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C2CD2 C2 calcium dependent domain containing 2 [ Homo sapiens (human) ]

Gene ID: 25966, updated on 3-Nov-2024

Summary

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Official Symbol
C2CD2provided by HGNC
Official Full Name
C2 calcium dependent domain containing 2provided by HGNC
Primary source
HGNC:HGNC:1266
See related
Ensembl:ENSG00000157617 MIM:617581; AllianceGenome:HGNC:1266
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TMEM24L; C21orf25; C21orf258
Summary
Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in adrenal (RPKM 38.9), fat (RPKM 23.4) and 21 other tissues See more
Orthologs
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Genomic context

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See C2CD2 in Genome Data Viewer
Location:
21q22.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (41885112..41954018, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (40275427..40344241, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (43305221..43374127, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724800 Neighboring gene Sharpr-MPRA regulatory region 172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43192149-43192696 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:43216480-43216980 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18485 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:43241376-43242575 Neighboring gene PR/SET domain 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43256373-43257080 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:43274198-43275397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18491 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43318691-43319691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43364315-43364815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43370715-43371220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43373099-43373873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43378985-43379952 Neighboring gene small nucleolar RNA, H/ACA box 91 Neighboring gene NANOG hESC enhancer GRCh37_chr21:43388567-43389068 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:43415728-43415930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13335 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13336 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13337 Neighboring gene zinc finger and BTB domain containing 21 Neighboring gene ZNF295 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43460101-43460604 Neighboring gene uncharacterized LOC107985502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43461111-43461614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43463997-43464496

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A complex of the lipid transport ER proteins TMEM24 and C2CD2 with band 4.1 at cell-cell contacts.
    Title: A complex of the lipid transport ER proteins TMEM24 and C2CD2 with band 4.1 at cell-cell contacts.
  2. Genotyping was accomplished on Infinium Human610-QUAD version 1. In the ilSIRENTE population, genetic variants in ZNF295 and C2CD2 (rs928874 and rs1788355) on chromosome 21q22.3, were significantly associated with the 4-meter gait speed
    Title: Genetic variants associated with physical performance and anthropometry in old age: a genome-wide association study in the ilSIRENTE cohort.
  3. The C2CD2/C21orf25 promoter is activated by Trichostatin A (TSA) treatment and by serum depletion according to promoter reporter assays in HEK 293 cells.
    Title: Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC71445, DKFZp686O198, DKFZp586F0422

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in cytosol HDA PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus HDA PubMed 

General protein information

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Preferred Names
C2 domain-containing protein 2
Names
TMEM24 related geme
transmembrane protein 24-like

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_015500.2 → NP_056315.1  C2 domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_056315.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB047784, AP001619
    Consensus CDS
    CCDS42933.1
    UniProtKB/Swiss-Prot
    Q5R2V7, Q6AHX8, Q9NSE6, Q9Y426
    Related
    ENSP00000369853.3, ENST00000380486.4
    Conserved Domains (1) summary
    cd08678
    Location:265 → 391
    C2_C21orf25-like; C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein

  2. NM_199050.3 → NP_950251.1  C2 domain-containing protein 2 isoform 2

    See identical proteins and their annotated locations for NP_950251.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AI143200, AL833323, AP001619
    Consensus CDS
    CCDS13677.1
    UniProtKB/Swiss-Prot
    Q9Y426
    Related
    ENSP00000329302.7, ENST00000329623.11
    Conserved Domains (1) summary
    cd08678
    Location:110 → 236
    C2_C21orf25-like; C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein

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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    41885112..41954018 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011529522.3 → XP_011527824.1  C2 domain-containing protein 2 isoform X1

    Conserved Domains (1) summary
    cd08678
    Location:276 → 402
    C2_C21orf25-like; C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein

  2. XM_011529523.3 → XP_011527825.1  C2 domain-containing protein 2 isoform X2

    Conserved Domains (1) summary
    cd08678
    Location:185 → 311
    C2_C21orf25-like; C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein

  3. XM_005261109.5 → XP_005261166.1  C2 domain-containing protein 2 isoform X3

    See identical proteins and their annotated locations for XP_005261166.1

    UniProtKB/Swiss-Prot
    Q9Y426
    Conserved Domains (1) summary
    cd08678
    Location:110 → 236
    C2_C21orf25-like; C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    40275427..40344241 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324425.1 → XP_054180400.1  C2 domain-containing protein 2 isoform X1

  2. XM_054324426.1 → XP_054180401.1  C2 domain-containing protein 2 isoform X2

  3. XM_054324427.1 → XP_054180402.1  C2 domain-containing protein 2 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y426.2 GenPept UniProtKB/Swiss-Prot:Q9Y426

Gene LinkOut

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