Human Gene RGPD6 (uc021vmh.1) Description and Page Index
  Description: Homo sapiens RANBP2-like and GRIP domain containing 6 (RGPD6), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:111,271,379-111,336,309 Size: 64,931 Total Exon Count: 24 Strand: -
Coding Region
   Position: hg19 chr2:111,273,188-111,334,601 Size: 61,414 Coding Exon Count: 23 

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 (chr2:111,271,379-111,336,309)mRNA (may differ from genome)Protein (1765 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: RGPD5_HUMAN
DESCRIPTION: RecName: Full=RANBP2-like and GRIP domain-containing protein 5/6; AltName: Full=Ran-binding protein 2-like 1/2; Short=RanBP2-like 1/2; Short=RanBP2L1; Short=RanBP2L2; AltName: Full=Sperm membrane protein BS-63;
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Expressed in testis.
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.

-  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: 0.10 RPKM in Testis
Total median expression: 1.57 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 -201.40533-0.378 Picture PostScript Text
3' UTR -476.121809-0.263 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
PF13432 - 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 Q99666
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 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:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  CR936614 - Homo sapiens mRNA; cDNA DKFZp686I1842 (from clone DKFZp686I1842).
EU794682 - Homo sapiens epididymis luminal protein 161 (HEL161) mRNA, complete cds.
HM005639 - Homo sapiens clone HTL-S-226n testis secretory sperm-binding protein Li 226n mRNA, complete cds.
AF012086 - Homo sapiens Ran binding protein 2 (RanBP2alpha) mRNA, partial cds.
AB209082 - Homo sapiens mRNA for RAN-binding protein 2-like 1 isoform 1 variant protein.
U64675 - Homo sapiens sperm membrane protein BS-63 mRNA, complete cds.
BC020901 - Homo sapiens similar to RAN-binding protein 2-like 1, mRNA (cDNA clone IMAGE:4719329), partial cds.
JD350420 - Sequence 331444 from Patent EP1572962.
JD503810 - Sequence 484834 from Patent EP1572962.
JD503809 - Sequence 484833 from Patent EP1572962.
JD171376 - Sequence 152400 from Patent EP1572962.
JD510789 - Sequence 491813 from Patent EP1572962.
JD071549 - Sequence 52573 from Patent EP1572962.
JD548036 - Sequence 529060 from Patent EP1572962.
JD510545 - Sequence 491569 from Patent EP1572962.
JD524941 - Sequence 505965 from Patent EP1572962.
JD279457 - Sequence 260481 from Patent EP1572962.
JD214070 - Sequence 195094 from Patent EP1572962.
JD439942 - Sequence 420966 from Patent EP1572962.
JD420702 - Sequence 401726 from Patent EP1572962.
JD396796 - Sequence 377820 from Patent EP1572962.
JD367735 - Sequence 348759 from Patent EP1572962.
JD268562 - Sequence 249586 from Patent EP1572962.
JD146535 - Sequence 127559 from Patent EP1572962.
JD490729 - Sequence 471753 from Patent EP1572962.
JD245139 - Sequence 226163 from Patent EP1572962.
JD366792 - Sequence 347816 from Patent EP1572962.
JD185465 - Sequence 166489 from Patent EP1572962.
JD117663 - Sequence 98687 from Patent EP1572962.
JD149548 - Sequence 130572 from Patent EP1572962.
JD415430 - Sequence 396454 from Patent EP1572962.
JD224373 - Sequence 205397 from Patent EP1572962.
JD324910 - Sequence 305934 from Patent EP1572962.
JD280306 - Sequence 261330 from Patent EP1572962.
JD295341 - Sequence 276365 from Patent EP1572962.
JD092891 - Sequence 73915 from Patent EP1572962.
JD184115 - Sequence 165139 from Patent EP1572962.
JD268478 - Sequence 249502 from Patent EP1572962.
JD229244 - Sequence 210268 from Patent EP1572962.
JD281737 - Sequence 262761 from Patent EP1572962.
JD072665 - Sequence 53689 from Patent EP1572962.
JD444679 - Sequence 425703 from Patent EP1572962.
JD291657 - Sequence 272681 from Patent EP1572962.
JD480037 - Sequence 461061 from Patent EP1572962.
JD472563 - Sequence 453587 from Patent EP1572962.
JD294225 - Sequence 275249 from Patent EP1572962.
JD294224 - Sequence 275248 from Patent EP1572962.
JD327246 - Sequence 308270 from Patent EP1572962.
JD432582 - Sequence 413606 from Patent EP1572962.
JD101250 - Sequence 82274 from Patent EP1572962.
JD101251 - Sequence 82275 from Patent EP1572962.
JD304902 - Sequence 285926 from Patent EP1572962.
JD268289 - Sequence 249313 from Patent EP1572962.
JD209604 - Sequence 190628 from Patent EP1572962.
JD511935 - Sequence 492959 from Patent EP1572962.
JD415801 - Sequence 396825 from Patent EP1572962.
JD354696 - Sequence 335720 from Patent EP1572962.
JD283620 - Sequence 264644 from Patent EP1572962.
EF491794 - Homo sapiens clone RGPD5 mRNA, partial sequence; alternatively spliced.
AK056675 - Homo sapiens cDNA FLJ32113 fis, clone OCBBF2001687, highly similar to Homo sapiens sperm membrane protein BS-63 mRNA.
AL136868 - Homo sapiens mRNA; cDNA DKFZp434P144 (from clone DKFZp434P144); complete cds.
BC148413 - Synthetic construct Homo sapiens clone IMAGE:100015385, MGC:183015 RANBP2-like and GRIP domain containing 5 (RGPD5) mRNA, encodes complete protein.
BC156282 - Synthetic construct Homo sapiens clone IMAGE:100061673, MGC:190070 RANBP2-like and GRIP domain containing 7 (RGPD7) mRNA, encodes complete protein.
DQ582662 - Homo sapiens piRNA piR-32774, complete sequence.
JD093214 - Sequence 74238 from Patent EP1572962.
DQ586100 - Homo sapiens piRNA piR-53212, complete sequence.
JD213830 - Sequence 194854 from Patent EP1572962.
JD278168 - Sequence 259192 from Patent EP1572962.
JD405997 - Sequence 387021 from Patent EP1572962.
JD461245 - Sequence 442269 from Patent EP1572962.
JD042990 - Sequence 24014 from Patent EP1572962.
JD040864 - Sequence 21888 from Patent EP1572962.
JD168992 - Sequence 150016 from Patent EP1572962.
JD436188 - Sequence 417212 from Patent EP1572962.
JD103033 - Sequence 84057 from Patent EP1572962.
JD091751 - Sequence 72775 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001123363, NP_001116835, Q53QN2, Q53T03, Q59GM7, Q99666, Q9H0B2, RANBP2L1, RANBP2L2, RGP5, RGP6, RGP7, RGPD5, RGPD5_HUMAN, RGPD7
UCSC ID: uc021vmh.1
RefSeq Accession: NM_001123363
Protein: Q99666 (aka RGPD5_HUMAN)
CCDS: CCDS46388.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001123363.3
exon count: 24CDS single in 3' UTR: no RNA size: 7640
ORF size: 5298CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 10495.00frame shift in genome: no % Coverage: 100.00
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.