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Aliases for CIB2 Gene

Aliases for CIB2 Gene

  • Calcium And Integrin Binding Family Member 2 2 3 5
  • KIP2 3 4
  • DNA-Dependent Protein Kinase Catalytic Subunit-Interacting Protein 2 3
  • Calcium And Integrin-Binding Family Member 2 3
  • Usher Syndrome 1J (Autosomal Recessive) 2
  • Deafness, Autosomal Recessive 48 2
  • Kinase-Interacting Protein 2 4
  • DFNB48 3
  • USH1J 3
  • KIP 2 4

External Ids for CIB2 Gene

Previous HGNC Symbols for CIB2 Gene

  • DFNB48
  • USH1J

Previous GeneCards Identifiers for CIB2 Gene

  • GC15M076113
  • GC15M076184
  • GC15M078396
  • GC15M055154

Summaries for CIB2 Gene

Entrez Gene Summary for CIB2 Gene

  • 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]

GeneCards Summary for CIB2 Gene

CIB2 (Calcium And Integrin Binding Family Member 2) is a Protein Coding gene. Diseases associated with CIB2 include Usher Syndrome, Type Ij and Deafness, Autosomal Recessive 48. GO annotations related to this gene include calcium ion binding and integrin binding. An important paralog of this gene is CIB3.

UniProtKB/Swiss-Prot for CIB2 Gene

  • Calcium-binding protein critical for proper photoreceptor cell maintenance and function. Plays a role in intracellular calcium homeostasis by decreasing ATP-induced calcium release (PubMed:23023331, PubMed:26173970, PubMed:26426422). May be involved in the mechanotransduction process (By similarity).

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CIB2 Gene

Genomics for CIB2 Gene

Regulatory Elements for CIB2 Gene

Enhancers for CIB2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH15G078128 1.3 Ensembl ENCODE 46.4 +1.1 1121 3.6 HDGF PKNOX1 ARNT CREB3L1 SIN3A ARID4B DMAP1 ZNF2 ZBTB7B ZNF143 CIB2 ENSG00000259562 IREB2 TBC1D2B IDH3A PIR50456
GH15G078166 1.4 Ensembl ENCODE dbSUPER 21.7 -39.0 -38995 8.6 TBP PKNOX1 TBL1XR1 ZBTB40 ZNF766 CBX5 RELB IKZF2 CREM JUNB CIB2 IDH3A TBC1D2B SH2D7 ENSG00000199633 GC15P078155 PIR56006
GH15G078100 1.2 Ensembl ENCODE 24.4 +28.0 27997 6.0 HDGF PKNOX1 ZNF2 ZBTB7B ZNF121 ZNF143 ZHX2 REST ZNF623 TBX21 CIB2 TBC1D2B SH2D7 PIR50456 GC15M078092 ENSG00000199633
GH15G078046 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10.7 +78.4 78380 14.3 HDGF SIN3A ZNF48 ZNF121 GATA2 ZNF143 FOS SP5 ZHX2 JUNB TBC1D2B LOC645752 SH2D7 ADAMTS7P3 ENSG00000199633 ENSG00000259562 ENSG00000260988 CIB2 IREB2 LOC440292
GH15G078156 0.8 dbSUPER 23.1 -25.4 -25440 1.5 HDAC1 FEZF1 YY1 SCRT2 CEBPB OVOL3 TSHZ1 ZNF843 NR2F2 MAFF CIB2 IDH3A ENSG00000199633 SH2D7 TBC1D2B GC15P078155 PIR56006
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CIB2 on UCSC Golden Path with GeneCards custom track

Promoters for CIB2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000079700 221 1401 HDGF PKNOX1 FOXA2 ARNT CREB3L1 ZFP64 SIN3A ARID4B DMAP1 ZNF2

Genomic Location for CIB2 Gene

Chromosome:
15
Start:
78,104,606 bp from pter
End:
78,131,721 bp from pter
Size:
27,116 bases
Orientation:
Minus strand

Genomic View for CIB2 Gene

Genes around CIB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CIB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CIB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CIB2 Gene

Proteins for CIB2 Gene

  • Protein details for CIB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75838-CIB2_HUMAN
    Recommended name:
    Calcium and integrin-binding family member 2
    Protein Accession:
    O75838
    Secondary Accessions:
    • B4DDF0
    • H0YM71
    • Q05BT6

    Protein attributes for CIB2 Gene

    Size:
    187 amino acids
    Molecular mass:
    21644 Da
    Quaternary structure:
    • Homodimer (PubMed:23023331). Interacts with WHRN and MYO7A (PubMed:23023331, PubMed:26426422). Interacts with ITGA2B (via C-terminus cytoplasmic tail region) and ITGA7 (via C-terminus cytoplasmic tail region); the interactions are stabilized/increased in a calcium and magnesium-dependent manner (PubMed:22779914).
    Miscellaneous:
    • The binding of either calcium or magnesium significantly increases the structural stability of the protein in comparison to apo-CIB (calcium- and magnesium-free form) (PubMed:22779914).

    Alternative splice isoforms for CIB2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CIB2 Gene

Post-translational modifications for CIB2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CIB2 Gene

Domains & Families for CIB2 Gene

Protein Domains for CIB2 Gene

Suggested Antigen Peptide Sequences for CIB2 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CIB2: view

No data available for UniProtKB/Swiss-Prot for CIB2 Gene

Function for CIB2 Gene

Molecular function for CIB2 Gene

UniProtKB/Swiss-Prot Function:
Calcium-binding protein critical for proper photoreceptor cell maintenance and function. Plays a role in intracellular calcium homeostasis by decreasing ATP-induced calcium release (PubMed:23023331, PubMed:26173970, PubMed:26426422). May be involved in the mechanotransduction process (By similarity).

Gene Ontology (GO) - Molecular Function for CIB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000287 magnesium ion binding IDA 22779914
GO:0005178 integrin binding IEA --
GO:0005509 calcium ion binding IDA,IEA 22779914
GO:0005515 protein binding IPI 22779914
GO:0032403 protein complex binding IEA --
genes like me logo Genes that share ontologies with CIB2: view
genes like me logo Genes that share phenotypes with CIB2: view

Human Phenotype Ontology for CIB2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CIB2 Gene

MGI Knock Outs for CIB2:
  • Cib2 tm1b(EUCOMM)Wtsi

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CIB2 Gene

Localization for CIB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CIB2 Gene

Cytoplasm. Cell projection, stereocilium. Photoreceptor inner segment. Cell projection, cilium, photoreceptor outer segment. Cell membrane, sarcolemma. Note=Colocalized with ITGA7 at the myotendinous junctions (MTJ) and at the neuromuscular junctions (NMJ) (By similarity). Localizes in the cuticular plate along and at the tip of the stereocilia of vestibular sensory hair cells (PubMed:26173970, PubMed:26426422). {ECO:0000250 UniProtKB:Q9Z309, ECO:0000269 PubMed:26173970, ECO:0000269 PubMed:26426422}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CIB2 gene
Compartment Confidence
extracellular 5
cytoskeleton 5
plasma membrane 3
nucleus 3
mitochondrion 2
cytosol 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for CIB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001750 photoreceptor outer segment ISS --
GO:0001917 photoreceptor inner segment ISS --
GO:0005737 cytoplasm ISS --
GO:0005886 plasma membrane IEA --
GO:0005927 muscle tendon junction IEA --
genes like me logo Genes that share ontologies with CIB2: view

Pathways & Interactions for CIB2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CIB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007204 positive regulation of cytosolic calcium ion concentration IDA 23023331
GO:0045494 photoreceptor cell maintenance ISS --
GO:0055074 calcium ion homeostasis ISS --
GO:0071318 cellular response to ATP IDA 23023331
genes like me logo Genes that share ontologies with CIB2: view

No data available for Pathways by source and SIGNOR curated interactions for CIB2 Gene

Drugs & Compounds for CIB2 Gene

No Compound Related Data Available

Transcripts for CIB2 Gene

Unigene Clusters for CIB2 Gene

Calcium and integrin binding family member 2:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for CIB2 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b
SP1: - - - -
SP2: - - -
SP3: - - - -
SP4: - - - - - - -
SP5: - - - -
SP6:

Relevant External Links for CIB2 Gene

GeneLoc Exon Structure for
CIB2
ECgene alternative splicing isoforms for
CIB2

Expression for CIB2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CIB2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CIB2 Gene

This gene is overexpressed in Heart - Atrial Appendage (x6.8).

Protein differential expression in normal tissues from HIPED for CIB2 Gene

This gene is overexpressed in Urine (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CIB2 Gene



Protein tissue co-expression partners for CIB2 Gene

NURSA nuclear receptor signaling pathways regulating expression of CIB2 Gene:

CIB2

SOURCE GeneReport for Unigene cluster for CIB2 Gene:

Hs.129867

mRNA Expression by UniProt/SwissProt for CIB2 Gene:

O75838-CIB2_HUMAN
Tissue specificity: Widely expressed (PubMed:23023331).

Evidence on tissue expression from TISSUES for CIB2 Gene

  • Nervous system(4.2)
  • Skin(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CIB2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • immune
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • face
  • head
  • inner ear
  • middle ear
  • nose
  • outer ear
  • skull
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with CIB2: view

Primer Products

Orthologs for CIB2 Gene

This gene was present in the common ancestor of animals.

Orthologs for CIB2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CIB2 34 35
  • 99.82 (n)
dog
(Canis familiaris)
Mammalia CIB2 34 35
  • 91.8 (n)
cow
(Bos Taurus)
Mammalia CIB2 34 35
  • 90.73 (n)
mouse
(Mus musculus)
Mammalia Cib2 34 16 35
  • 90.2 (n)
rat
(Rattus norvegicus)
Mammalia Cib2 34
  • 90.2 (n)
oppossum
(Monodelphis domestica)
Mammalia CIB2 35
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves CIB2 34 35
  • 71.66 (n)
lizard
(Anolis carolinensis)
Reptilia CIB2 35
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cib2 34
  • 71.48 (n)
zebrafish
(Danio rerio)
Actinopterygii cib2 34 35
  • 67.91 (n)
zgc73079 34
fruit fly
(Drosophila melanogaster)
Insecta CG9236 34 35
  • 60.25 (n)
worm
(Caenorhabditis elegans)
Secernentea calm-1 34 35
  • 53.33 (n)
Species where no ortholog for CIB2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CIB2 Gene

ENSEMBL:
Gene Tree for CIB2 (if available)
TreeFam:
Gene Tree for CIB2 (if available)

Paralogs for CIB2 Gene

Paralogs for CIB2 Gene

genes like me logo Genes that share paralogs with CIB2: view

Variants for CIB2 Gene

Sequence variations from dbSNP and Humsavar for CIB2 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs145415848 Pathogenic, Usher syndrome 1J (USH1J) [MIM:614869] 78,111,171(+) CGGAG(C/G/T)TCTGG intron-variant, nc-transcript-variant, reference, synonymous-codon
rs370359511 Deafness, autosomal recessive, 48 (DFNB48) [MIM:609439] 78,105,319(+) GATCC(A/G/T)GATGT nc-transcript-variant, downstream-variant-500B, reference, synonymous-codon, missense
rs370965183 Pathogenic, Deafness, autosomal recessive, 48 (DFNB48) [MIM:609439] 78,109,284(+) GACTC(A/C/G)CAGAG nc-transcript-variant, reference, synonymous-codon
rs397515411 Pathogenic, Deafness, autosomal recessive, 48 (DFNB48) [MIM:609439] 78,109,309(-) CGACT(C/T)TGTGG nc-transcript-variant, reference, missense
rs397515412 Pathogenic, Deafness, autosomal recessive, 48 (DFNB48) [MIM:609439] 78,105,913(-) CTTCA(C/T)CTGCA nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for CIB2 Gene

Variant ID Type Subtype PubMed ID
esv274890 CNV gain+loss 21479260
esv3581778 CNV loss 25503493
esv3636979 CNV gain 21293372
nsv1116464 OTHER inversion 24896259
nsv526717 CNV loss 19592680
nsv94529 CNV deletion 16902084
nsv94621 CNV deletion 16902084

Variation tolerance for CIB2 Gene

Residual Variation Intolerance Score: 51.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.54; 29.84% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CIB2 Gene

Human Gene Mutation Database (HGMD)
CIB2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CIB2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CIB2 Gene

Disorders for CIB2 Gene

MalaCards: The human disease database

(12) MalaCards diseases for CIB2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
usher syndrome, type ij
  • usher syndrome type 1j
deafness, autosomal recessive 48
  • autosomal recessive nonsyndromic deafness 48
usher syndrome, type 1b
  • usher syndrome type 1
dfnb48 nonsyndromic hearing loss and deafness
  • dfnb48
autosomal recessive non-syndromic sensorineural deafness type dfnb
  • autosomal recessive isolated neurosensory deafness type dfnb
- elite association - COSMIC cancer census association via MalaCards
Search CIB2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CIB2_HUMAN
  • Deafness, autosomal recessive, 48 (DFNB48) [MIM:609439]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DFNB48 patients have prelingual onset of severe to profound sensorineural hearing loss affecting all frequencies. {ECO:0000269 PubMed:23023331, ECO:0000269 PubMed:26173970, ECO:0000269 PubMed:26426422}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Usher syndrome 1J (USH1J) [MIM:614869]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH1 is characterized by profound congenital sensorineural deafness, absent vestibular function and prepubertal onset of progressive retinitis pigmentosa leading to blindness. {ECO:0000269 PubMed:23023331}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CIB2

Genetic Association Database (GAD)
CIB2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CIB2
genes like me logo Genes that share disorders with CIB2: view

No data available for Genatlas for CIB2 Gene

Publications for CIB2 Gene

  1. Structure, expression profile and chromosomal location of an isolog of DNA-PKcs interacting protein (KIP) gene. (PMID: 9931475) Seki N. … Saito T. (Biochim. Biophys. Acta 1999) 2 3 4 22 64
  2. Alterations of the CIB2 calcium- and integrin-binding protein cause Usher syndrome type 1J and nonsyndromic deafness DFNB48. (PMID: 23023331) Riazuddin S. … Ahmed Z.M. (Nat. Genet. 2012) 2 3 4 64
  3. Novel and recurrent CIB2 variants, associated with nonsyndromic deafness, do not affect calcium buffering and localization in hair cells. (PMID: 26173970) Seco C.Z. … Kremer H. (Eur. J. Hum. Genet. 2015) 3 4 64
  4. A Novel C-Terminal CIB2 (Calcium and Integrin Binding Protein 2) Mutation Associated with Non-Syndromic Hearing Loss in a Hispanic Family. (PMID: 26426422) Patel K. … Morrow B.E. (PLoS ONE 2015) 3 4 64
  5. Biophysical and structural studies of the human calcium- and integrin-binding protein family: understanding their functional similarities and differences. (PMID: 22779914) Huang H. … Vogel H.J. (Biochem. Cell Biol. 2012) 3 4 64

Products for CIB2 Gene

Sources for CIB2 Gene

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