Human Gene RUNDC3A (uc002igl.4)
  Description: Homo sapiens RUN domain containing 3A (RUNDC3A), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr17:42,385,927-42,396,038 Size: 10,112 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr17:42,386,201-42,395,606 Size: 9,406 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
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 (chr17:42,385,927-42,396,038)mRNA (may differ from genome)Protein (446 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RUN3A_HUMAN
DESCRIPTION: RecName: Full=RUN domain-containing protein 3A; AltName: Full=Rap2-interacting protein 8; Short=RPIP-8;
FUNCTION: May act as an effector of RAP2A in neuronal cells (By similarity).
SUBUNIT: Interacts with the GTP-bound form of RAP2A (By similarity).
SIMILARITY: Belongs to the RUNDC3 family.
SIMILARITY: Contains 1 RUN domain.
SEQUENCE CAUTION: Sequence=BAD93039.1; Type=Erroneous initiation;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: RUNDC3A
Diseases sorted by gene-association score: dementia, frontotemporal (1)

-  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: 201.15 RPKM in Brain - Cortex
Total median expression: 1807.11 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 -139.00274-0.507 Picture PostScript Text
3' UTR -167.08432-0.387 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
IPR004012 - Run

Pfam Domains:
PF02759 - RUN domain

ModBase Predicted Comparative 3D Structure on Q59EK9
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:0005515 protein binding
GO:0030250 guanylate cyclase activator activity
GO:0030695 GTPase regulator activity
GO:0051428 peptide hormone receptor binding

Biological Process:
GO:0007264 small GTPase mediated signal transduction
GO:0030828 positive regulation of cGMP biosynthetic process
GO:0031284 positive regulation of guanylate cyclase activity
GO:0050790 regulation of catalytic activity

Cellular Component:
GO:0005829 cytosol
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  AL133657 - Homo sapiens mRNA; cDNA DKFZp434A1727 (from clone DKFZp434A1727).
LP896051 - Sequence 915 from Patent EP3253886.
LF209376 - JP 2014500723-A/16879: Polycomb-Associated Non-Coding RNAs.
AB209802 - Homo sapiens mRNA for RaP2 interacting protein 8 variant protein.
AK226045 - Homo sapiens mRNA for RaP2 interacting protein 8 variant, clone: FCC101B04.
BC006194 - Homo sapiens RUN domain containing 3A, mRNA (cDNA clone MGC:1161 IMAGE:2823366), complete cds.
AK313669 - Homo sapiens cDNA, FLJ94252, Homo sapiens RaP2 interacting protein 8 (RPIP8), mRNA.
BX537443 - Homo sapiens mRNA; cDNA DKFZp686G19272 (from clone DKFZp686G19272); complete cds.
JD475229 - Sequence 456253 from Patent EP1572962.
JD396741 - Sequence 377765 from Patent EP1572962.
AF055026 - Homo sapiens clone 24444 RaP2 interacting protein 8 (RPIP8) mRNA, complete cds.
JD474618 - Sequence 455642 from Patent EP1572962.
CU675291 - Synthetic construct Homo sapiens gateway clone IMAGE:100019259 5' read RUNDC3A mRNA.
CR456748 - Homo sapiens full open reading frame cDNA clone RZPDo834A0711D for gene RPIP8, RaP2 interacting protein 8; complete cds, incl. stopcodon.
HQ447276 - Synthetic construct Homo sapiens clone IMAGE:100070586; CCSB004465_01 RaP2 interacting protein 8 (RUNDC3A) gene, encodes complete protein.
KJ898307 - Synthetic construct Homo sapiens clone ccsbBroadEn_07701 RUNDC3A gene, encodes complete protein.
U93871 - Homo sapiens RaP2 interacting protein 8 (RPIP8) mRNA, complete cds.
AK123330 - Homo sapiens cDNA FLJ41336 fis, clone BRAMY3000213, highly similar to Homo sapiens RaP2 interacting protein 8 (RPIP8) mRNA.
LF328069 - JP 2014500723-A/135572: Polycomb-Associated Non-Coding RNAs.
LF328070 - JP 2014500723-A/135573: Polycomb-Associated Non-Coding RNAs.
LF209377 - JP 2014500723-A/16880: Polycomb-Associated Non-Coding RNAs.
LF328071 - JP 2014500723-A/135574: Polycomb-Associated Non-Coding RNAs.
LF328072 - JP 2014500723-A/135575: Polycomb-Associated Non-Coding RNAs.
LF328073 - JP 2014500723-A/135576: Polycomb-Associated Non-Coding RNAs.
BC013240 - Homo sapiens RUN domain containing 3A, mRNA (cDNA clone IMAGE:4179132).
LF328074 - JP 2014500723-A/135577: Polycomb-Associated Non-Coding RNAs.
JD024300 - Sequence 5324 from Patent EP1572962.
LF328075 - JP 2014500723-A/135578: Polycomb-Associated Non-Coding RNAs.
JD033166 - Sequence 14190 from Patent EP1572962.
LF209378 - JP 2014500723-A/16881: Polycomb-Associated Non-Coding RNAs.
MA563646 - JP 2018138019-A/135572: Polycomb-Associated Non-Coding RNAs.
MA563647 - JP 2018138019-A/135573: Polycomb-Associated Non-Coding RNAs.
MA563648 - JP 2018138019-A/135574: Polycomb-Associated Non-Coding RNAs.
MA563649 - JP 2018138019-A/135575: Polycomb-Associated Non-Coding RNAs.
MA563650 - JP 2018138019-A/135576: Polycomb-Associated Non-Coding RNAs.
MA563651 - JP 2018138019-A/135577: Polycomb-Associated Non-Coding RNAs.
MA563652 - JP 2018138019-A/135578: Polycomb-Associated Non-Coding RNAs.
MA444953 - JP 2018138019-A/16879: Polycomb-Associated Non-Coding RNAs.
MA444954 - JP 2018138019-A/16880: Polycomb-Associated Non-Coding RNAs.
MA444955 - JP 2018138019-A/16881: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B2R974, NM_001144825, NP_001138297, O15483, O60651, Q59EK9, Q7Z3S2, Q9UF50, RAP2IP, RPIP8, RUN3A_HUMAN
UCSC ID: uc002igl.4
RefSeq Accession: NM_001144825
Protein: Q59EK9 (aka RUN3A_HUMAN)
CCDS: CCDS45698.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001144825.1
exon count: 11CDS single in 3' UTR: no RNA size: 2047
ORF size: 1341CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1932.00frame 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: 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.