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CC2D1A coiled-coil and C2 domain containing 1A [ Homo sapiens (human) ]

Gene ID: 54862, updated on 5-May-2024

Summary

Official Symbol
CC2D1Aprovided by HGNC
Official Full Name
coiled-coil and C2 domain containing 1Aprovided by HGNC
Primary source
HGNC:HGNC:30237
See related
Ensembl:ENSG00000132024 MIM:610055; AllianceGenome:HGNC:30237
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
Lgd2; MRT3; TAPE; Aki-1; FREUD-1; Freud-1/Aki1
Summary
This gene encodes a transcriptional repressor that binds to a conserved 14-bp 5'-repressor element and regulates expression of the 5-hydroxytryptamine (serotonin) receptor 1A gene in neuronal cells. The DNA binding and transcriptional repressor activities of the protein are inhibited by calcium. A mutation in this gene results in a nonsyndromic form of cognitive disability (MRT3). [provided by RefSeq, Jul 2017]
Expression
Ubiquitous expression in duodenum (RPKM 16.8), small intestine (RPKM 12.5) and 25 other tissues See more
Orthologs
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Genomic context

Location:
19p13.12
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (13906201..13930879)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (14032358..14057039)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (14017014..14041692)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene nanos C2HC-type zinc finger 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13993737-13994582 Neighboring gene microRNA 181d Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14000391-14000892 Neighboring gene break repair meiotic recombinase recruitment factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10218 Neighboring gene MPRA-validated peak3378 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14046993-14047750 Neighboring gene podocan like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14069830-14070403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14070404-14070976 Neighboring gene DDB1 and CUL4 associated factor 15 Neighboring gene regulatory factor X1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14090312-14090838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14090839-14091365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14091366-14091891 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14093768-14094294 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14096053-14096944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14097836-14098726 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14116358-14116886 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14116887-14117414 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14117415-14117942

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human coiled-coil and C2 domain containing 1A (CC2D1A) at amino acid residues 783-784 by the HIV-1 protease 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

Clone Names

  • FLJ20241, FLJ41160

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in centrosome IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in endosome membrane IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular exosome HDA PubMed 
located_in fibrillar center IDA
Inferred from Direct Assay
more info
 
located_in membrane HDA PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
coiled-coil and C2 domain-containing protein 1A
Names
Akt kinase-interacting protein 1
FRE under dual repression-binding protein 1
TBK1-associated protein in endolysosomes
five prime repressor element under dual repression-binding protein 1
five repressor element under dual repression-binding protein 1
lethal (2) giant discs homolog 2
putative NF-kappa-B-activating protein 023N
putative NFkB activating protein

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.

Genomic

  1. NG_013089.1 RefSeqGene

    Range
    5059..29737
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001411138.1NP_001398067.1  coiled-coil and C2 domain-containing protein 1A isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC020916
    Consensus CDS
    CCDS92537.1
    Related
    ENSP00000467526.1, ENST00000589606.5
  2. NM_017721.5NP_060191.3  coiled-coil and C2 domain-containing protein 1A isoform 1

    See identical proteins and their annotated locations for NP_060191.3

    Status: REVIEWED

    Source sequence(s)
    BC064981, DB065701
    Consensus CDS
    CCDS42512.1
    UniProtKB/Swiss-Prot
    Q6P1N0, Q7Z435, Q86XV0, Q8NF89, Q9H603, Q9NXI1
    Related
    ENSP00000313601.6, ENST00000318003.11
    Conserved Domains (2) summary
    smart00685
    Location:349407
    DM14; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241
    cd08690
    Location:652809
    C2_Freud-1; C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    13906201..13930879
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439012.1XP_047294968.1  coiled-coil and C2 domain-containing protein 1A isoform X1

  2. XM_047439014.1XP_047294970.1  coiled-coil and C2 domain-containing protein 1A isoform X2

  3. XM_047439015.1XP_047294971.1  coiled-coil and C2 domain-containing protein 1A isoform X3

  4. XM_047439017.1XP_047294973.1  coiled-coil and C2 domain-containing protein 1A isoform X5

  5. XM_047439016.1XP_047294972.1  coiled-coil and C2 domain-containing protein 1A isoform X4

  6. XM_047439018.1XP_047294974.1  coiled-coil and C2 domain-containing protein 1A isoform X6

  7. XM_047439019.1XP_047294975.1  coiled-coil and C2 domain-containing protein 1A isoform X7

  8. XM_047439020.1XP_047294976.1  coiled-coil and C2 domain-containing protein 1A isoform X8

    Related
    ENSP00000506358.1, ENST00000680977.1

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160022.1 Reference GRCh38.p14 PATCHES

    Range
    118042..142720
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332691.1XP_054188666.1  coiled-coil and C2 domain-containing protein 1A isoform X1

  2. XM_054332692.1XP_054188667.1  coiled-coil and C2 domain-containing protein 1A isoform X2

  3. XM_054332693.1XP_054188668.1  coiled-coil and C2 domain-containing protein 1A isoform X3

  4. XM_054332695.1XP_054188670.1  coiled-coil and C2 domain-containing protein 1A isoform X5

  5. XM_054332694.1XP_054188669.1  coiled-coil and C2 domain-containing protein 1A isoform X4

  6. XM_054332696.1XP_054188671.1  coiled-coil and C2 domain-containing protein 1A isoform X6

  7. XM_054332697.1XP_054188672.1  coiled-coil and C2 domain-containing protein 1A isoform X7

  8. XM_054332698.1XP_054188673.1  coiled-coil and C2 domain-containing protein 1A isoform X8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    14032358..14057039
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321331.1XP_054177306.1  coiled-coil and C2 domain-containing protein 1A isoform X1

  2. XM_054321332.1XP_054177307.1  coiled-coil and C2 domain-containing protein 1A isoform X2

  3. XM_054321333.1XP_054177308.1  coiled-coil and C2 domain-containing protein 1A isoform X3

  4. XM_054321335.1XP_054177310.1  coiled-coil and C2 domain-containing protein 1A isoform X5

  5. XM_054321334.1XP_054177309.1  coiled-coil and C2 domain-containing protein 1A isoform X4

  6. XM_054321336.1XP_054177311.1  coiled-coil and C2 domain-containing protein 1A isoform X6

  7. XM_054321337.1XP_054177312.1  coiled-coil and C2 domain-containing protein 1A isoform X7

  8. XM_054321338.1XP_054177313.1  coiled-coil and C2 domain-containing protein 1A isoform X8