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

Gene ID: 10518, updated on 17-Sep-2024

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; AllianceGenome:HGNC:24579
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
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Genomic context

See CIB2 in Genome Data Viewer
Location:
15q25.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (78104606..78131535, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (75967162..75994101, complement)
RS_2024_09 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 ATAC-STARR-seq lymphoblastoid active region 9900 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:78376354-78376854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9909 Neighboring gene SH2 domain containing 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6705 Neighboring gene uncharacterized LOC124903534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9911 Neighboring gene isocitrate dehydrogenase (NAD(+)) 3 catalytic subunit alpha Neighboring gene acyl-CoA synthetase bubblegum family member 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What'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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

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

NEW Try the new Transcript table

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_033006.2 RefSeqGene

    Range
    5090..31929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    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)
    AC090260
    Consensus CDS
    CCDS61722.1
    UniProtKB/Swiss-Prot
    O75838
    Related
    ENSP00000442459.1, ENST00000539011.5
    Conserved Domains (1) summary
    COG5126
    Location:25135
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  2. NM_001271889.2NP_001258818.1  calcium and integrin-binding family member 2 isoform 3

    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)
    AC090260
    Consensus CDS
    CCDS61723.1
    UniProtKB/Swiss-Prot
    O75838
    Related
    ENSP00000453488.1, ENST00000557846.5
    Conserved Domains (1) summary
    COG5126
    Location:19129
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  3. NM_001301224.2NP_001288153.1  calcium and integrin-binding family member 2 isoform 4

    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)
    AC090260
    UniProtKB/Swiss-Prot
    O75838
    Conserved Domains (1) summary
    cl25352
    Location:69183
    EFh_PEF; The penta-EF hand (PEF) family
  4. NM_006383.4NP_006374.1  calcium and integrin-binding family member 2 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AC090260
    Consensus CDS
    CCDS10296.1
    UniProtKB/Swiss-Prot
    B4DDF0, H0YM71, O75838, Q05BT6
    UniProtKB/TrEMBL
    Q5TZX7
    Related
    ENSP00000258930.3, ENST00000258930.8
    Conserved Domains (1) summary
    COG5126
    Location:68178
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

RNA

  1. NR_125435.2 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)
    AC090260

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    78104606..78131535 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005254126.4XP_005254183.1  calcium and integrin-binding family member 2 isoform X1

    UniProtKB/TrEMBL
    Q5TZX7
    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
  2. XM_011521161.2XP_011519463.1  calcium and integrin-binding family member 2 isoform X3

    UniProtKB/TrEMBL
    H0YKC8
    Related
    ENSP00000452752.1, ENST00000560618.5
    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
  3. XM_047432110.1XP_047288066.1  calcium and integrin-binding family member 2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    75967162..75994101 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377207.1XP_054233182.1  calcium and integrin-binding family member 2 isoform X1

    UniProtKB/TrEMBL
    Q5TZX7
  2. XM_054377209.1XP_054233184.1  calcium and integrin-binding family member 2 isoform X3

    UniProtKB/TrEMBL
    H0YKC8
  3. XM_054377208.1XP_054233183.1  calcium and integrin-binding family member 2 isoform X2