Human Gene RIC1 (uc003zjh.4)
  Description: Homo sapiens RIC1 (RIC1), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:5,629,119-5,769,454 Size: 140,336 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg19 chr9:5,629,310-5,769,330 Size: 140,021 Coding Exon Count: 22 

Page IndexSequence and LinksPrimersGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:5,629,119-5,769,454)mRNA (may differ from genome)Protein (1165 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
LynxMGIOMIMPubMedReactomeUniProtKB
BioGrid 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


+  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: 19.98 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 289.55 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 -108.20191-0.566 Picture PostScript Text
3' UTR -24.20124-0.195 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:
PF07064 - RIC1

SCOP Domains:
50960 - TolB, C-terminal domain
101898 - NHL repeat
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain

ModBase Predicted Comparative 3D Structure on Q4ADV7-2
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     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  LF385283 - JP 2014500723-A/192786: Polycomb-Associated Non-Coding RNAs.
LF385475 - JP 2014500723-A/192978: Polycomb-Associated Non-Coding RNAs.
AL136875 - Homo sapiens mRNA; cDNA DKFZp434D105 (from clone DKFZp434D105).
BC136616 - Homo sapiens KIAA1432, mRNA (cDNA clone MGC:168229 IMAGE:9020606), complete cds.
BC144296 - Homo sapiens KIAA1432, mRNA (cDNA clone MGC:177833 IMAGE:9052816), complete cds.
AB205401 - Homo sapiens CIP150 mRNA for connexin43-interacting protein of 150 kDa, complete cds.
AK124394 - Homo sapiens cDNA FLJ42403 fis, clone ASTRO3000177, weakly similar to Drosophila melanogaster BcDNA.GH03694 (BcDNA.GH03694) mRNA.
AK022642 - Homo sapiens cDNA FLJ12580 fis, clone NT2RM4001116, weakly similar to HYPOTHETICAL 216.3 KD PROTEIN R06F6.8 IN CHROMOSOME II.
AB037853 - Homo sapiens mRNA for KIAA1432 protein, partial cds.
AB527173 - Synthetic construct DNA, clone: pF1KA1432, Homo sapiens KIAA1432 gene for KIAA1432, without stop codon, in Flexi system.
AK074150 - Homo sapiens mRNA for FLJ00223 protein.
BC030576 - Homo sapiens KIAA1432, mRNA (cDNA clone IMAGE:4077122), partial cds.
MA620860 - JP 2018138019-A/192786: Polycomb-Associated Non-Coding RNAs.
MA621052 - JP 2018138019-A/192978: Polycomb-Associated Non-Coding RNAs.
JD109793 - Sequence 90817 from Patent EP1572962.
JD468950 - Sequence 449974 from Patent EP1572962.
JD428544 - Sequence 409568 from Patent EP1572962.
JD206490 - Sequence 187514 from Patent EP1572962.
JD301616 - Sequence 282640 from Patent EP1572962.
JD154748 - Sequence 135772 from Patent EP1572962.
JD315186 - Sequence 296210 from Patent EP1572962.
LF345332 - JP 2014500723-A/152835: Polycomb-Associated Non-Coding RNAs.
JD079965 - Sequence 60989 from Patent EP1572962.
JD186607 - Sequence 167631 from Patent EP1572962.
LF345335 - JP 2014500723-A/152838: Polycomb-Associated Non-Coding RNAs.
JD091887 - Sequence 72911 from Patent EP1572962.
LF345342 - JP 2014500723-A/152845: Polycomb-Associated Non-Coding RNAs.
MA580909 - JP 2018138019-A/152835: Polycomb-Associated Non-Coding RNAs.
MA580912 - JP 2018138019-A/152838: Polycomb-Associated Non-Coding RNAs.
MA580919 - JP 2018138019-A/152845: Polycomb-Associated Non-Coding RNAs.
LF345345 - JP 2014500723-A/152848: Polycomb-Associated Non-Coding RNAs.
DQ570742 - Homo sapiens piRNA piR-30854, complete sequence.
MA580922 - JP 2018138019-A/152848: Polycomb-Associated Non-Coding RNAs.

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

Protein Q4ADV7 (Reactome details) participates in the following event(s):

R-HSA-6811428 RIC1:RGP1 recruits RAB6:GDP to the TGN
R-HSA-8847887 RAB33B:GTP binds RIC1:RGP1
R-HSA-6811431 RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived vesicles
R-HSA-6811429 RIC1:RGP1 stimulates nucleotide RAB6 nucleotide exchange
R-HSA-8876193 RIC1-RGP1 exchanges GTP for GDP on RAB6
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network
R-HSA-6811438 Intra-Golgi traffic
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
R-HSA-199991 Membrane Trafficking
R-HSA-9007101 Rab regulation of trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: CIP150, KIAA1432, NM_001135920, NP_001129392, Q4ADV7-2, uc003zjh.3
UCSC ID: uc003zjh.4
RefSeq Accession: NM_001135920
Protein: Q4ADV7-2, splice isoform of Q4ADV7 CCDS: CCDS47949.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001135920.2
exon count: 22CDS single in 3' UTR: no RNA size: 3831
ORF size: 3498CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7060.50frame shift in genome: no % Coverage: 99.53
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: 198# 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.