Human Gene CALB2 (uc002fac.4) Description and Page Index
  Description: Homo sapiens calbindin 2 (CALB2), transcript variant CALB2c, mRNA.
RefSeq Summary (NM_007088): This gene encodes an intracellular calcium-binding protein belonging to the troponin C superfamily. Members of this protein family have six EF-hand domains which bind calcium. This protein plays a role in diverse cellular functions, including message targeting and intracellular calcium buffering. It also functions as a modulator of neuronal excitability, and is a diagnostic marker for some human diseases, including Hirschsprung disease and some cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2010].
Transcript (Including UTRs)
   Position: hg19 chr16:71,392,616-71,424,342 Size: 31,727 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr16:71,392,696-71,419,525 Size: 26,830 Coding Exon Count: 8 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:71,392,616-71,424,342)mRNA (may differ from genome)Protein (192 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHuman Cortex Gene ExpressionLynxMGIOMIM
PubMedStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CALB2
CDC HuGE Published Literature: CALB2

-  MalaCards Disease Associations
  MalaCards Gene Search: CALB2
Diseases sorted by gene-association score: adenomatoid tumor (15), adenofibroma (15), sex cord-gonadal stromal tumor (15), sertoli cell tumor (13), sertoli-leydig cell tumor (11), malignant pleural mesothelioma (8), ovarian serous cystadenofibroma (7), lymphohistiocytoid mesothelioma (6), benign mesothelioma (6), pseudo-meigs syndrome (6), mesothelioma, somatic (5), ovarian cancer, somatic (5), cystadenofibroma (4), malignant biphasic mesothelioma (4), clear cell cystadenofibroma (4), ovarian fibrothecoma (4), ovarian serous adenofibroma (4), colon adenocarcinoma (4), gynandroblastoma (4), fibroma (3), ovarian serous carcinoma (3), sarcoma, synovial (3), liposarcoma (3), status epilepticus (3), thymus cancer (3), fallopian tube endometrioid adenocarcinoma (3), synucleinopathy (3), mucinous bronchioloalveolar adenocarcinoma (3), rete testis adenoma (3), lung cancer susceptibility 3 (2), fallopian tube carcinosarcoma (2), horseshoe kidney (2), papillary thymic adenocarcinoma (2), keratocystic odontogenic tumor (2), cervix endometriosis (2), fallopian tube adenocarcinoma (2), wilms tumor susceptibility-5 (2), pleural cancer (2), inverted follicular keratosis (2), deafness, autosomal recessive 89 (2), reproductive organ benign neoplasm (2), large cell carcinoma with rhabdoid phenotype (2), pericardium cancer (2), ovarian melanoma (2), malignant epithelial mesothelioma (2), schizophrenia (2), pericardial mesothelioma (1), rete testis neoplasm (1), venous hemangioma (1), mucinous ovarian cystadenoma (1), rete testis adenocarcinoma (1), hirschsprung disease 1 (1), bile duct cystadenocarcinoma (1), spermatocele (1), neurogenic bowel (1), pneumatosis cystoides intestinalis (1), pancreatic mucinous cystadenoma (1), spindle cell liposarcoma (1), clear cell adenofibroma (1), functional colonic disease (1), proliferative fasciitis (1), colonic pseudo-obstruction (1), ovarian brenner tumor (1), mixed ductal-endocrine carcinoma (1), malignant leydig cell tumor (1), pleomorphic lipoma (1), lung sarcoma (1), dysgerminoma of ovary (1), amyotrophic lateral sclerosis 1 (1), retinitis pigmentosa (0)

-  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: 172.70 RPKM in Brain - Hypothalamus
Total median expression: 727.06 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 -38.6080-0.482 Picture PostScript Text
3' UTR -256.73717-0.358 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
IPR002048 - EF_hand_Ca-bd

Pfam Domains:
PF00036 - EF hand
PF13202 - EF hand
PF13405 - EF-hand domain
PF13499 - EF-hand domain pair

SCOP Domains:
47473 - EF-hand

ModBase Predicted Comparative 3D Structure on A6NER6
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    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding

Cellular Component:
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  JD336564 - Sequence 317588 from Patent EP1572962.
AK291096 - Homo sapiens cDNA FLJ77118 complete cds, highly similar to Homo sapiens calbindin 2, 29kDa (calretinin) (CALB2), transcript variant CALB2, mRNA.
AK222495 - Homo sapiens mRNA for calbindin 2 full length protein isoform variant, clone: adKA03490.
AK222648 - Homo sapiens mRNA for calbindin 2 full length protein isoform variant, clone: CBL05474.
HM005548 - Homo sapiens clone HTL-S-8 testicular secretory protein Li 8 mRNA, complete cds.
JD230164 - Sequence 211188 from Patent EP1572962.
JD269787 - Sequence 250811 from Patent EP1572962.
BC015484 - Homo sapiens calbindin 2, mRNA (cDNA clone MGC:8907 IMAGE:3847342), complete cds.
X56667 - Human mRNA for calretinin.
JD107866 - Sequence 88890 from Patent EP1572962.
JD465087 - Sequence 446111 from Patent EP1572962.
JD218357 - Sequence 199381 from Patent EP1572962.
JD400288 - Sequence 381312 from Patent EP1572962.
JD123292 - Sequence 104316 from Patent EP1572962.
JD505002 - Sequence 486026 from Patent EP1572962.
JD105423 - Sequence 86447 from Patent EP1572962.
JD346922 - Sequence 327946 from Patent EP1572962.
JD097361 - Sequence 78385 from Patent EP1572962.
JD188010 - Sequence 169034 from Patent EP1572962.
JD411015 - Sequence 392039 from Patent EP1572962.
JD253278 - Sequence 234302 from Patent EP1572962.
JD389208 - Sequence 370232 from Patent EP1572962.
JD384822 - Sequence 365846 from Patent EP1572962.
JD489485 - Sequence 470509 from Patent EP1572962.
JD365833 - Sequence 346857 from Patent EP1572962.
JD298479 - Sequence 279503 from Patent EP1572962.
JD502233 - Sequence 483257 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NER6, A6NER6_HUMAN, hCG_2011413, NM_007088, NP_009019
UCSC ID: uc002fac.4
RefSeq Accession: NM_007088
Protein: A6NER6

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_007088.3
exon count: 9CDS single in 3' UTR: no RNA size: 1391
ORF size: 579CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1086.00frame shift in genome: no % Coverage: 98.92
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.