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Cc2d2a coiled-coil and C2 domain containing 2A [ Mus musculus (house mouse) ]

Gene ID: 231214, updated on 12-May-2024

Summary

Official Symbol
Cc2d2aprovided by MGI
Official Full Name
coiled-coil and C2 domain containing 2Aprovided by MGI
Primary source
MGI:MGI:1924487
See related
Ensembl:ENSMUSG00000039765 AllianceGenome:MGI:1924487
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
b2b1035Clo; 5730509K17Rik
Summary
Involved in cilium assembly and protein localization to ciliary transition zone. Acts upstream of or within several processes, including animal organ development; cilium assembly; and neural tube closure. Located in ciliary transition zone. Part of MKS complex. Used to study Meckel syndrome and visceral heterotaxy. Human ortholog(s) of this gene implicated in Joubert syndrome 9; Meckel syndrome 6; and intellectual disability. Orthologous to human CC2D2A (coiled-coil and C2 domain containing 2A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bladder adult (RPKM 4.8), cerebellum adult (RPKM 3.2) and 22 other tissues See more
Orthologs
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Genomic context

See Cc2d2a in Genome Data Viewer
Location:
5 B3; 5 23.78 cM
Exon count:
43
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (43819715..43898317)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (43662374..43740975)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_12970 Neighboring gene predicted gene 43699 Neighboring gene STARR-seq mESC enhancer starr_12971 Neighboring gene C1q and tumor necrosis factor related protein 7 Neighboring gene STARR-seq mESC enhancer starr_12973 Neighboring gene predicted gene 15866 Neighboring gene predicted gene, 35762 Neighboring gene F-box and leucine-rich repeat protein 5 Neighboring gene STARR-seq mESC enhancer starr_12974 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:44215949-44216168 Neighboring gene STARR-positive B cell enhancer ABC_E8052 Neighboring gene bone marrow stromal cell antigen 1

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Chemically induced (ENU) (1) 
  • Endonuclease-mediated (1) 
  • Gene trapped (1) 
  • Targeted (3)  1 citation

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within axoneme assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within camera-type eye development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell projection organization IEA
Inferred from Electronic Annotation
more info
 
involved_in cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within determination of left/right symmetry IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within embryonic brain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within heart development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within motile cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within neural tube closure IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in non-motile cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within non-motile cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in protein localization to ciliary transition zone IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in protein localization to ciliary transition zone IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within smoothened signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of MKS complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in cell projection IEA
Inferred from Electronic Annotation
more info
 
is_active_in ciliary transition zone IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in ciliary transition zone IDA
Inferred from Direct Assay
more info
PubMed 
located_in cilium IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
coiled-coil and C2 domain-containing protein 2A

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_001359903.1NP_001346832.1  coiled-coil and C2 domain-containing protein 2A isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC140277, AC161536
    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (2) summary
    pfam15625
    Location:646819
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    cl14603
    Location:10981136
    C2; C2 domain
  2. NM_001359904.1NP_001346833.1  coiled-coil and C2 domain-containing protein 2A isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC140277, AC161536
    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (3) summary
    pfam15625
    Location:646820
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:137383
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:11031141
    C2; C2 domain
  3. NM_001359905.1NP_001346834.1  coiled-coil and C2 domain-containing protein 2A isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks two alternate in-frame exons compared to variant 1. The resulting isoform (d) has the same N- and C-termini but is shorter compared to isoform a. Variants 4 and 5 both encode the same isoform (d).
    Source sequence(s)
    AC140277, AC161536
    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (3) summary
    pfam15625
    Location:646820
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:137383
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:10981136
    C2; C2 domain
  4. NM_001359906.1NP_001346835.1  coiled-coil and C2 domain-containing protein 2A isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (d) has the same N- and C-termini but is shorter compared to isoform a. Variants 4 and 5 both encode the same isoform (d).
    Source sequence(s)
    AC140277, AC161536
    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (3) summary
    pfam15625
    Location:646820
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:137383
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:10981136
    C2; C2 domain
  5. NM_172274.2NP_758478.1  coiled-coil and C2 domain-containing protein 2A isoform a

    See identical proteins and their annotated locations for NP_758478.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    BC032290, CJ129212
    Consensus CDS
    CCDS39080.1
    UniProtKB/Swiss-Prot
    Q8BP57, Q8CFW7
    UniProtKB/TrEMBL
    F6YZ61
    Related
    ENSMUSP00000048320.9, ENSMUST00000048150.15
    Conserved Domains (3) summary
    COG1340
    Location:377551
    COG1340; Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]
    pfam15625
    Location:646817
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    cl14603
    Location:11031141
    C2; C2 domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    43819715..43898317
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036165058.1XP_036020951.1  coiled-coil and C2 domain-containing protein 2A isoform X7

    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (3) summary
    pfam15625
    Location:676850
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:137413
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:11331171
    C2; C2 domain
  2. XM_036165053.1XP_036020946.1  coiled-coil and C2 domain-containing protein 2A isoform X1

    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (3) summary
    pfam15625
    Location:676850
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:137413
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:11331171
    C2; C2 domain
  3. XM_036165055.1XP_036020948.1  coiled-coil and C2 domain-containing protein 2A isoform X2

    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (3) summary
    pfam15625
    Location:676850
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:137413
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:11281166
    C2; C2 domain
  4. XM_036165059.1XP_036020952.1  coiled-coil and C2 domain-containing protein 2A isoform X9

    Conserved Domains (2) summary
    pfam15625
    Location:131305
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    cl14603
    Location:583621
    C2; C2 domain
  5. XM_006503938.4XP_006504001.1  coiled-coil and C2 domain-containing protein 2A isoform X8

    Conserved Domains (2) summary
    pfam15625
    Location:131305
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    cl14603
    Location:588626
    C2; C2 domain
  6. XM_036165054.1XP_036020947.1  coiled-coil and C2 domain-containing protein 2A isoform X1

    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (3) summary
    pfam15625
    Location:676850
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:137413
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:11331171
    C2; C2 domain
  7. XM_006503934.5XP_006503997.1  coiled-coil and C2 domain-containing protein 2A isoform X3

    See identical proteins and their annotated locations for XP_006503997.1

    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (3) summary
    pfam15625
    Location:646820
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:137383
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:11031141
    C2; C2 domain
  8. XM_030254387.2XP_030110247.1  coiled-coil and C2 domain-containing protein 2A isoform X3

    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (3) summary
    pfam15625
    Location:646820
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:137383
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:11031141
    C2; C2 domain
  9. XM_036165056.1XP_036020949.1  coiled-coil and C2 domain-containing protein 2A isoform X4

    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (3) summary
    pfam15625
    Location:627801
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:88364
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:10841122
    C2; C2 domain
  10. XM_006503936.4XP_006503999.1  coiled-coil and C2 domain-containing protein 2A isoform X5

    UniProtKB/TrEMBL
    F6YZ61
    Conserved Domains (3) summary
    pfam15625
    Location:597771
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:88334
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:10541092
    C2; C2 domain
  11. XM_036165057.1XP_036020950.1  coiled-coil and C2 domain-containing protein 2A isoform X6

    UniProtKB/TrEMBL
    F6YZ61
    Related
    ENSMUSP00000114349.3, ENSMUST00000125866.4
    Conserved Domains (3) summary
    pfam15625
    Location:597771
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    pfam17661
    Location:88334
    DUF5523; Family of unknown function (DUF5523)
    cl14603
    Location:10491087
    C2; C2 domain