U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 128387, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    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. Located in mitochondrion. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 5.5), fat (RPKM 5.4) and 25 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See TATDN3 in Genome Data Viewer
    Location:
    1q32.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (212791894..212816830)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (212036861..212061805)
    RS_2024_09 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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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 (12) 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

    Go to the top of the page Help

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

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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 mitochondrion HTP PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    putative deoxyribonuclease TATDN3

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools