Human Gene RCN2 (uc002bcd.3)
  Description: Homo sapiens reticulocalbin 2, EF-hand calcium binding domain (RCN2), transcript variant 1, mRNA.
RefSeq Summary (NM_002902): The protein encoded by this gene is a calcium-binding protein located in the lumen of the ER. The protein contains six conserved regions with similarity to a high affinity Ca(+2)-binding motif, the EF-hand. This gene maps to the same region as type 4 Bardet-Biedl syndrome, suggesting a possible causative role for this gene in the disorder. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2012].
Transcript (Including UTRs)
   Position: hg19 chr15:77,223,962-77,242,601 Size: 18,640 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr15:77,224,183-77,241,563 Size: 17,381 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:77,223,962-77,242,601)mRNA (may differ from genome)Protein (317 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RCN2_HUMAN
DESCRIPTION: RecName: Full=Reticulocalbin-2; AltName: Full=Calcium-binding protein ERC-55; AltName: Full=E6-binding protein; Short=E6BP; Flags: Precursor;
FUNCTION: Not known. Binds calcium.
SUBCELLULAR LOCATION: Endoplasmic reticulum lumen.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the CREC family.
SIMILARITY: Contains 6 EF-hand domains.

-  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): RCN2
CDC HuGE Published Literature: RCN2
Positive Disease Associations: Body Weight
Related Studies:
  1. 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.

-  MalaCards Disease Associations
  MalaCards Gene Search: RCN2
Diseases sorted by gene-association score: bardet-biedl syndrome (1)

-  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: 48.34 RPKM in Testis
Total median expression: 1005.29 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 -84.90221-0.384 Picture PostScript Text
3' UTR -245.671038-0.237 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:
PF13202 - EF hand
PF13499 - EF-hand domain pair

SCOP Domains:
47473 - EF-hand

ModBase Predicted Comparative 3D Structure on Q14257
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 DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0046872 metal ion binding

Cellular Component:
GO:0005730 nucleolus
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen


-  Descriptions from all associated GenBank mRNAs
  LF208503 - JP 2014500723-A/16006: Polycomb-Associated Non-Coding RNAs.
AK313833 - Homo sapiens cDNA, FLJ94458, Homo sapiens reticulocalbin 2, EF-hand calcium binding domain(RCN2), mRNA.
X78669 - H.sapiens ERC-55 mRNA.
BC004892 - Homo sapiens reticulocalbin 2, EF-hand calcium binding domain, mRNA (cDNA clone MGC:1650 IMAGE:3505241), complete cds.
LF377151 - JP 2014500723-A/184654: Polycomb-Associated Non-Coding RNAs.
CU678788 - Synthetic construct Homo sapiens gateway clone IMAGE:100023417 5' read RCN2 mRNA.
KJ905306 - Synthetic construct Homo sapiens clone ccsbBroadEn_14826 RCN2 gene, encodes complete protein.
BT009790 - Homo sapiens reticulocalbin 2, EF-hand calcium binding domain mRNA, complete cds.
HQ448215 - Synthetic construct Homo sapiens clone IMAGE:100071614; CCSB003509_03 reticulocalbin 2, EF-hand calcium binding domain (RCN2) gene, encodes complete protein.
LF377153 - JP 2014500723-A/184656: Polycomb-Associated Non-Coding RNAs.
LF377154 - JP 2014500723-A/184657: Polycomb-Associated Non-Coding RNAs.
AL110102 - Homo sapiens EST from clone 43449, 5' end.
LF377157 - JP 2014500723-A/184660: Polycomb-Associated Non-Coding RNAs.
AK126522 - Homo sapiens cDNA FLJ44558 fis, clone UTERU3008280.
LF377160 - JP 2014500723-A/184663: Polycomb-Associated Non-Coding RNAs.
LF377163 - JP 2014500723-A/184666: Polycomb-Associated Non-Coding RNAs.
LF377164 - JP 2014500723-A/184667: Polycomb-Associated Non-Coding RNAs.
LF377166 - JP 2014500723-A/184669: Polycomb-Associated Non-Coding RNAs.
LF377167 - JP 2014500723-A/184670: Polycomb-Associated Non-Coding RNAs.
LF377168 - JP 2014500723-A/184671: Polycomb-Associated Non-Coding RNAs.
JD025372 - Sequence 6396 from Patent EP1572962.
JD028262 - Sequence 9286 from Patent EP1572962.
JD289805 - Sequence 270829 from Patent EP1572962.
LF377169 - JP 2014500723-A/184672: Polycomb-Associated Non-Coding RNAs.
JD023288 - Sequence 4312 from Patent EP1572962.
JD035841 - Sequence 16865 from Patent EP1572962.
MA444080 - JP 2018138019-A/16006: Polycomb-Associated Non-Coding RNAs.
MA612728 - JP 2018138019-A/184654: Polycomb-Associated Non-Coding RNAs.
MA612730 - JP 2018138019-A/184656: Polycomb-Associated Non-Coding RNAs.
MA612731 - JP 2018138019-A/184657: Polycomb-Associated Non-Coding RNAs.
MA612734 - JP 2018138019-A/184660: Polycomb-Associated Non-Coding RNAs.
MA612737 - JP 2018138019-A/184663: Polycomb-Associated Non-Coding RNAs.
MA612740 - JP 2018138019-A/184666: Polycomb-Associated Non-Coding RNAs.
MA612741 - JP 2018138019-A/184667: Polycomb-Associated Non-Coding RNAs.
MA612743 - JP 2018138019-A/184669: Polycomb-Associated Non-Coding RNAs.
MA612744 - JP 2018138019-A/184670: Polycomb-Associated Non-Coding RNAs.
MA612745 - JP 2018138019-A/184671: Polycomb-Associated Non-Coding RNAs.
MA612746 - JP 2018138019-A/184672: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8MTG6, ERC55, NM_002902, NP_002893, Q14257, Q53XN8, RCN2_HUMAN
UCSC ID: uc002bcd.3
RefSeq Accession: NM_002902
Protein: Q14257 (aka RCN2_HUMAN)
CCDS: CCDS10291.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002902.2
exon count: 7CDS single in 3' UTR: no RNA size: 2213
ORF size: 954CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2432.00frame 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.