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REXO4 REX4 homolog, 3'-5' exonuclease [ Homo sapiens (human) ]

Gene ID: 57109, updated on 2-Nov-2024

Summary

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Official Symbol
REXO4provided by HGNC
Official Full Name
REX4 homolog, 3'-5' exonucleaseprovided by HGNC
Primary source
HGNC:HGNC:12820
See related
Ensembl:ENSG00000148300 MIM:602930; AllianceGenome:HGNC:12820
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
REX4; XPMC2; XPMC2H
Summary
Enables DNA binding activity and nuclease activity. Involved in DNA catabolic process and DNA repair. Located in nuclear speck and nucleolus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in ovary (RPKM 10.2), testis (RPKM 9.8) and 25 other tissues See more
Orthologs
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Genomic context

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See REXO4 in Genome Data Viewer
Location:
9q34.2
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (133406058..133418172, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (145620490..145632600, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (136271182..136283292, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29237 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136234564-136235235 Neighboring gene surfeit 2 Neighboring gene surfeit 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20455 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20456 Neighboring gene serine/threonine kinase like domain containing 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:136257045-136257682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136265498-136266135 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136267839-136268006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136269742-136270242 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29238 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20458 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136295843-136296052 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136321575-136321727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136322178-136323045 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136327558-136328114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29242 Neighboring gene uncharacterized LOC124902295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20462 Neighboring gene calcium channel flower domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136344231-136344732 Neighboring gene solute carrier family 2 member 6

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 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 XPMC2H: cDNA cloning, mapping to 9q34, genomic structure, and evaluation as TSC1. Kwiatkowska J, et al. Genomics, 1997 Sep 15. PMID 9325058
  2. The exonuclease activity of hPMC2 is required for transcriptional regulation of the QR gene and repair of estrogen-induced abasic sites. Krishnamurthy N, et al. Oncogene, 2011 Nov 24. PMID 21602889, Free PMC Article
  3. Identification and characterization of a novel factor that regulates quinone reductase gene transcriptional activity. Montano MM, et al. J Biol Chem, 2000 Nov 3. PMID 10908561
  4. Application of gene network analysis techniques identifies AXIN1/PDIA2 and endoglin haplotypes associated with bicuspid aortic valve. Wooten EC, et al. PLoS One, 2010 Jan 21. PMID 20098615, Free PMC Article
  5. Functional proteomic analysis of human nucleolus. Scherl A, et al. Mol Biol Cell, 2002 Nov. PMID 12429849, Free PMC Article

See all (75) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. determined that the catalytic activity of hPMC2 is required for repair of abasic sites that result from estrogen-induced DNA damage
    Title: The exonuclease activity of hPMC2 is required for transcriptional regulation of the QR gene and repair of estrogen-induced abasic sites.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Application of gene network analysis techniques identifies AXIN1/PDIA2 and endoglin haplotypes associated with bicuspid aortic valve.
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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3'-5' exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding HDA PubMed 
enables double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables single-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in DNA catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in RNA processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in rRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
RNA exonuclease 4
Names
REX4, RNA exonuclease 4 homolog
XPMC2 prevents mitotic catastrophe 2 homolog
Xenopus prevents mitotic catastrophe 2 homolog
exonuclease XPMC2

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_001279349.2 → NP_001266278.1  RNA exonuclease 4 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region and lacks two coding exons, which results in a region containing a frameshift, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK304547, AL136894, BX333016
    Consensus CDS
    CCDS65179.1
    UniProtKB/TrEMBL
    A0A0C4DG31
    Related
    ENSP00000361003.2, ENST00000371935.6
    Conserved Domains (1) summary
    cl10012
    Location:114 → 222
    DnaQ_like_exo; DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily

  2. NM_001279350.2 → NP_001266279.1  RNA exonuclease 4 isoform 3

    See identical proteins and their annotated locations for NP_001266279.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site near the 5' end and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK304547, AL136894, BC009274
    UniProtKB/TrEMBL
    B4E331
    Conserved Domains (1) summary
    cd06144
    Location:107 → 257
    REX4_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins

  3. NM_001279351.1 → NP_001266280.1  RNA exonuclease 4 isoform 4

    See identical proteins and their annotated locations for NP_001266280.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' exon and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK295982, AL136894, BC009274, BM984937
    UniProtKB/TrEMBL
    B4DJ95
    Conserved Domains (2) summary
    cd06144
    Location:151 → 301
    REX4_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins
    COG0847
    Location:148 → 312
    DnaQ; DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair]

  4. NM_020385.4 → NP_065118.2  RNA exonuclease 4 isoform 1

    See identical proteins and their annotated locations for NP_065118.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL136894, BC009274, DC387839
    Consensus CDS
    CCDS6969.1
    UniProtKB/Swiss-Prot
    B2RAT2, Q5T8S4, Q5T8S5, Q5T8S6, Q9GZR2, Q9GZW3
    Related
    ENSP00000361010.3, ENST00000371942.8
    Conserved Domains (1) summary
    cd06144
    Location:244 → 394
    REX4_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins

RNA

  1. NR_103995.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
    Source sequence(s)
    AK310164, AL136894, DC387839

  2. NR_103996.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
    Source sequence(s)
    BC071691, DC387839

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    133406058..133418172 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447612.2 → XP_024303380.1  RNA exonuclease 4 isoform X1

    UniProtKB/TrEMBL
    B4E331
    Conserved Domains (1) summary
    cd06144
    Location:107 → 257
    REX4_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins

  2. XM_024447611.2 → XP_024303379.1  RNA exonuclease 4 isoform X1

    UniProtKB/TrEMBL
    B4E331
    Conserved Domains (1) summary
    cd06144
    Location:107 → 257
    REX4_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins

  3. XM_047423608.1 → XP_047279564.1  RNA exonuclease 4 isoform X2

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646201.1 Reference GRCh38.p14 PATCHES

    Range
    232152..244266 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331583.1 → XP_054187558.1  RNA exonuclease 4 isoform X1

    UniProtKB/TrEMBL
    B4E331

  2. XM_054331582.1 → XP_054187557.1  RNA exonuclease 4 isoform X1

    UniProtKB/TrEMBL
    B4E331

  3. XM_054331584.1 → XP_054187559.1  RNA exonuclease 4 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    145620490..145632600 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054363316.1 → XP_054219291.1  RNA exonuclease 4 isoform X1

    UniProtKB/TrEMBL
    B4E331

  2. XM_054363315.1 → XP_054219290.1  RNA exonuclease 4 isoform X1

    UniProtKB/TrEMBL
    B4E331

  3. XM_054363317.1 → XP_054219292.1  RNA exonuclease 4 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9GZR2.2 GenPept UniProtKB/Swiss-Prot:Q9GZR2

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