Human Gene CIB2 (uc002bdb.2) Description and Page Index
  Description: Homo sapiens calcium and integrin binding family member 2 (CIB2), transcript variant 1, mRNA.
RefSeq Summary (NM_006383): The protein encoded by this gene is similar to that of KIP/CIB, calcineurin B, and calmodulin. The encoded protein is a calcium-binding regulatory protein that interacts with DNA-dependent protein kinase catalytic subunits (DNA-PKcs), and it is involved in photoreceptor cell maintenance. Mutations in this gene cause deafness, autosomal recessive, 48 (DFNB48), and also Usher syndrome 1J (USH1J). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014].
Transcript (Including UTRs)
   Position: hg19 chr15:78,396,948-78,423,877 Size: 26,930 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr15:78,397,653-78,423,557 Size: 25,905 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:78,396,948-78,423,877)mRNA (may differ from genome)Protein (187 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: CIB2_HUMAN
DESCRIPTION: RecName: Full=Calcium and integrin-binding family member 2; AltName: Full=Kinase-interacting protein 2; Short=KIP 2;
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Contains 3 EF-hand domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CIB2
CDC HuGE Published Literature: CIB2
Positive Disease Associations: Leukocyte Count
Related Studies:
  1. Leukocyte Count
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: CIB2
Diseases sorted by gene-association score: usher syndrome, type ij* (1319), deafness, autosomal recessive 48* (1260), dfnb48 nonsyndromic hearing loss and deafness* (500), usher syndrome, type 1b* (313), autosomal recessive non-syndromic sensorineural deafness type dfnb* (55), deafness, autosomal recessive (29), usher syndrome (21), deafness, autosomal dominant 48 (7), usher syndrome type 2 (7), deafness, autosomal recessive 67 (7), perrault syndrome (5), nonsyndromic deafness (2), retinitis pigmentosa (1)
* = Manually curated disease association

-  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: 18.81 RPKM in Heart - Atrial Appendage
Total median expression: 199.73 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 -202.10320-0.632 Picture PostScript Text
3' UTR -244.85705-0.347 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:
PF13499 - EF-hand domain pair

SCOP Domains:
47473 - EF-hand

ModBase Predicted Comparative 3D Structure on O75838
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 BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000287 magnesium ion binding
GO:0005178 integrin binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0042803 protein homodimerization activity
GO:0044877 macromolecular complex binding
GO:0046872 metal ion binding

Biological Process:
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0045494 photoreceptor cell maintenance
GO:0055074 calcium ion homeostasis
GO:0071318 cellular response to ATP

Cellular Component:
GO:0001750 photoreceptor outer segment
GO:0001917 photoreceptor inner segment
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005927 muscle tendon junction
GO:0005929 cilium
GO:0016020 membrane
GO:0031594 neuromuscular junction
GO:0032420 stereocilium
GO:0032437 cuticular plate
GO:0042383 sarcolemma
GO:0042995 cell projection
GO:0072562 blood microparticle


-  Descriptions from all associated GenBank mRNAs
  BC047381 - Homo sapiens calcium and integrin binding family member 2, mRNA (cDNA clone MGC:48487 IMAGE:5287072), complete cds.
BC057292 - Homo sapiens calcium and integrin binding family member 2, mRNA (cDNA clone IMAGE:5286502).
BC033108 - Homo sapiens calcium and integrin binding family member 2, mRNA (cDNA clone MGC:45698 IMAGE:4841632), complete cds.
AB012955 - Homo sapiens mRNA for KIP2, complete cds.
JD366032 - Sequence 347056 from Patent EP1572962.
JD224356 - Sequence 205380 from Patent EP1572962.
JD377573 - Sequence 358597 from Patent EP1572962.
JD133244 - Sequence 114268 from Patent EP1572962.
JD154142 - Sequence 135166 from Patent EP1572962.
JD512415 - Sequence 493439 from Patent EP1572962.
JD477050 - Sequence 458074 from Patent EP1572962.
JD252079 - Sequence 233103 from Patent EP1572962.
JD270697 - Sequence 251721 from Patent EP1572962.
JD520280 - Sequence 501304 from Patent EP1572962.
JD054213 - Sequence 35237 from Patent EP1572962.
JD215100 - Sequence 196124 from Patent EP1572962.
JD121384 - Sequence 102408 from Patent EP1572962.
JD504647 - Sequence 485671 from Patent EP1572962.
AL110098 - Homo sapiens EST from clone 669324, 5' end.
AK293167 - Homo sapiens cDNA FLJ59581 complete cds, highly similar to Calcium and integrin-binding protein 2.
CU690402 - Synthetic construct Homo sapiens gateway clone IMAGE:100020837 5' read CIB2 mRNA.
HQ447978 - Synthetic construct Homo sapiens clone IMAGE:100071344; CCSB010655_01 calcium and integrin binding family member 2 (CIB2) gene, encodes complete protein.
KJ898233 - Synthetic construct Homo sapiens clone ccsbBroadEn_07627 CIB2 gene, encodes complete protein.
KJ904655 - Synthetic construct Homo sapiens clone ccsbBroadEn_14049 CIB2 gene, encodes complete protein.
BT019962 - Homo sapiens DNA-dependent protein kinase catalytic subunit-interacting protein 2 mRNA, complete cds.
AB528675 - Synthetic construct DNA, clone: pF1KB6824, Homo sapiens CIB2 gene for calcium and integrin binding family member 2, without stop codon, in Flexi system.

-  Other Names for This Gene
  Alternate Gene Symbols: CIB2_HUMAN, KIP2, NM_006383, NP_001258817, O75838, uc002bdb.1
UCSC ID: uc002bdb.2
RefSeq Accession: NM_006383
Protein: O75838 (aka CIB2_HUMAN)
CCDS: CCDS10296.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CIB2:
usher1 (Usher Syndrome Type I)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006383.3
exon count: 6CDS single in 3' UTR: no RNA size: 1623
ORF size: 564CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1282.00frame shift in genome: no % Coverage: 97.84
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.