Human Gene EFCAB3 (uc010wpc.2) Description and Page Index
  Description: Homo sapiens EF-hand calcium binding domain 3 (EFCAB3), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr17:60,447,579-60,493,839 Size: 46,261 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr17:60,447,650-60,493,690 Size: 46,041 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:60,447,579-60,493,839)mRNA (may differ from genome)Protein (490 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCHPRDLynxMGIPubMedStanford SOURCE
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: J3KQM8_HUMAN
DESCRIPTION: SubName: Full=EF-hand calcium-binding domain-containing protein 3;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): EFCAB3
CDC HuGE Published Literature: EFCAB3

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • D000111 Acetylcysteine
  • D003042 Cocaine
  • D004052 Diethylnitrosamine
  • C016517 indole-3-carbinol

+  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: 3.33 RPKM in Testis
Total median expression: 3.33 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 -9.9071-0.139 Picture PostScript Text
3' UTR -21.30149-0.143 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
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR018249 - EF_HAND_2

Pfam Domains:
PF13202 - EF hand
PF13833 - EF-hand domain pair

SCOP Domains:
47473 - EF-hand

ModBase Predicted Comparative 3D Structure on J3KQM8
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK098684 - Homo sapiens cDNA FLJ25818 fis, clone TST07538.
BC101752 - Homo sapiens EF-hand calcium binding domain 3, mRNA (cDNA clone MGC:126801 IMAGE:8069258), complete cds.
BC101778 - Homo sapiens EF-hand calcium binding domain 3, mRNA (cDNA clone MGC:126827 IMAGE:8069284), complete cds.
KJ900239 - Synthetic construct Homo sapiens clone ccsbBroadEn_09633 EFCAB3 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: J3KQM8, J3KQM8_HUMAN, NM_001144933, NP_001138405
UCSC ID: uc010wpc.2
RefSeq Accession: NM_001144933
Protein: J3KQM8 CCDS: CCDS45751.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001144933.1
exon count: 12CDS single in 3' UTR: no RNA size: 1694
ORF size: 1473CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3132.50frame shift in genome: no % Coverage: 99.94
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.