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CIB2 calcium and integrin binding family member 2 [ Homo sapiens (human) ]

Gene ID: 10518, updated on 5-Aug-2018

Summary

Official Symbol
CIB2provided by HGNC
Official Full Name
calcium and integrin binding family member 2provided by HGNC
Primary source
HGNC:HGNC:24579
See related
Ensembl:ENSG00000136425 MIM:605564; Vega:OTTHUMG00000143731
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KIP2; USH1J; DFNB48
Summary
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]
Expression
Broad expression in small intestine (RPKM 6.5), testis (RPKM 5.9) and 23 other tissues See more
Orthologs

Genomic context

See CIB2 in Genome Data Viewer
Location:
15q25.1
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 15 NC_000015.10 (78104606..78131976, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (78396948..78423877, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene TBC1 domain family member 2B Neighboring gene SH2 domain containing 7 Neighboring gene isocitrate dehydrogenase 3 (NAD(+)) alpha Neighboring gene acyl-CoA synthetase bubblegum family member 1 Neighboring gene uncharacterized LOC105370911

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 replication, specifically viral entry, requires CIB1 and CIB2 expression as shRNA knockdown of each impairs replication in Jurkat and primary CD4+ T cells PubMed
Screening in Jurkat T-cells with a short-hairpin-RNA (shRNA) library identifies calcium and integrin binding family member 2 (CIB2) is important for HIV-1 replication PubMed
Knockdown of calcium and integrin binding family member 2 (CIB2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
integrin binding IEA
Inferred from Electronic Annotation
more info
 
magnesium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
calcium ion homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to ATP IDA
Inferred from Direct Assay
more info
PubMed 
photoreceptor cell maintenance ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cytosolic calcium ion concentration IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
blood microparticle HDA PubMed 
cuticular plate IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
muscle tendon junction IEA
Inferred from Electronic Annotation
more info
 
neuromuscular junction IEA
Inferred from Electronic Annotation
more info
 
photoreceptor inner segment ISS
Inferred from Sequence or Structural Similarity
more info
 
photoreceptor outer segment ISS
Inferred from Sequence or Structural Similarity
more info
 
sarcolemma IEA
Inferred from Electronic Annotation
more info
 
stereocilium IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
calcium and integrin-binding family member 2
Names
DNA-dependent protein kinase catalytic subunit-interacting protein 2

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033006.1 RefSeqGene

    Range
    5001..31929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001271888.1NP_001258817.1  calcium and integrin-binding family member 2 isoform 2

    See identical proteins and their annotated locations for NP_001258817.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon, and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AA731290, AC090260, BC033108, CN371149
    Consensus CDS
    CCDS61722.1
    UniProtKB/Swiss-Prot
    O75838
    Related
    ENSP00000442459.1, OTTHUMP00000248800, ENST00000539011.5, OTTHUMT00000419331
    Conserved Domains (1) summary
    cl25352
    Location:25135
    EFh_PEF; The penta-EF hand (PEF) family
  2. NM_001271889.1NP_001258818.1  calcium and integrin-binding family member 2 isoform 3

    See identical proteins and their annotated locations for NP_001258818.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two alternate exons resulting in the loss of an in-frame segment in the 5' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AA731290, AC090260, BC033108, BU556614
    Consensus CDS
    CCDS61723.1
    UniProtKB/Swiss-Prot
    O75838
    Related
    ENSP00000453488.1, OTTHUMP00000248801, ENST00000557846.5, OTTHUMT00000419332
    Conserved Domains (1) summary
    cl25352
    Location:19129
    EFh_PEF; The penta-EF hand (PEF) family
  3. NM_001301224.1NP_001288153.1  calcium and integrin-binding family member 2 isoform 4

    See identical proteins and their annotated locations for NP_001288153.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (4) is longer than isoform 1.
    Source sequence(s)
    AA731290, AC090260, AI857912, BC033108, BM908035
    UniProtKB/Swiss-Prot
    O75838
    Conserved Domains (1) summary
    cl25352
    Location:69183
    EFh_PEF; The penta-EF hand (PEF) family
  4. NM_006383.3NP_006374.1  calcium and integrin-binding family member 2 isoform 1

    See identical proteins and their annotated locations for NP_006374.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AA731290, AB012955, AC090260, BC033108, CN371149
    Consensus CDS
    CCDS10296.1
    UniProtKB/Swiss-Prot
    O75838
    Related
    ENSP00000258930.3, OTTHUMP00000184905, ENST00000258930.7, OTTHUMT00000289798
    Conserved Domains (1) summary
    cl25352
    Location:68178
    EFh_PEF; The penta-EF hand (PEF) family

RNA

  1. NR_125435.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA731290, AC090260, AI817087, BC033108, BU556614

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p12 Primary Assembly

    Range
    78104606..78131976 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006720374.2XP_006720437.1  calcium and integrin-binding family member 2 isoform X2

    See identical proteins and their annotated locations for XP_006720437.1

    UniProtKB/Swiss-Prot
    O75838
    Conserved Domains (1) summary
    cl25352
    Location:25135
    EFh_PEF; The penta-EF hand (PEF) family
  2. XM_005254126.3XP_005254183.1  calcium and integrin-binding family member 2 isoform X1

    See identical proteins and their annotated locations for XP_005254183.1

    UniProtKB/Swiss-Prot
    O75838
    Conserved Domains (2) summary
    cd00051
    Location:107174
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    pfam13499
    Location:111173
    EF-hand_7; EF-hand domain pair
  3. XM_011521161.2XP_011519463.1  calcium and integrin-binding family member 2 isoform X3

    UniProtKB/TrEMBL
    H0YKC8
    Related
    ENSP00000452752.1, OTTHUMP00000248803, ENST00000560618.5, OTTHUMT00000419334
    Conserved Domains (2) summary
    cd00051
    Location:64131
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    pfam13499
    Location:68130
    EF-hand_7; EF-hand domain pair

RNA

  1. XR_001751051.1 RNA Sequence

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