Human Gene GDAP2 (uc001ehf.3) Description and Page Index
  Description: Homo sapiens ganglioside induced differentiation associated protein 2 (GDAP2), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:118,406,107-118,472,302 Size: 66,196 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr1:118,413,191-118,462,980 Size: 49,790 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:118,406,107-118,472,302)mRNA (may differ from genome)Protein (497 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: GDAP2_HUMAN
DESCRIPTION: RecName: Full=Ganglioside-induced differentiation-associated protein 2;
SIMILARITY: Belongs to the GDAP2 family.
SIMILARITY: Contains 1 CRAL-TRIO domain.
SIMILARITY: Contains 1 Macro domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GDAP2
CDC HuGE Published Literature: GDAP2
Positive Disease Associations: Mortality
Related Studies:
  1. Mortality
    Kathryn L Lunetta et al. BMC medical genetics 2007, Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study., BMC medical genetics. [PubMed 17903295]
    Longevity and aging traits are associated with SNPs on the Affymetrix 100K GeneChip. None of the associations achieved genome-wide significance. These data generate hypotheses and serve as a resource for replication as more genes and biologic pathways are proposed as contributing to longevity and healthy aging.

-  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: 2.42 RPKM in Testis
Total median expression: 60.53 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 -120.01299-0.401 Picture PostScript Text
3' UTR -1850.157084-0.261 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
IPR002589 - A1pp
IPR001251 - CRAL-TRIO_dom

Pfam Domains:
PF01661 - Macro domain
PF13716 - Divergent CRAL/TRIO domain

SCOP Domains:
52087 - CRAL/TRIO domain
52949 - Macro domain-like

ModBase Predicted Comparative 3D Structure on Q9NXN4
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 orthologGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
 Gene Details Gene Details  
 Gene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0032526 response to retinoic acid

Cellular Component:
GO:0005765 lysosomal membrane


-  Descriptions from all associated GenBank mRNAs
  BX647355 - Homo sapiens mRNA; cDNA DKFZp686K07244 (from clone DKFZp686K07244).
JD363200 - Sequence 344224 from Patent EP1572962.
JD354516 - Sequence 335540 from Patent EP1572962.
AK000149 - Homo sapiens cDNA FLJ20142 fis, clone COL07365.
JD305764 - Sequence 286788 from Patent EP1572962.
JD303080 - Sequence 284104 from Patent EP1572962.
JD563165 - Sequence 544189 from Patent EP1572962.
JD098755 - Sequence 79779 from Patent EP1572962.
JD177797 - Sequence 158821 from Patent EP1572962.
JD188383 - Sequence 169407 from Patent EP1572962.
JD334058 - Sequence 315082 from Patent EP1572962.
JD051845 - Sequence 32869 from Patent EP1572962.
JD240129 - Sequence 221153 from Patent EP1572962.
JD353934 - Sequence 334958 from Patent EP1572962.
JD168135 - Sequence 149159 from Patent EP1572962.
JD096125 - Sequence 77149 from Patent EP1572962.
JD278764 - Sequence 259788 from Patent EP1572962.
JD404224 - Sequence 385248 from Patent EP1572962.
JD559524 - Sequence 540548 from Patent EP1572962.
JD137084 - Sequence 118108 from Patent EP1572962.
BC013324 - Homo sapiens cDNA clone IMAGE:4070372, containing frame-shift errors.
BC013132 - Homo sapiens ganglioside induced differentiation associated protein 2, mRNA (cDNA clone MGC:4972 IMAGE:3448678), complete cds.
KJ894071 - Synthetic construct Homo sapiens clone ccsbBroadEn_03465 GDAP2 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: GDAP2_HUMAN, NM_017686, NP_060156, Q96DZ0, Q9NXN4
UCSC ID: uc001ehf.3
RefSeq Accession: NM_017686
Protein: Q9NXN4 (aka GDAP2_HUMAN)
CCDS: CCDS44201.1, CCDS897.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene GDAP2:
ataxias (Hereditary Ataxia Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_017686.3
exon count: 14CDS single in 3' UTR: no RNA size: 8885
ORF size: 1494CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2469.00frame shift in genome: no % Coverage: 99.91
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.