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TATDN3 TatD DNase domain containing 3 [ Homo sapiens (human) ]

Gene ID: 128387, updated on 5-Mar-2024

Summary

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Official Symbol
TATDN3provided by HGNC
Official Full Name
TatD DNase domain containing 3provided by HGNC
Primary source
HGNC:HGNC:27010
See related
Ensembl:ENSG00000203705 AllianceGenome:HGNC:27010
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
Summary
Predicted to enable metal ion binding activity and nuclease activity. Predicted to be involved in nucleic acid phosphodiester bond hydrolysis. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 5.5), fat (RPKM 5.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1q32.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (212791894..212816830)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (212036861..212061805)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (212965236..212990172)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1805 Neighboring gene basic leucine zipper ATF-like transcription factor 3 Neighboring gene NANOG hESC enhancer GRCh37_chr1:212885887-212886440 Neighboring gene MPRA-validated peak687 silencer Neighboring gene NSL1 component of MIS12 kinetochore complex Neighboring gene MPRA-validated peak688 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:212932746-212933595 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:212933596-212934444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:212963792-212964570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2517 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:212967459-212967959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2519 Neighboring gene RPS5 pseudogene 4 Neighboring gene spermatogenesis associated 45

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. Human and bacterial TatD enzymes exhibit apurinic/apyrimidinic (AP) endonuclease activity. Dorival J, et al. Nucleic Acids Res, 2023 Apr 11. PMID 36881763, Free PMC Article
  2. NotI flanking sequences: a tool for gene discovery and verification of the human genome. Kutsenko AS, et al. Nucleic Acids Res, 2002 Jul 15. PMID 12136098, Free PMC Article
  3. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. Wang AG, et al. Biochem Biophys Res Commun, 2006 Jul 7. PMID 16712791
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. Hendrickson SL, et al. PLoS One, 2010 Sep 21. PMID 20877624, Free PMC Article
  5. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Fei T, et al. Proc Natl Acad Sci U S A, 2017 Jun 27. PMID 28611215, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Human and bacterial TatD enzymes exhibit apurinic/apyrimidinic (AP) endonuclease activity.
    Title: Human and bacterial TatD enzymes exhibit apurinic/apyrimidinic (AP) endonuclease activity.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
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

  • MGC142198

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nuclease activity IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
putative deoxyribonuclease TATDN3

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_001042552.3 → NP_001036017.1  putative deoxyribonuclease TATDN3 isoform 1

    See identical proteins and their annotated locations for NP_001036017.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AC104333, BC113638, DB351940
    Consensus CDS
    CCDS31019.1
    UniProtKB/Swiss-Prot
    A6NGS3, B7Z1C1, B7Z978, B7ZLQ6, E9PJE5, E9PNH3, G3V151, Q17R31, Q4G0L1
    Related
    ENSP00000355941.4, ENST00000366974.9
    Conserved Domains (1) summary
    pfam01026
    Location:9 → 265
    TatD_DNase; TatD related DNase

  2. NM_001042553.3 → NP_001036018.1  putative deoxyribonuclease TATDN3 isoform 2

    See identical proteins and their annotated locations for NP_001036018.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. This results in a shorter protein (isoform 2) compared to isoform 1.
    Source sequence(s)
    AC104333, BC143956, DB351940
    Consensus CDS
    CCDS41465.1
    UniProtKB/Swiss-Prot
    Q17R31
    Related
    ENSP00000355940.4, ENST00000366973.8
    Conserved Domains (1) summary
    pfam01026
    Location:9 → 264
    TatD_DNase; TatD related DNase

  3. NM_001146169.2 → NP_001139641.1  putative deoxyribonuclease TATDN3 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses two alternate splice sites in the 3' coding region compared to variant 1, one of which results in a frameshift. The encoded isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC104333, BC143957, DB351940
    Consensus CDS
    CCDS53476.1
    UniProtKB/Swiss-Prot
    Q17R31
    Related
    ENSP00000433755.1, ENST00000531963.5
    Conserved Domains (1) summary
    cd01310
    Location:8 → 233
    TatD_DNAse; TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity.

  4. NM_001146170.2 → NP_001139642.1  putative deoxyribonuclease TATDN3 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AC104333, AK304557, DB351940
    Consensus CDS
    CCDS53477.1
    UniProtKB/Swiss-Prot
    Q17R31
    Related
    ENSP00000434801.1, ENST00000526641.5
    Conserved Domains (1) summary
    pfam01026
    Location:9 → 244
    TatD_DNase; TatD related DNase

  5. NM_001146171.2 → NP_001139643.1  putative deoxyribonuclease TATDN3 isoform 5

    See identical proteins and their annotated locations for NP_001139643.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. This results in a longer protein (isoform 5) compared to isoform 1.
    Source sequence(s)
    AC104333, AK293129, BC143957, DB351940
    Consensus CDS
    CCDS53475.1
    UniProtKB/Swiss-Prot
    Q17R31
    Related
    ENSP00000431376.1, ENST00000532324.5
    Conserved Domains (1) summary
    pfam01026
    Location:9 → 272
    TatD_DNase; TatD related DNase

  6. NM_001363589.2 → NP_001350518.1  putative deoxyribonuclease TATDN3 isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks an exon in the 3' coding region which causes a frameshift compared to variant 1. The encoded isoform (6) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC104333
    Conserved Domains (1) summary
    cl00281
    Location:8 → 161
    metallo-dependent_hydrolases; Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a ...

  7. NM_001363590.2 → NP_001350519.1  putative deoxyribonuclease TATDN3 isoform 7

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses an alternate splice site and lacks an exon in the 3' coding region which causes a frameshift compared to variant 1. The encoded isoform (7) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC104333
    Consensus CDS
    CCDS86050.1
    UniProtKB/TrEMBL
    E9PP81
    Related
    ENSP00000436364.1, ENST00000526997.5
    Conserved Domains (1) summary
    cl00281
    Location:8 → 161
    metallo-dependent_hydrolases; Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a ...

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    212791894..212816830
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000330.3 → XP_016855819.1  putative deoxyribonuclease TATDN3 isoform X3

  2. XM_017000328.3 → XP_016855817.1  putative deoxyribonuclease TATDN3 isoform X1

  3. XM_017000329.2 → XP_016855818.1  putative deoxyribonuclease TATDN3 isoform X2

  4. XM_047446340.1 → XP_047302296.1  putative deoxyribonuclease TATDN3 isoform X5

  5. XM_024453283.2 → XP_024309051.1  putative deoxyribonuclease TATDN3 isoform X4

    UniProtKB/TrEMBL
    B7Z2Z9
    Conserved Domains (1) summary
    pfam01026
    Location:2 → 212
    TatD_DNase; TatD related DNase

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    212036861..212061805
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334463.1 → XP_054190438.1  putative deoxyribonuclease TATDN3 isoform X3

  2. XM_054334461.1 → XP_054190436.1  putative deoxyribonuclease TATDN3 isoform X1

  3. XM_054334462.1 → XP_054190437.1  putative deoxyribonuclease TATDN3 isoform X2

  4. XM_054334465.1 → XP_054190440.1  putative deoxyribonuclease TATDN3 isoform X5

  5. XM_054334464.1 → XP_054190439.1  putative deoxyribonuclease TATDN3 isoform X4

    UniProtKB/TrEMBL
    B7Z2Z9
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q17R31.1 GenPept UniProtKB/Swiss-Prot:Q17R31

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