Human Gene EFCAB4B (uc010sen.1) Description and Page Index
  Description: Homo sapiens EF-hand calcium binding domain 4B (EFCAB4B), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr12:3,724,101-3,862,366 Size: 138,266 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr12:3,724,521-3,806,165 Size: 81,645 Coding Exon Count: 17 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:3,724,101-3,862,366)mRNA (may differ from genome)Protein (731 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIOMIM
PubMedReactomeStanford SOURCEUniProtKB

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): EFCAB4B
CDC HuGE Published Literature: EFCAB4B
Positive Disease Associations: Cytomegalovirus Vaccines , Infertility, Male , male infertility , Myocardial Infarction , Nonalcoholic Fatty Liver Disease , Parkinson Disease
Related Studies:
  1. Cytomegalovirus Vaccines
    T Kuparinen et al. Genes and immunity 2012, Genome-wide association study does not reveal major genetic determinants for anti-cytomegalovirus antibody response., Genes and immunity. [PubMed 21993531]
  2. Infertility, Male
    Kenneth I Aston et al. Journal of andrology 2010, Genome-wide study of single-nucleotide polymorphisms associated with azoospermia and severe oligozoospermia., Journal of andrology. [PubMed 19478329]
  3. male infertility
    Aston ,et al. 2009, Genome-wide Study of Single Nucleotide Polymorphisms Associated with Azoospermia and Severe Oligozoospermia, Journal of andrology 2010 30- 6 : 711-25. [PubMed 19478329]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.56 RPKM in Minor Salivary Gland
Total median expression: 25.68 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 -249.70572-0.437 Picture PostScript Text
3' UTR -128.19420-0.305 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:
PF00025 - ADP-ribosylation factor family
PF00071 - Ras family
PF01926 - 50S ribosome-binding GTPase
PF08477 - Ras of Complex, Roc, domain of DAPkinase
PF13202 - EF hand
PF13499 - EF-hand domain pair
PF13833 - EF-hand domain pair

SCOP Domains:
47473 - EF-hand
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q9BSW2-2
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
  AK304017 - Homo sapiens cDNA FLJ61047 complete cds, weakly similar to Homo sapiens RAS and EF-hand domain containing (RASEF), mRNA.
BC004524 - Homo sapiens EF-hand calcium binding domain 4B, mRNA (cDNA clone IMAGE:3531511), complete cds.
BC150643 - Homo sapiens EF-hand calcium binding domain 4B, mRNA (cDNA clone MGC:183553 IMAGE:9057013), complete cds.
JF432156 - Synthetic construct Homo sapiens clone IMAGE:100073302 EF-hand calcium binding domain 4B (EFCAB4B) gene, encodes complete protein.
KJ895028 - Synthetic construct Homo sapiens clone ccsbBroadEn_04422 EFCAB4B gene, encodes complete protein.
CU678750 - Synthetic construct Homo sapiens gateway clone IMAGE:100019219 5' read EFCAB4B mRNA.
AK091124 - Homo sapiens cDNA FLJ33805 fis, clone CTONG2000819, weakly similar to YPT1-RELATED PROTEIN 2.
AX746791 - Sequence 316 from Patent EP1308459.
JD071308 - Sequence 52332 from Patent EP1572962.
JD436375 - Sequence 417399 from Patent EP1572962.
CR627161 - Homo sapiens mRNA; cDNA DKFZp686G13246 (from clone DKFZp686G13246).
AK057608 - Homo sapiens cDNA FLJ33046 fis, clone THYMU2000570.
JD482447 - Sequence 463471 from Patent EP1572962.
JD104031 - Sequence 85055 from Patent EP1572962.
JD377514 - Sequence 358538 from Patent EP1572962.
JD467636 - Sequence 448660 from Patent EP1572962.
JD115064 - Sequence 96088 from Patent EP1572962.
JD121079 - Sequence 102103 from Patent EP1572962.
JD078610 - Sequence 59634 from Patent EP1572962.
JD453115 - Sequence 434139 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9BSW2 (Reactome details) participates in the following event(s):

R-HSA-6798749 Exocytosis of specific granule lumen proteins
R-HSA-6798695 Neutrophil degranulation
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: CRACR2A, NM_001144958, NP_001138430, Q9BSW2-2
UCSC ID: uc010sen.1
RefSeq Accession: NM_001144958
Protein: Q9BSW2-2, splice isoform of Q9BSW2 CCDS: CCDS44803.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001144958.1
exon count: 20CDS single in 3' UTR: no RNA size: 2795
ORF size: 2196CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4314.50frame 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.