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CDADC1 cytidine and dCMP deaminase domain containing 1 [ Homo sapiens (human) ]

Gene ID: 81602, updated on 11-Apr-2024

Summary

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Official Symbol
CDADC1provided by HGNC
Official Full Name
cytidine and dCMP deaminase domain containing 1provided by HGNC
Primary source
HGNC:HGNC:20299
See related
Ensembl:ENSG00000102543 MIM:618997; AllianceGenome:HGNC:20299
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
NYD-SP15; bA103J18.1
Summary
Enables several functions, including cytidine deaminase activity; importin-alpha family protein binding activity; and protein homodimerization activity. Involved in DNA cytosine deamination and cytidine deamination. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in thyroid (RPKM 5.8), testis (RPKM 5.7) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
13q14.2
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (49247925..49293485)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (48469229..48514699)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (49822061..49867621)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370203 Neighboring gene THAP domain containing 12 pseudogene 10 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:49821922-49822484 Neighboring gene Sharpr-MPRA regulatory region 13963 Neighboring gene Sharpr-MPRA regulatory region 6847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:49880333-49880832 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:49888093-49889292 Neighboring gene calcium binding protein 39 like Neighboring gene NANOG hESC enhancer GRCh37_chr13:49961302-49961803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7746 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:50018017-50018789 Neighboring gene SETDB2-PHF11 readthrough Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:50018790-50019563 Neighboring gene SET domain bifurcated histone lysine methyltransferase 2 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 14

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
  • 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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Related articles in PubMed

  1. Structural and biological function of NYD-SP15 as a new member of cytidine deaminases. Xu Y, et al. Gene, 2016 May 25. PMID 26945630
  2. NYD-SP15: a novel gene potentially involved in regulating testicular development and spermatogenesis. Liu Q, et al. Biochem Genet, 2006 Oct. PMID 16955368
  3. Insight into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma with those of corresponding noncancerous liver. Xu XR, et al. Proc Natl Acad Sci U S A, 2001 Dec 18. PMID 11752456, Free PMC Article
  4. The p300/YY1/miR-500a-5p/HDAC2 signalling axis regulates cell proliferation in human colorectal cancer. Tang W, et al. Nat Commun, 2019 Feb 8. PMID 30737378, Free PMC Article
  5. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Boldt K, et al. Nat Commun, 2016 May 13. PMID 27173435, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NYD-SP15 contained nuclear localization sequence and nuclear export-signal and could dynamically shuttle between the nucleus and cytoplasm.
    Title: Structural and biological function of NYD-SP15 as a new member of cytidine deaminases.
  2. NYD-SP15 protein plays an important role in testicular development and spermatogenesis
    Title: NYD-SP15: a novel gene potentially involved in regulating testicular development and spermatogenesis.
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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC41774, MGC57136, MGC150615

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cytidine deaminase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables dCMP deaminase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables importin-alpha family protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA cytosine deamination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cytidine deamination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cytidine deamination IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in nucleus IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
cytidine and dCMP deaminase domain-containing protein 1
Names
cytidine deaminase
protein kinase NYD-SP15
testis development protein NYD-SP15
NP_001180407.1
NP_112173.1
XP_006719934.1
XP_011533552.1
XP_011533553.1
XP_047286645.1
XP_047286646.1
XP_047286648.1
XP_054231027.1
XP_054231028.1
XP_054231029.1
XP_054231030.1
XP_054231031.1
XP_054231032.1

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_001193478.2 → NP_001180407.1  cytidine and dCMP deaminase domain-containing protein 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate splice site in the last splice junction compared to variant 1. The resulting isoform (2) is shorter than isoform 1 at the C-terminus.
    Source sequence(s)
    BC048092, BC125203, DA400049
    UniProtKB/TrEMBL
    B2R742
    Conserved Domains (2) summary
    cd01286
    Location:319 → 454
    deoxycytidylate_deaminase; Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the ...
    cl00269
    Location:79 → 151
    cytidine_deaminase-like; Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members ...

  2. NM_030911.4 → NP_112173.1  cytidine and dCMP deaminase domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_112173.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    BC048092, BC125202, DA400049
    Consensus CDS
    CCDS9415.1
    UniProtKB/Swiss-Prot
    Q49A08, Q4G119, Q5TAW9, Q7Z764, Q9BWV3, Q9NT36
    UniProtKB/TrEMBL
    B2R742
    Related
    ENSP00000251108.6, ENST00000251108.10
    Conserved Domains (2) summary
    cd01286
    Location:319 → 454
    deoxycytidylate_deaminase; Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the ...
    cl00269
    Location:79 → 151
    cytidine_deaminase-like; Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members ...

RNA

  1. NR_036439.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an exon in the CDS, resulting in a premature stop codon, compared to variant 1. The transcript is a nonsense-mediated mRNA decay candidate and does not encode a functional protein.
    Source sequence(s)
    AK297400, BC048092, BC125202, DA400049

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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    49247925..49293485
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535251.2 → XP_011533553.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X5

    See identical proteins and their annotated locations for XP_011533553.1

    UniProtKB/TrEMBL
    B2R742
    Conserved Domains (2) summary
    cd01286
    Location:274 → 409
    deoxycytidylate_deaminase; Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the ...
    cl00269
    Location:34 → 106
    cytidine_deaminase-like; Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members ...

  2. XM_011535250.3 → XP_011533552.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    B2R742
    Conserved Domains (2) summary
    cd01286
    Location:333 → 468
    deoxycytidylate_deaminase; Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the ...
    cl00269
    Location:93 → 165
    cytidine_deaminase-like; Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members ...

  3. XM_047430689.1 → XP_047286645.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X2

  4. XM_047430692.1 → XP_047286648.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X4

  5. XM_006719871.4 → XP_006719934.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X3

    UniProtKB/TrEMBL
    B4DMC8
    Conserved Domains (1) summary
    cd01286
    Location:180 → 315
    deoxycytidylate_deaminase; Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the ...

  6. XM_047430690.1 → XP_047286646.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    48469229..48514699
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054375057.1 → XP_054231032.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X5

  2. XM_054375052.1 → XP_054231027.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X1

  3. XM_054375053.1 → XP_054231028.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X2

  4. XM_054375056.1 → XP_054231031.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X4

  5. XM_054375054.1 → XP_054231029.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X3

  6. XM_054375055.1 → XP_054231030.1  cytidine and dCMP deaminase domain-containing protein 1 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BWV3.1 GenPept UniProtKB/Swiss-Prot:Q9BWV3

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