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

    Gene ID: 57109, updated on 10-Dec-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, Dec 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 10.2), testis (RPKM 9.8) and 25 other tissues See more
    Orthologs
    mouse all
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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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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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    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_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

    Gene LinkOut

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

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