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    REXO5 RNA exonuclease 5 [ Homo sapiens (human) ]

    Gene ID: 81691, updated on 3-Nov-2024

    Summary

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    Official Symbol
    REXO5provided by HGNC
    Official Full Name
    RNA exonuclease 5provided by HGNC
    Primary source
    HGNC:HGNC:24661
    See related
    Ensembl:ENSG00000005189 AllianceGenome:HGNC:24661
    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
    NEF-sp
    Summary
    Predicted to enable exonuclease activity. Located in nucleolus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward testis (RPKM 183.5) See more
    Orthologs
    mouse all
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    Genomic context

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    See REXO5 in Genome Data Viewer
    Location:
    16p12.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (20806425..20849665)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (20737356..20780580)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (20817849..20860987)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene acyl-CoA synthetase medium chain family member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10535 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10539 Neighboring gene THUMP domain containing 1 Neighboring gene RNA, U6 small nuclear 944, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:20816990-20817935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10541 Neighboring gene uncharacterized LOC105371121 Neighboring gene ERI1 exoribonuclease family member 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:20878222-20878722 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:20876915-20878114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10544 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10545 Neighboring gene defective in cullin neddylation 1 domain containing 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:20911499-20912284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10546 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:20912285-20913070 Neighboring gene LYR motif containing 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:20982344-20983543 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:20985044-20985544 Neighboring gene dynein axonemal heavy chain 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7247 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:21059143-21059715 Neighboring gene uncharacterized LOC107984888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10547

    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. Characterization of the mammalian RNA exonuclease 5/NEF-sp as a testis-specific nuclear 3' → 5' exoribonuclease. Silva S, et al. RNA, 2017 Sep. PMID 28539487, Free PMC Article
    2. The Conserved RNA Exonuclease Rexo5 Is Required for 3' End Maturation of 28S rRNA, 5S rRNA, and snoRNAs. Gerstberger S, et al. Cell Rep, 2017 Oct 17. PMID 29045842, Free PMC Article
    3. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. Loftus BJ, et al. Genomics, 1999 Sep 15. PMID 10493829
    4. Acetylation-Mimic Mutation of TRIM28-Lys304 to Gln Attenuates the Interaction with KRAB-Zinc-Finger Proteins and Affects Gene Expression in Leukemic K562 Cells. Chang YJ, et al. Int J Mol Sci, 2023 Jun 6. PMID 37372979, Free PMC Article
    5. Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance. Pech MF, et al. Elife, 2019 Aug 27. PMID 31452512, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    • DKFZp434J0315

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in rRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    RNA exonuclease 5
    Names
    exonuclease NEF-sp
    putative RNA exonuclease NEF-sp

    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_001144924.2 → NP_001138396.1  RNA exonuclease 5 isoform 2

      See identical proteins and their annotated locations for NP_001138396.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC004381, AL136763, BC068503
      Consensus CDS
      CCDS45437.1
      UniProtKB/Swiss-Prot
      Q96IC2
      Related
      ENSP00000261378.8, ENST00000348433.10
      Conserved Domains (3) summary
      cd06145
      Location:229 → 377
      REX1_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins
      COG0847
      Location:258 → 394
      DnaQ; DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair]
      cl17169
      Location:571 → 641
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. NM_001199053.2 → NP_001185982.1  RNA exonuclease 5 isoform 1

      See identical proteins and their annotated locations for NP_001185982.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 both encode the same isoform (1).
      Source sequence(s)
      AC004381, AK314458, BC007646, DB059505
      Consensus CDS
      CCDS10591.1
      UniProtKB/Swiss-Prot
      B2RB19, O60364, Q96IC2, Q96MB1, Q9BXH9, Q9H0K2, Q9NSM2
      Related
      ENSP00000457616.1, ENST00000564274.5
      Conserved Domains (3) summary
      cd06145
      Location:229 → 377
      REX1_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins
      cd12273
      Location:506 → 576
      RRM1_NEFsp; RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp
      cl17169
      Location:602 → 672
      RRM_SF; RNA recognition motif (RRM) superfamily

    3. NM_030941.3 → NP_112203.2  RNA exonuclease 5 isoform 1

      See identical proteins and their annotated locations for NP_112203.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 3 both encode the same isoform (1).
      Source sequence(s)
      AC004381, BC007646
      Consensus CDS
      CCDS10591.1
      UniProtKB/Swiss-Prot
      B2RB19, O60364, Q96IC2, Q96MB1, Q9BXH9, Q9H0K2, Q9NSM2
      Related
      ENSP00000261377.6, ENST00000261377.11
      Conserved Domains (3) summary
      cd06145
      Location:229 → 377
      REX1_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins
      cd12273
      Location:506 → 576
      RRM1_NEFsp; RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp
      cl17169
      Location:602 → 672
      RRM_SF; RNA recognition motif (RRM) superfamily

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      20806425..20849665
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011545963.3 → XP_011544265.1  RNA exonuclease 5 isoform X1

      See identical proteins and their annotated locations for XP_011544265.1

      UniProtKB/Swiss-Prot
      B2RB19, O60364, Q96IC2, Q96MB1, Q9BXH9, Q9H0K2, Q9NSM2
      Conserved Domains (3) summary
      cd06145
      Location:229 → 377
      REX1_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins
      cd12273
      Location:506 → 576
      RRM1_NEFsp; RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp
      cl17169
      Location:602 → 672
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. XM_047434726.1 → XP_047290682.1  RNA exonuclease 5 isoform X2

    3. XM_005255604.3 → XP_005255661.1  RNA exonuclease 5 isoform X1

      See identical proteins and their annotated locations for XP_005255661.1

      UniProtKB/Swiss-Prot
      B2RB19, O60364, Q96IC2, Q96MB1, Q9BXH9, Q9H0K2, Q9NSM2
      Conserved Domains (3) summary
      cd06145
      Location:229 → 377
      REX1_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins
      cd12273
      Location:506 → 576
      RRM1_NEFsp; RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp
      cl17169
      Location:602 → 672
      RRM_SF; RNA recognition motif (RRM) superfamily

    4. XM_017023739.3 → XP_016879228.1  RNA exonuclease 5 isoform X2

      UniProtKB/Swiss-Prot
      Q96IC2
      Conserved Domains (3) summary
      cd06145
      Location:229 → 377
      REX1_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins
      COG0847
      Location:258 → 394
      DnaQ; DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair]
      cl17169
      Location:571 → 641
      RRM_SF; RNA recognition motif (RRM) superfamily

    5. XM_011545964.3 → XP_011544266.1  RNA exonuclease 5 isoform X3

      Conserved Domains (4) summary
      cd06145
      Location:229 → 377
      REX1_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins
      COG0847
      Location:258 → 394
      DnaQ; DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair]
      cd12273
      Location:471 → 541
      RRM1_NEFsp; RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp
      cd12274
      Location:567 → 637
      RRM2_NEFsp; RNA recognition motif 2 in vertebrate putative RNA exonuclease NEF-sp

    6. XM_011545965.3 → XP_011544267.1  RNA exonuclease 5 isoform X4

      Conserved Domains (3) summary
      cd06145
      Location:229 → 377
      REX1_like; DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins
      COG0847
      Location:258 → 394
      DnaQ; DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair]
      cl17169
      Location:536 → 606
      RRM_SF; RNA recognition motif (RRM) superfamily

    7. XM_047434727.1 → XP_047290683.1  RNA exonuclease 5 isoform X5

    8. XM_047434725.1 → XP_047290681.1  RNA exonuclease 5 isoform X1

      UniProtKB/Swiss-Prot
      B2RB19, O60364, Q96IC2, Q96MB1, Q9BXH9, Q9H0K2, Q9NSM2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      20737356..20780580
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314063.1 → XP_054170038.1  RNA exonuclease 5 isoform X1

      UniProtKB/Swiss-Prot
      B2RB19, O60364, Q96IC2, Q96MB1, Q9BXH9, Q9H0K2, Q9NSM2

    2. XM_054314062.1 → XP_054170037.1  RNA exonuclease 5 isoform X1

      UniProtKB/Swiss-Prot
      B2RB19, O60364, Q96IC2, Q96MB1, Q9BXH9, Q9H0K2, Q9NSM2

    3. XM_054314066.1 → XP_054170041.1  RNA exonuclease 5 isoform X2

    4. XM_054314065.1 → XP_054170040.1  RNA exonuclease 5 isoform X2

    5. XM_054314067.1 → XP_054170042.1  RNA exonuclease 5 isoform X3

    6. XM_054314068.1 → XP_054170043.1  RNA exonuclease 5 isoform X4

    7. XM_054314069.1 → XP_054170044.1  RNA exonuclease 5 isoform X5

    8. XM_054314064.1 → XP_054170039.1  RNA exonuclease 5 isoform X1

      UniProtKB/Swiss-Prot
      B2RB19, O60364, Q96IC2, Q96MB1, Q9BXH9, Q9H0K2, Q9NSM2
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96IC2.1 GenPept UniProtKB/Swiss-Prot:Q96IC2

    Gene LinkOut

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

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