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EXD3 exonuclease 3'-5' domain containing 3 [ Homo sapiens (human) ]

Gene ID: 54932, updated on 13-Mar-2020

Summary

Official Symbol
EXD3provided by HGNC
Official Full Name
exonuclease 3'-5' domain containing 3provided by HGNC
Primary source
HGNC:HGNC:26023
See related
Ensembl:ENSG00000187609
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
Nbr; mut-7
Expression
Ubiquitous expression in spleen (RPKM 2.6), fat (RPKM 2.4) and 25 other tissues See more
Orthologs

Genomic context

See EXD3 in Genome Data Viewer
Location:
9q34.3
Exon count:
32
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (137306896..137423262, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140201346..140317714, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene 9q34.3 TOR4A distal recombination region Neighboring gene NOTCH regulated ankyrin repeat protein Neighboring gene NADPH oxidase activator 1 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 8 Neighboring gene microRNA 7114 Neighboring gene NMDA receptor synaptonuclear signaling and neuronal migration factor

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20433, FLJ30442, MGC74981, MGC131904

Gene Ontology Provided by GOA

Function Evidence Code Pubs
3'-5' exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
nucleic acid binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
nucleic acid phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
exonuclease mut-7 homolog
Names
exonuclease 3'-5' domain-containing protein 3
nibbler homolog
probable exonuclease mut-7 homolog, isoform 5
testicular tissue protein Li 125

NCBI Reference Sequences (RefSeq)

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_001286823.2NP_001273752.1  exonuclease mut-7 homolog isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks several 3' exons but includes an alternate 3' exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is significantly shorter than isoform a.
    Source sequence(s)
    BC037355, BC069205, BX322799
    Consensus CDS
    CCDS75942.1
    UniProtKB/Swiss-Prot
    Q8N9H8
    Related
    ENSP00000431859.1, ENST00000479452.5
  2. NM_017820.5NP_060290.3  exonuclease mut-7 homolog isoform a

    See identical proteins and their annotated locations for NP_060290.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
    Source sequence(s)
    AI682614, AK094438, AL536907, BC131749, BX322799, HM005438
    Consensus CDS
    CCDS48066.1
    UniProtKB/Swiss-Prot
    Q8N9H8
    UniProtKB/TrEMBL
    A0A140VJP9
    Related
    ENSP00000340474.4, ENST00000340951.9
    Conserved Domains (2) summary
    cd06146
    Location:373568
    mut-7_like_exo; DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins
    cl19501
    Location:631850
    Mut7-C; Mut7-C RNAse domain

RNA

  1. NR_104598.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) includes three additional exons in the 5' region, and lacks several 3' exons but includes an alternate 3' exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC033079, BC069205, BX322799
    Related
    ENST00000460390.6
  2. NR_104599.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) shares two 5' exons but lacks the remaining exons found in variant 1, and it includes an alternate 3' exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    BC039252, BC065002
    Related
    ENST00000465160.2

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    137306896..137423262 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518810.1XP_011517112.1  exonuclease mut-7 homolog isoform X2

    Conserved Domains (2) summary
    cd06146
    Location:497693
    mut-7_like_exo; DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins
    cl19501
    Location:756852
    Mut7-C; Mut7-C RNAse domain
  2. XM_017014861.1XP_016870350.1  exonuclease mut-7 homolog isoform X1

  3. XM_017014863.1XP_016870352.1  exonuclease mut-7 homolog isoform X4

  4. XM_017014862.1XP_016870351.1  exonuclease mut-7 homolog isoform X3

  5. XM_024447589.1XP_024303357.1  exonuclease mut-7 homolog isoform X7

    Conserved Domains (2) summary
    cd06146
    Location:53249
    mut-7_like_exo; DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins
    cl19501
    Location:312408
    Mut7-C; Mut7-C RNAse domain
  6. XM_017014865.1XP_016870354.1  exonuclease mut-7 homolog isoform X5

  7. XM_017014864.1XP_016870353.1  exonuclease mut-7 homolog isoform X5

  8. XM_024447588.1XP_024303356.1  exonuclease mut-7 homolog isoform X6

    Conserved Domains (2) summary
    cd06146
    Location:325521
    mut-7_like_exo; DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins
    cl19501
    Location:584680
    Mut7-C; Mut7-C RNAse domain
  9. XM_011518814.1XP_011517116.1  exonuclease mut-7 homolog isoform X7

    See identical proteins and their annotated locations for XP_011517116.1

    Conserved Domains (2) summary
    cd06146
    Location:53249
    mut-7_like_exo; DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins
    cl19501
    Location:312408
    Mut7-C; Mut7-C RNAse domain
  10. XM_011518815.2XP_011517117.1  exonuclease mut-7 homolog isoform X7

    See identical proteins and their annotated locations for XP_011517117.1

    Conserved Domains (2) summary
    cd06146
    Location:53249
    mut-7_like_exo; DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins
    cl19501
    Location:312408
    Mut7-C; Mut7-C RNAse domain
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