Human Gene SNX13 (uc003stv.3) Description and Page Index
  Description: Homo sapiens sorting nexin 13 (SNX13), mRNA.
RefSeq Summary (NM_015132): This gene encodes a PHOX domain- and RGS domain-containing protein that belongs to the sorting nexin (SNX) family and the regulator of G protein signaling (RGS) family. The PHOX domain is a phosphoinositide binding domain, and the SNX family members are involved in intracellular trafficking. The RGS family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. The RGS domain of this protein interacts with G alpha(s), accelerates its GTP hydrolysis, and attenuates G alpha(s)-mediated signaling. Overexpression of this protein delayes lysosomal degradation of the epidermal growth factor receptor. Because of its bifunctional role, this protein may link heterotrimeric G protein signaling and vesicular trafficking. [provided by RefSeq, Jul 2008]. ##Evidence-Data-START## Transcript exon combination :: SRR1803614.264128.1, SRR1803614.113921.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000428135.7/ ENSP00000398789.2 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr7:17,830,385-17,980,131 Size: 149,747 Total Exon Count: 26 Strand: -
Coding Region
   Position: hg19 chr7:17,833,669-17,979,918 Size: 146,250 Coding Exon Count: 26 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:17,830,385-17,980,131)mRNA (may differ from genome)Protein (957 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SNX13
CDC HuGE Published Literature: SNX13

-  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: 5.66 RPKM in Testis
Total median expression: 185.50 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 -96.60213-0.454 Picture PostScript Text
3' UTR -810.013284-0.247 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:
PF00615 - Regulator of G protein signaling domain
PF00787 - PX domain
PF02194 - PXA domain
PF08628 - Sorting nexin C terminal

SCOP Domains:
46785 - "Winged helix" DNA-binding domain
48097 - Regulator of G-protein signaling, RGS
64268 - PX domain

ModBase Predicted Comparative 3D Structure on Q9Y5W8-2
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 orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Descriptions from all associated GenBank mRNAs
  LP895579 - Sequence 443 from Patent EP3253886.
AB018256 - Homo sapiens mRNA for KIAA0713 protein, partial cds.
BC045667 - Homo sapiens sorting nexin 13, mRNA (cDNA clone MGC:44494 IMAGE:5298570), complete cds.
BC041844 - Homo sapiens sorting nexin 13, mRNA (cDNA clone IMAGE:5269355), with apparent retained intron.
AF420470 - Homo sapiens RGS-PX1 mRNA, complete cds.
AK294582 - Homo sapiens cDNA FLJ56070 complete cds, highly similar to Sorting nexin-13.
AK315135 - Homo sapiens cDNA, FLJ96101, Homo sapiens sorting nexin 13 (SNX13), mRNA.
AK001861 - Homo sapiens cDNA FLJ10999 fis, clone PLACE1002529, highly similar to Homo sapiens mRNA for KIAA0713 protein.
AL353943 - Homo sapiens mRNA; cDNA DKFZp761E0611 (from clone DKFZp761E0611).
BC022060 - Homo sapiens, Similar to sorting nexin 13, clone IMAGE:4719518, mRNA, partial cds.
JD093546 - Sequence 74570 from Patent EP1572962.
JD130197 - Sequence 111221 from Patent EP1572962.
JD490621 - Sequence 471645 from Patent EP1572962.
AK023740 - Homo sapiens cDNA FLJ13678 fis, clone PLACE1012031, highly similar to Sorting nexin-13.
AK026643 - Homo sapiens cDNA: FLJ22990 fis, clone KAT11852, highly similar to AF121862 Homo sapiens sorting nexin 13 (SNX13) mRNA.
AF121862 - Homo sapiens sorting nexin 13 (SNX13) mRNA, partial cds.
AK307453 - Homo sapiens cDNA, FLJ97401.
JD089250 - Sequence 70274 from Patent EP1572962.
GQ129429 - Synthetic construct Homo sapiens clone HAIB:100068618; DKFZo008G0535 sorting nexin 13 protein (SNX13) gene, complete cds.
GQ129428 - Synthetic construct Homo sapiens clone HAIB:100068715; DKFZo004G0536 sorting nexin 13 protein (SNX13) gene, partial cds.
AB384514 - Synthetic construct DNA, clone: pF1KA0713, Homo sapiens SNX13 gene for sorting nexin-13, complete cds, without stop codon, in Flexi system.
DQ597831 - Homo sapiens piRNA piR-35897, complete sequence.
BC050289 - Homo sapiens sorting nexin 13, mRNA (cDNA clone IMAGE:5271192), with apparent retained intron.
JD411769 - Sequence 392793 from Patent EP1572962.
JD197043 - Sequence 178067 from Patent EP1572962.
JD215528 - Sequence 196552 from Patent EP1572962.
JD396584 - Sequence 377608 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA0713, NM_015132, NP_055947, Q9Y5W8-2
UCSC ID: uc003stv.3
RefSeq Accession: NM_015132
Protein: Q9Y5W8-2, splice isoform of Q9Y5W8 CCDS: CCDS47551.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015132.4
exon count: 26CDS single in 3' UTR: no RNA size: 6371
ORF size: 2874CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5789.00frame 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.