Human Gene RGPD4 (uc010ywk.2) Description and Page Index
  Description: Homo sapiens RANBP2-like and GRIP domain containing 4 (RGPD4), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:108,443,388-108,509,000 Size: 65,613 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr2:108,443,470-108,507,187 Size: 63,718 Coding Exon Count: 23 

Page IndexSequence and LinksUniProtKB CommentsGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:108,443,388-108,509,000)mRNA (may differ from genome)Protein (1758 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: RGPD4_HUMAN
DESCRIPTION: RecName: Full=RanBP2-like and GRIP domain-containing protein 4;
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 2 TPR repeats.

+  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: 2.90 RPKM in Testis
Total median expression: 4.16 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 -30.3082-0.370 Picture PostScript Text
3' UTR -466.261813-0.257 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
PF13181 - Tetratricopeptide repeat
PF16704 - Rab binding domain

SCOP Domains:
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like
50729 - PH domain-like

ModBase Predicted Comparative 3D Structure on Q7Z3J3
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 orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008536 Ran GTPase binding
GO:0005096 GTPase activator activity

Biological Process:
GO:0000082 G1/S transition of mitotic cell cycle
GO:0006405 RNA export from nucleus
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006606 protein import into nucleus
GO:0007051 spindle organization
GO:0043547 positive regulation of GTPase activity
GO:0046604 positive regulation of mitotic centrosome separation
GO:0046907 intracellular transport

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005813 centrosome


-  Descriptions from all associated GenBank mRNAs
  BX537861 - Homo sapiens mRNA; cDNA DKFZp686P0288 (from clone DKFZp686P0288); complete cds.
AK302921 - Homo sapiens cDNA FLJ59078 complete cds, highly similar to Ran-binding protein 2-like 6.
DQ578622 - Homo sapiens piRNA piR-46734, complete sequence.
DQ586100 - Homo sapiens piRNA piR-53212, complete sequence.
JD168593 - Sequence 149617 from Patent EP1572962.
JD317802 - Sequence 298826 from Patent EP1572962.
JD354696 - Sequence 335720 from Patent EP1572962.
JD415801 - Sequence 396825 from Patent EP1572962.
JD511935 - Sequence 492959 from Patent EP1572962.
JD209604 - Sequence 190628 from Patent EP1572962.
JD268289 - Sequence 249313 from Patent EP1572962.
JD304902 - Sequence 285926 from Patent EP1572962.
JD432583 - Sequence 413607 from Patent EP1572962.
JD294226 - Sequence 275250 from Patent EP1572962.
JD472564 - Sequence 453588 from Patent EP1572962.
JD291657 - Sequence 272681 from Patent EP1572962.
JD444679 - Sequence 425703 from Patent EP1572962.
JD072665 - Sequence 53689 from Patent EP1572962.
JD281737 - Sequence 262761 from Patent EP1572962.
JD229244 - Sequence 210268 from Patent EP1572962.
JD268478 - Sequence 249502 from Patent EP1572962.
JD184115 - Sequence 165139 from Patent EP1572962.
JD092891 - Sequence 73915 from Patent EP1572962.
JD295341 - Sequence 276365 from Patent EP1572962.
JD280306 - Sequence 261330 from Patent EP1572962.
JD224373 - Sequence 205397 from Patent EP1572962.
JD324910 - Sequence 305934 from Patent EP1572962.
JD415430 - Sequence 396454 from Patent EP1572962.
JD185465 - Sequence 166489 from Patent EP1572962.
JD366792 - Sequence 347816 from Patent EP1572962.
JD149548 - Sequence 130572 from Patent EP1572962.
JD117663 - Sequence 98687 from Patent EP1572962.
JD245139 - Sequence 226163 from Patent EP1572962.
JD490729 - Sequence 471753 from Patent EP1572962.
JD159705 - Sequence 140729 from Patent EP1572962.
JD268562 - Sequence 249586 from Patent EP1572962.
JD367735 - Sequence 348759 from Patent EP1572962.
JD537690 - Sequence 518714 from Patent EP1572962.
JD420702 - Sequence 401726 from Patent EP1572962.
JD439942 - Sequence 420966 from Patent EP1572962.
JD214070 - Sequence 195094 from Patent EP1572962.
JD279457 - Sequence 260481 from Patent EP1572962.
JD548036 - Sequence 529060 from Patent EP1572962.
JD510545 - Sequence 491569 from Patent EP1572962.
JD071549 - Sequence 52573 from Patent EP1572962.
JD510789 - Sequence 491813 from Patent EP1572962.
JD171376 - Sequence 152400 from Patent EP1572962.
JD503810 - Sequence 484834 from Patent EP1572962.
JD503809 - Sequence 484833 from Patent EP1572962.
JD510013 - Sequence 491037 from Patent EP1572962.
JD350420 - Sequence 331444 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B9A029, NM_182588, NP_872394, Q7Z3J3, RGP4, RGPD4_HUMAN
UCSC ID: uc010ywk.2
RefSeq Accession: NM_182588
Protein: Q7Z3J3 (aka RGPD4_HUMAN)
CCDS: CCDS46381.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_182588.2
exon count: 23CDS single in 3' UTR: no RNA size: 7172
ORF size: 5277CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 10751.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # 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.