Human Gene RIN3 (uc001yap.3) Description and Page Index
  Description: Homo sapiens Ras and Rab interactor 3 (RIN3), mRNA.
RefSeq Summary (NM_024832): This protein encoded by this gene is a member of the RIN family of Ras interaction-interference proteins, which are binding partners to the RAB5 small GTPases. The protein functions as a guanine nucleotide exchange for RAB5B and RAB31. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016].
Transcript (Including UTRs)
   Position: hg19 chr14:92,980,125-93,155,334 Size: 175,210 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr14:92,980,277-93,154,597 Size: 174,321 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:92,980,125-93,155,334)mRNA (may differ from genome)Protein (985 aa)
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UniProtKB

-  Comments and Description Text from UniProtKB
  ID: RIN3_HUMAN
DESCRIPTION: RecName: Full=Ras and Rab interactor 3; AltName: Full=Ras interaction/interference protein 3;
FUNCTION: Potential Ras effector protein. May function as a guanine nucleotide exchange (GEF), by exchanging bound GDP for free GTP.
SUBUNIT: Interacts with RAB5B and BIN1.
INTERACTION: P16333:NCK1; NbExp=2; IntAct=EBI-1570523, EBI-389883; P19174:PLCG1; NbExp=3; IntAct=EBI-1570523, EBI-79387;
SUBCELLULAR LOCATION: Cytoplasm. Cytoplasmic vesicle. Early endosome. Note=Activation of tyrosine phosphorylation signaling induces translocation to cytoplasmic vesicles.
TISSUE SPECIFICITY: Widely expressed.
SIMILARITY: Belongs to the RIN (Ras interaction/interference) family.
SIMILARITY: Contains 1 Ras-associating domain.
SIMILARITY: Contains 1 SH2 domain.
SIMILARITY: Contains 1 VPS9 domain.
SEQUENCE CAUTION: Sequence=BAB13888.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing; Sequence=BAB15357.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAC03432.1; Type=Miscellaneous discrepancy; Note=Intron retention;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RIN3
CDC HuGE Published Literature: RIN3
Positive Disease Associations: Hemoglobins , Paget's disease , smoking cessation
Related Studies:
  1. Hemoglobins
    Qiong Yang et al. BMC medical genetics 2007, Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903294]
    Using genome-wide association methodology, we have successfully identified a SNP in complete LD with a sequence variant previously shown to be strongly associated with factor VII, providing proof of principle for this approach. Further study of additional strongly associated SNPs and linked regions may identify novel variants that influence the inter-individual variability in hemostatic factors and hematological phenotypes.
  2. Paget's disease
    Omar M E Albagha et al. Nature genetics 2011, Genome-wide association identifies three new susceptibility loci for Paget's disease of bone., Nature genetics. [PubMed 21623375]
  3. smoking cessation
    Uhl ,et al. Pharmacogenomics 2010, Genome-wide association for smoking cessation success: participants in the Patch in Practice trial of nicotine replacement , Pharmacogenomics 2010 11- 3 : 357-67. [PubMed 20235792]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: RIN3
Diseases sorted by gene-association score: paget's disease of bone (3)

-  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: 44.89 RPKM in Whole Blood
Total median expression: 244.58 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 -96.40152-0.634 Picture PostScript Text
3' UTR -293.43737-0.398 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
IPR000159 - Ras-assoc
IPR000980 - SH2
IPR003123 - VPS9
IPR013995 - VPS9_subgr

Pfam Domains:
PF02204 - Vacuolar sorting protein 9 (VPS9) domain

SCOP Domains:
109993 - VPS9 domain (Pfam 02204)
55550 - SH2 domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3U23
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8TB24
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
  Molecular Function:
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0017112 Rab guanyl-nucleotide exchange factor activity
GO:0017137 Rab GTPase binding

Biological Process:
GO:0006897 endocytosis
GO:0007165 signal transduction
GO:0043547 positive regulation of GTPase activity

Cellular Component:
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005829 cytosol
GO:0031410 cytoplasmic vesicle


-  Descriptions from all associated GenBank mRNAs
  AK021762 - Homo sapiens cDNA FLJ11700 fis, clone HEMBA1005050.
BC032614 - Homo sapiens cDNA clone IMAGE:5557263, containing frame-shift errors.
BC070062 - Homo sapiens Ras and Rab interactor 3, mRNA (cDNA clone MGC:87258 IMAGE:30332851), complete cds.
BX248258 - human full-length cDNA clone CS0DM003YJ21 of Fetal liver of Homo sapiens (human).
AB081753 - Homo sapiens mRNA for RIN3, complete cds.
AK128338 - Homo sapiens cDNA FLJ46480 fis, clone THYMU3025683, weakly similar to Ras interaction/interference protein 1.
AK096145 - Homo sapiens cDNA FLJ38826 fis, clone LIVER2009118.
BC034153 - Homo sapiens Ras and Rab interactor 3, mRNA (cDNA clone IMAGE:4704191), with apparent retained intron.
BC025248 - Homo sapiens Ras and Rab interactor 3, mRNA (cDNA clone IMAGE:4842507), partial cds.
JD331164 - Sequence 312188 from Patent EP1572962.
JD122725 - Sequence 103749 from Patent EP1572962.
JD119456 - Sequence 100480 from Patent EP1572962.
JD076117 - Sequence 57141 from Patent EP1572962.
JD094046 - Sequence 75070 from Patent EP1572962.
JD395911 - Sequence 376935 from Patent EP1572962.
AK090451 - Homo sapiens mRNA for FLJ00372 protein.
JD439174 - Sequence 420198 from Patent EP1572962.
JD117566 - Sequence 98590 from Patent EP1572962.
JD414391 - Sequence 395415 from Patent EP1572962.
AB060338 - Homo sapiens mRNA for RIN3, partial cds.
JD387900 - Sequence 368924 from Patent EP1572962.
AK026092 - Homo sapiens cDNA: FLJ22439 fis, clone HRC09236.
JD095731 - Sequence 76755 from Patent EP1572962.
JD397420 - Sequence 378444 from Patent EP1572962.
AK074176 - Homo sapiens mRNA for FLJ00249 protein.
CR936654 - Homo sapiens mRNA; cDNA DKFZp762H1613 (from clone DKFZp762H1613).
JD205723 - Sequence 186747 from Patent EP1572962.
JD058160 - Sequence 39184 from Patent EP1572962.
JD100342 - Sequence 81366 from Patent EP1572962.
JD304338 - Sequence 285362 from Patent EP1572962.
JD551613 - Sequence 532637 from Patent EP1572962.
JD113425 - Sequence 94449 from Patent EP1572962.
JD184783 - Sequence 165807 from Patent EP1572962.
JD170559 - Sequence 151583 from Patent EP1572962.
JD099217 - Sequence 80241 from Patent EP1572962.
JD464375 - Sequence 445399 from Patent EP1572962.
JD321593 - Sequence 302617 from Patent EP1572962.
JD318172 - Sequence 299196 from Patent EP1572962.
JD456954 - Sequence 437978 from Patent EP1572962.
JD338985 - Sequence 320009 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8TB24 (Reactome details) participates in the following event(s):

R-HSA-8875320 RAB5 GEFs exchange GTP for GDP on RAB5
R-HSA-8877311 RAB31 GEFs exchange GTP for GDP on RAB31
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
R-HSA-9007101 Rab regulation of trafficking
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: NM_024832, NP_079108, Q76LB3, Q8NF30, Q8TB24, Q8TEE8, Q8WYP4, Q9H6A5, Q9HAG1, RIN3_HUMAN
UCSC ID: uc001yap.3
RefSeq Accession: NM_024832
Protein: Q8TB24 (aka RIN3_HUMAN)
CCDS: CCDS32144.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024832.3
exon count: 10CDS single in 3' UTR: no RNA size: 3869
ORF size: 2958CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5277.00frame shift in genome: no % Coverage: 99.43
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.