Human Gene RGPD1 (uc002ssc.3)
  Description: Homo sapiens RANBP2-like and GRIP domain containing 1 (RGPD1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:87,203,276-87,241,099 Size: 37,824 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr2:87,204,733-87,239,670 Size: 34,938 Coding Exon Count: 8 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:87,203,276-87,241,099)mRNA (may differ from genome)Protein (1013 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkHGNC
HPRDLynxMGIneXtProtPubMedUniProtKB

-  Comments and Description Text from UniProtKB
  ID: RGPD1_HUMAN
DESCRIPTION: RecName: Full=RANBP2-like and GRIP domain-containing protein 1; AltName: Full=Ran-binding protein 2-like 6; Short=RanBP2-like 6; Short=RanBP2L6;
MISCELLANEOUS: One of the 8 copies of RANBP2 clustered close to the chromosome 2 centromere.
SIMILARITY: Contains 1 GRIP domain.
SIMILARITY: Contains 2 RanBD1 domains.
SIMILARITY: Contains 3 TPR repeats.

-  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): RGPD1
CDC HuGE Published Literature: RGPD1

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

+  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: 2.12 RPKM in Testis
Total median expression: 3.45 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 -66.14304-0.218 Picture PostScript Text
3' UTR -394.961429-0.276 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
IPR000237 - GRIP
IPR011993 - PH_like_dom
IPR000156 - Ran_bind_dom
IPR001440 - TPR-1
IPR013026 - TPR-contain_dom
IPR011990 - TPR-like_helical
IPR019734 - TPR_repeat

Pfam Domains:
PF00638 - RanBP1 domain
PF01465 - GRIP domain
PF16704 - Rab binding domain

SCOP Domains:
50729 - PH domain-like

ModBase Predicted Comparative 3D Structure on P0DJD0
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0046907 intracellular transport

Cellular Component:
GO:0005622 intracellular


-  Descriptions from all associated GenBank mRNAs
  AK302429 - Homo sapiens cDNA FLJ56975 complete cds, highly similar to Ran-binding protein 2-like 6.
BC172352 - Synthetic construct Homo sapiens clone IMAGE:100069046, MGC:199057 RANBP2-like and GRIP domain containing 1 (RGPD1) mRNA, encodes complete protein.
CR749330 - Homo sapiens mRNA; cDNA DKFZp781D1923 (from clone DKFZp781D1923).
AK300352 - Homo sapiens cDNA FLJ54456 complete cds, highly similar to Ran-binding protein 2-like 6.
JD374809 - Sequence 355833 from Patent EP1572962.
AY354203 - Homo sapiens RAN-binding protein 2-like 1 short isoform mRNA, complete cds, alternatively spliced.
AK303443 - Homo sapiens cDNA FLJ58076 complete cds, highly similar to Ran-binding protein 2-like 6.
JD168593 - Sequence 149617 from Patent EP1572962.
AK300276 - Homo sapiens cDNA FLJ54501 complete cds, highly similar to Ran-binding protein 2-like 6.
AK298885 - Homo sapiens cDNA FLJ54867 complete cds, highly similar to Ran-binding protein 2-like 6.
JD081039 - Sequence 62063 from Patent EP1572962.
JD189224 - Sequence 170248 from Patent EP1572962.
AF086151 - Homo sapiens full length insert cDNA clone ZB50A07.

-  Other Names for This Gene
  Alternate Gene Symbols: AY354203, P0C839, P0DJD0, Q68DN6, Q6V1X0, RANBP2L6, RGP1, RGPD1_HUMAN
UCSC ID: uc002ssc.3
RefSeq Accession: NM_001024457
Protein: P0DJD0 (aka RGPD1_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AY354203.1
exon count: 10CDS single in 3' UTR: no RNA size: 3504
ORF size: 3042CDS single in intron: no Alignment % ID: 99.97
txCdsPredict score: 5788.50frame shift in genome: no % Coverage: 99.20
has start codon: yes stop codon in genome: no # of Alignments: 2
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.