Human Gene SRGAP3 (uc003brg.2)
  Description: Homo sapiens SLIT-ROBO Rho GTPase activating protein 3 (SRGAP3), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:9,022,276-9,291,369 Size: 269,094 Total Exon Count: 22 Strand: -
Coding Region
   Position: hg19 chr3:9,027,203-9,290,635 Size: 263,433 Coding Exon Count: 22 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:9,022,276-9,291,369)mRNA (may differ from genome)Protein (1075 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedReactomeUniProtKBWikipediaBioGrid 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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SRGAP3
CDC HuGE Published Literature: SRGAP3
Positive Disease Associations: Amyotrophic Lateral Sclerosis , Body Weight , Coronary Artery Disease , Glucose , smoking cessation , Stroke , Triglycerides
Related Studies:
  1. Amyotrophic Lateral Sclerosis
    Simon Cronin et al. Human molecular genetics 2008, A genome-wide association study of sporadic ALS in a homogenous Irish population., Human molecular genetics. [PubMed 18057069]
  2. Body Weight
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Coronary Artery Disease
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SRGAP3
Diseases sorted by gene-association score: pilocytic astrocytoma* (145), 3p- syndrome (11), obstructive hydrocephalus (5)
* = Manually curated disease association

-  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: 21.96 RPKM in Brain - Cerebellum
Total median expression: 144.68 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 -262.10734-0.357 Picture PostScript Text
3' UTR -1687.844927-0.343 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:
PF00018 - SH3 domain
PF00611 - Fes/CIP4, and EFC/F-BAR homology domain
PF00620 - RhoGAP domain
PF07653 - Variant SH3 domain
PF14604 - Variant SH3 domain

SCOP Domains:
48350 - GTPase activation domain, GAP
50044 - SH3-domain

ModBase Predicted Comparative 3D Structure on O43295-2
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 orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Descriptions from all associated GenBank mRNAs
  AF427144 - Homo sapiens MEGAP transcript variant a mRNA, complete cds.
AF464189 - Homo sapiens WAVE-associated Rac GTPase activating protein mRNA, complete cds.
AB007871 - Homo sapiens KIAA0411 mRNA, partial cds.
BC172359 - Synthetic construct Homo sapiens clone IMAGE:100069053, MGC:199064 SLIT-ROBO Rho GTPase activating protein 3 (SRGAP3) mRNA, encodes complete protein.
AB384477 - Synthetic construct DNA, clone: pF1KA0411, Homo sapiens SRGAP3 gene for SLIT-ROBO Rho GTPase-activating protein 3, complete cds, without stop codon, in Flexi system.
BC039300 - Homo sapiens SLIT-ROBO Rho GTPase activating protein 3, mRNA (cDNA clone IMAGE:4830856), complete cds.
AK094355 - Homo sapiens cDNA FLJ37036 fis, clone BRACE2011592, moderately similar to RHO-GTPASE-ACTIVATING PROTEIN 4.
JD268106 - Sequence 249130 from Patent EP1572962.
JD245491 - Sequence 226515 from Patent EP1572962.
JD524273 - Sequence 505297 from Patent EP1572962.
JD168989 - Sequence 150013 from Patent EP1572962.
JD503305 - Sequence 484329 from Patent EP1572962.
JD378726 - Sequence 359750 from Patent EP1572962.
JD440618 - Sequence 421642 from Patent EP1572962.
JD215909 - Sequence 196933 from Patent EP1572962.
JD228508 - Sequence 209532 from Patent EP1572962.
JD142710 - Sequence 123734 from Patent EP1572962.
JD220504 - Sequence 201528 from Patent EP1572962.
JD227878 - Sequence 208902 from Patent EP1572962.
JD180689 - Sequence 161713 from Patent EP1572962.
JD481962 - Sequence 462986 from Patent EP1572962.
JD392985 - Sequence 374009 from Patent EP1572962.
JD305337 - Sequence 286361 from Patent EP1572962.
JD236650 - Sequence 217674 from Patent EP1572962.
JD287083 - Sequence 268107 from Patent EP1572962.
JD339592 - Sequence 320616 from Patent EP1572962.
JD087356 - Sequence 68380 from Patent EP1572962.
JD297883 - Sequence 278907 from Patent EP1572962.
JD127372 - Sequence 108396 from Patent EP1572962.
JD226578 - Sequence 207602 from Patent EP1572962.
JD285101 - Sequence 266125 from Patent EP1572962.
JD091379 - Sequence 72403 from Patent EP1572962.
JD080111 - Sequence 61135 from Patent EP1572962.
JD164323 - Sequence 145347 from Patent EP1572962.
JD324216 - Sequence 305240 from Patent EP1572962.
JD563469 - Sequence 544493 from Patent EP1572962.
JD167101 - Sequence 148125 from Patent EP1572962.
JD101332 - Sequence 82356 from Patent EP1572962.
JD329935 - Sequence 310959 from Patent EP1572962.
JD113902 - Sequence 94926 from Patent EP1572962.
JD445633 - Sequence 426657 from Patent EP1572962.
JD403712 - Sequence 384736 from Patent EP1572962.
JD272767 - Sequence 253791 from Patent EP1572962.
JD346836 - Sequence 327860 from Patent EP1572962.
JD038447 - Sequence 19471 from Patent EP1572962.
JD560341 - Sequence 541365 from Patent EP1572962.
JD025338 - Sequence 6362 from Patent EP1572962.
JD034145 - Sequence 15169 from Patent EP1572962.
JD084499 - Sequence 65523 from Patent EP1572962.
JD045844 - Sequence 26868 from Patent EP1572962.
JD035439 - Sequence 16463 from Patent EP1572962.
JD023515 - Sequence 4539 from Patent EP1572962.
JD148931 - Sequence 129955 from Patent EP1572962.
JD021908 - Sequence 2932 from Patent EP1572962.
JD180757 - Sequence 161781 from Patent EP1572962.
JD030260 - Sequence 11284 from Patent EP1572962.
JD252150 - Sequence 233174 from Patent EP1572962.
JD126443 - Sequence 107467 from Patent EP1572962.
JD208981 - Sequence 190005 from Patent EP1572962.
JD519392 - Sequence 500416 from Patent EP1572962.
JD394015 - Sequence 375039 from Patent EP1572962.
JD307676 - Sequence 288700 from Patent EP1572962.
JD130101 - Sequence 111125 from Patent EP1572962.
JD551175 - Sequence 532199 from Patent EP1572962.
JD179263 - Sequence 160287 from Patent EP1572962.
JD365670 - Sequence 346694 from Patent EP1572962.
JD073499 - Sequence 54523 from Patent EP1572962.
JD479913 - Sequence 460937 from Patent EP1572962.
JD511890 - Sequence 492914 from Patent EP1572962.
JD327914 - Sequence 308938 from Patent EP1572962.
JD058620 - Sequence 39644 from Patent EP1572962.
JD062083 - Sequence 43107 from Patent EP1572962.
JD248401 - Sequence 229425 from Patent EP1572962.
JD304470 - Sequence 285494 from Patent EP1572962.
JD187121 - Sequence 168145 from Patent EP1572962.
JD421642 - Sequence 402666 from Patent EP1572962.
JD494246 - Sequence 475270 from Patent EP1572962.
JD273459 - Sequence 254483 from Patent EP1572962.
JD210073 - Sequence 191097 from Patent EP1572962.
JD193787 - Sequence 174811 from Patent EP1572962.
JD227854 - Sequence 208878 from Patent EP1572962.
JD138548 - Sequence 119572 from Patent EP1572962.
AB032982 - Homo sapiens mRNA for KIAA1156 protein, partial cds.
KJ902035 - Synthetic construct Homo sapiens clone ccsbBroadEn_11429 SRGAP3 gene, encodes complete protein.
AK126331 - Homo sapiens cDNA FLJ44358 fis, clone TRACH3007391.
AK223293 - Homo sapiens mRNA, mouse double minute 4 homolog, SLIT-ROBO Rho GTPase-activating protein 2 variant, clone: SYN07773.
AK054831 - Homo sapiens cDNA FLJ30269 fis, clone BRACE2002649.
JD522043 - Sequence 503067 from Patent EP1572962.
BC140004 - Homo sapiens cDNA clone IMAGE:8860356.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04360 - Axon guidance

Reactome (by CSHL, EBI, and GO)

Protein O43295 (Reactome details) participates in the following event(s):

R-HSA-376145 SRGAP binds ROBO1:SLIT2
R-NUL-428517 SrGAP binds Robo:Slit
R-HSA-194922 GAPs inactivate Rho GTPase:GTP by hydrolysis
R-HSA-428533 Inactivation of CDC42
R-NUL-428519 Inactivation of Cdc42
R-HSA-428543 Inactivation of CDC42 and RAC1
R-HSA-194840 Rho GTPase cycle
R-HSA-376176 Signaling by ROBO receptors
R-HSA-194315 Signaling by Rho GTPases
R-HSA-422475 Axon guidance
R-HSA-162582 Signal Transduction
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: ARHGAP14, KIAA0411, KIAA1156, MEGAP, NM_001033117, NP_001028289, O43295-2, SRGAP2, uc003brg.1
UCSC ID: uc003brg.2
RefSeq Accession: NM_001033117
Protein: O43295-2, splice isoform of O43295 CCDS: CCDS2572.1, CCDS33689.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001033117.2
exon count: 22CDS single in 3' UTR: no RNA size: 8905
ORF size: 3228CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5791.50frame shift in genome: no % Coverage: 99.82
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.