628 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr20:34,129,847-34,145,275 Size: 15,429 Coding Exon Count: 14 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:34,129,778-34,145,405)mRNA (may differ from genome)Protein (388 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIOMIM
PubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  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


-  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: 131.26 RPKM in Testis
Total median expression: 2518.34 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 -36.2069-0.525 Picture PostScript Text
3' UTR -28.29130-0.218 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
  Pfam Domains:
PF07970 - Endoplasmic reticulum vesicle transporter
PF13850 - Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)

ModBase Predicted Comparative 3D Structure on Q9Y282-3
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 orthologGenome BrowserNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
  Ensembl  SGD
  Protein Sequence  Protein Sequence
  Alignment  Alignment

-  Descriptions from all associated GenBank mRNAs
  LF205980 - JP 2014500723-A/13483: Polycomb-Associated Non-Coding RNAs.
AF308298 - Homo sapiens serologically defined breast cancer antigen NY-BR-84 mRNA, partial cds.
AF077030 - Homo sapiens hypothetical 43.2 Kd protein mRNA, complete cds.
AF151812 - Homo sapiens CGI-54 protein mRNA, complete cds.
EF206690 - Homo sapiens endoplasmic reticulum-localized protein ERp43 mRNA, complete cds.
BC014014 - Homo sapiens ERGIC and golgi 3, mRNA (cDNA clone MGC:19896 IMAGE:3954269), complete cds.
JD127258 - Sequence 108282 from Patent EP1572962.
AK074550 - Homo sapiens cDNA FLJ90069 fis, clone HEMBA1003945, highly similar to Serologically defined breast cancer antigen 84.
BC009765 - Homo sapiens ERGIC and golgi 3, mRNA (cDNA clone MGC:13325 IMAGE:4283844), complete cds.
AK096484 - Homo sapiens cDNA FLJ39165 fis, clone OCBBF2002663.
AK300916 - Homo sapiens cDNA FLJ56701 complete cds, highly similar to Endoplasmic reticulum-Golgi intermediate compartment protein 3.
LF350336 - JP 2014500723-A/157839: Polycomb-Associated Non-Coding RNAs.
CU679479 - Synthetic construct Homo sapiens gateway clone IMAGE:100023404 5' read ERGIC3 mRNA.
CU680742 - Synthetic construct Homo sapiens gateway clone IMAGE:100017143 5' read ERGIC3 mRNA.
HQ448277 - Synthetic construct Homo sapiens clone IMAGE:100071680; CCSB007079_02 ERGIC and golgi 3 (ERGIC3) gene, encodes complete protein.
KJ893951 - Synthetic construct Homo sapiens clone ccsbBroadEn_03345 ERGIC3 gene, encodes complete protein.
KJ898933 - Synthetic construct Homo sapiens clone ccsbBroadEn_08327 ERGIC3 gene, encodes complete protein.
AF091085 - Homo sapiens clone 638 unknown mRNA, complete sequence.
AF116614 - Homo sapiens PRO0989 mRNA, complete cds.
LF350337 - JP 2014500723-A/157840: Polycomb-Associated Non-Coding RNAs.
DQ591872 - Homo sapiens piRNA piR-58984, complete sequence.
LF350338 - JP 2014500723-A/157841: Polycomb-Associated Non-Coding RNAs.
AL161963 - Homo sapiens mRNA; cDNA DKFZp547A2190 (from clone DKFZp547A2190).
LF350339 - JP 2014500723-A/157842: Polycomb-Associated Non-Coding RNAs.
LF350340 - JP 2014500723-A/157843: Polycomb-Associated Non-Coding RNAs.
LF350344 - JP 2014500723-A/157847: Polycomb-Associated Non-Coding RNAs.
LF350345 - JP 2014500723-A/157848: Polycomb-Associated Non-Coding RNAs.
LF350346 - JP 2014500723-A/157849: Polycomb-Associated Non-Coding RNAs.
JD164062 - Sequence 145086 from Patent EP1572962.
JD228513 - Sequence 209537 from Patent EP1572962.
JD295930 - Sequence 276954 from Patent EP1572962.
JD123698 - Sequence 104722 from Patent EP1572962.
LF350347 - JP 2014500723-A/157850: Polycomb-Associated Non-Coding RNAs.
JD105219 - Sequence 86243 from Patent EP1572962.
JD070757 - Sequence 51781 from Patent EP1572962.
JD193369 - Sequence 174393 from Patent EP1572962.
MA585913 - JP 2018138019-A/157839: Polycomb-Associated Non-Coding RNAs.
MA585914 - JP 2018138019-A/157840: Polycomb-Associated Non-Coding RNAs.
MA585915 - JP 2018138019-A/157841: Polycomb-Associated Non-Coding RNAs.
MA585916 - JP 2018138019-A/157842: Polycomb-Associated Non-Coding RNAs.
MA585917 - JP 2018138019-A/157843: Polycomb-Associated Non-Coding RNAs.
MA585921 - JP 2018138019-A/157847: Polycomb-Associated Non-Coding RNAs.
MA585922 - JP 2018138019-A/157848: Polycomb-Associated Non-Coding RNAs.
MA585923 - JP 2018138019-A/157849: Polycomb-Associated Non-Coding RNAs.
MA585924 - JP 2018138019-A/157850: Polycomb-Associated Non-Coding RNAs.
MA441557 - JP 2018138019-A/13483: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: C20orf47, CGI-54, ERV46, NM_198398, NP_938408, PRO0989, Q9Y282-3, SDBCAG84
UCSC ID: uc002xcs.3
RefSeq Accession: NM_198398
Protein: Q9Y282-3, splice isoform of Q9Y282 CCDS: CCDS13257.1, CCDS13258.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_198398.1
exon count: 14CDS single in 3' UTR: no RNA size: 1383
ORF size: 1167CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2534.00frame shift in genome: no % Coverage: 98.77
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.