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Aliases for XRN2 Gene

Aliases for XRN2 Gene

  • 5'-3' Exoribonuclease 2 2
  • 5-3 Exoribonuclease 2 2 3 5
  • DHM1-Like Protein 4
  • DHP Protein 4
  • EC 3.1.13.- 4
  • EC 3.1.13 61

External Ids for XRN2 Gene

Previous GeneCards Identifiers for XRN2 Gene

  • GC20P021272
  • GC20P021278
  • GC20P021231

Summaries for XRN2 Gene

Entrez Gene Summary for XRN2 Gene

  • This gene encodes a 5'-3' exonuclease that promotes transcription termination at cotranscriptional cleavage sites. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

GeneCards Summary for XRN2 Gene

XRN2 (5'-3' Exoribonuclease 2) is a Protein Coding gene. Diseases associated with XRN2 include Amyotrophic Lateral Sclerosis 4, Juvenile. Among its related pathways are mRNA Splicing - Major Pathway and Chaperonin-mediated protein folding. GO annotations related to this gene include nucleic acid binding and nuclease activity.

UniProtKB/Swiss-Prot for XRN2 Gene

  • Possesses 5->3 exoribonuclease activity (By similarity). May promote the termination of transcription by RNA polymerase II. During transcription termination, cleavage at the polyadenylation site liberates a 5 fragment which is subsequently processed to form the mature mRNA and a 3 fragment which remains attached to the elongating polymerase. The processive degradation of this 3 fragment by this protein may promote termination of transcription. Binds to RNA polymerase II (RNAp II) transcription termination R-loops formed by G-rich pause sites (PubMed:21700224).

Gene Wiki entry for XRN2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for XRN2 Gene

Genomics for XRN2 Gene

Regulatory Elements for XRN2 Gene

Enhancers for XRN2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20G021505 1.5 Ensembl ENCODE dbSUPER 15.2 +202.9 202905 2.3 SIN3A ZNF2 ZNF48 GLIS2 ZNF416 ZNF143 ZNF207 ZNF202 REST GLIS1 RPS15AP1 XRN2 ENSG00000278041 NKX2-2-AS1
GH20G021322 1.4 Ensembl ENCODE 12.4 +21.1 21106 3.2 HNRNPUL1 HDGF FOXA2 PKNOX1 CREB3L1 MLX ARID4B SIN3A DMAP1 FEZF1 XRN2 RPS15AP1 GC20P021326 GC20P021304
GH20G021514 1 ENCODE dbSUPER 15.2 +210.9 210914 0.2 FOXA2 MAX ZNF76 RBBP5 ZFHX2 ZNF366 PATZ1 PRDM10 KLF8 EZH2 RPS15AP1 XRN2 NKX2-2 GC20P021523
GH20G021302 1.1 ENCODE 0.7 +0.2 241 2.9 HDGF HNRNPUL1 PKNOX1 FOXA2 MLX CREB3L1 ARID4B SIN3A FEZF1 DMAP1 KIZ ENSG00000275457 XRN2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around XRN2 on UCSC Golden Path with GeneCards custom track

Promoters for XRN2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000135490 296 2401 HDGF HNRNPUL1 PKNOX1 FOXA2 MLX CREB3L1 ARID4B SIN3A FEZF1 DMAP1

Genomic Location for XRN2 Gene

Chromosome:
20
Start:
21,303,304 bp from pter
End:
21,389,827 bp from pter
Size:
86,524 bases
Orientation:
Plus strand

Genomic View for XRN2 Gene

Genes around XRN2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
XRN2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for XRN2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for XRN2 Gene

Proteins for XRN2 Gene

  • Protein details for XRN2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H0D6-XRN2_HUMAN
    Recommended name:
    5-3 exoribonuclease 2
    Protein Accession:
    Q9H0D6
    Secondary Accessions:
    • Q3L8N4
    • Q6KGZ9
    • Q9BQL1
    • Q9NTW0
    • Q9NXS6
    • Q9UL53

    Protein attributes for XRN2 Gene

    Size:
    950 amino acids
    Molecular mass:
    108582 Da
    Quaternary structure:
    • Interacts with POLR2A and SMN1/SMN2 (PubMed:26700805). Interacts with CDKN2AIP and NKRF (PubMed:24462208). Interacts with CDKN2AIPNL; the interaction is direct (PubMed:26779609).
    SequenceCaution:
    • Sequence=AAR24369.1; Type=Frameshift; Positions=73; Evidence={ECO:0000305}; Sequence=BAA90934.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for XRN2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for XRN2 Gene

Selected DME Specific Peptides for XRN2 Gene

Q9H0D6:
  • DDWVFMCFF
  • FFVGNDFLPHLPSLEIR
  • FEKGTKPF
  • DPGWKNLTVILSDASAPGEGEHKIMDYIRRQRAQPNHDPN
  • KERFDSNCITPGTEFMDNLAKCLRYYIADRLN
  • SPVPMLRDLTQN
  • AFRTLGH
  • EDEMMVA
  • EFDNLYLDMNGIIHPCTHPED
  • FRWLSRKYP
  • EDSDSEPEPEDN
  • DGVAPRAKMNQQRSRRFR
  • PQLGFNRDR
  • YVEGLCWVLRYYYQGC
  • WQGVALLPF
  • KECNGVK
  • LGLATHEP
  • PNTHHCL
  • DFYPEDF
  • YYYQGCASW
  • PAPKNEDEM
  • VNLQRVQMIMLAVGEVEDSIFKKRKDD

Post-translational modifications for XRN2 Gene

  • Ubiquitination at Lys172, Lys517, and isoforms=2533
  • Modification sites at PhosphoSitePlus

Other Protein References for XRN2 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for XRN2 (XRN2)
  • Abcam antibodies for XRN2
  • Santa Cruz Biotechnology (SCBT) Antibodies for XRN2

Domains & Families for XRN2 Gene

Suggested Antigen Peptide Sequences for XRN2 Gene

Graphical View of Domain Structure for InterPro Entry

Q9H0D6

UniProtKB/Swiss-Prot:

XRN2_HUMAN :
  • Belongs to the 5-3 exonuclease family. XRN2/RAT1 subfamily.
Family:
  • Belongs to the 5-3 exonuclease family. XRN2/RAT1 subfamily.
genes like me logo Genes that share domains with XRN2: view

No data available for Gene Families for XRN2 Gene

Function for XRN2 Gene

Molecular function for XRN2 Gene

GENATLAS Biochemistry:
murine DHM1 gene homolog,5-3 exoribonuclease 2,highly expressed in the testis,involved in homologous recomnbination
UniProtKB/Swiss-Prot CatalyticActivity:
Exonucleolytic cleavage in the 5- to 3-direction to yield nucleoside 5-phosphates.
UniProtKB/Swiss-Prot Function:
Possesses 5->3 exoribonuclease activity (By similarity). May promote the termination of transcription by RNA polymerase II. During transcription termination, cleavage at the polyadenylation site liberates a 5 fragment which is subsequently processed to form the mature mRNA and a 3 fragment which remains attached to the elongating polymerase. The processive degradation of this 3 fragment by this protein may promote termination of transcription. Binds to RNA polymerase II (RNAp II) transcription termination R-loops formed by G-rich pause sites (PubMed:21700224).

Enzyme Numbers (IUBMB) for XRN2 Gene

Gene Ontology (GO) - Molecular Function for XRN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000175 3-5-exoribonuclease activity EXP 23482395
GO:0001147 transcription termination site sequence-specific DNA binding IDA 21700224
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IDA 22658674
genes like me logo Genes that share ontologies with XRN2: view
genes like me logo Genes that share phenotypes with XRN2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for XRN2

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for XRN2 Gene

Localization for XRN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for XRN2 Gene

Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for XRN2 gene
Compartment Confidence
nucleus 5
mitochondrion 1
cytosol 1

Gene Ontology (GO) - Cellular Components for XRN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,TAS --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA,IEA 12429849
GO:0016020 membrane IDA 19946888
GO:0016235 aggresome IDA --
genes like me logo Genes that share ontologies with XRN2: view

Pathways & Interactions for XRN2 Gene

genes like me logo Genes that share pathways with XRN2: view

Pathways by source for XRN2 Gene

Gene Ontology (GO) - Biological Process for XRN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000738 DNA catabolic process, exonucleolytic IDA 15565158
GO:0006139 nucleobase-containing compound metabolic process IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006353 DNA-templated transcription, termination IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with XRN2: view

No data available for SIGNOR curated interactions for XRN2 Gene

Transcripts for XRN2 Gene

Unigene Clusters for XRN2 Gene

5-3 exoribonuclease 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for XRN2 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^
SP1: - - -
SP2: - - - -
SP3: -
SP4: - - - - - - - - - - - - - - - - - - - - - -
SP5: -
SP6:
SP7:

ExUns: 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31a · 31b
SP1: -
SP2: -
SP3:
SP4: - - - - - - - - - -
SP5:
SP6:
SP7:

Relevant External Links for XRN2 Gene

GeneLoc Exon Structure for
XRN2
ECgene alternative splicing isoforms for
XRN2

Expression for XRN2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for XRN2 Gene

Protein differential expression in normal tissues from HIPED for XRN2 Gene

This gene is overexpressed in Lymph node (12.1), Serum (10.5), and Peripheral blood mononuclear cells (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for XRN2 Gene



Protein tissue co-expression partners for XRN2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of XRN2 Gene:

XRN2

SOURCE GeneReport for Unigene cluster for XRN2 Gene:

Hs.255932

mRNA Expression by UniProt/SwissProt for XRN2 Gene:

Q9H0D6-XRN2_HUMAN
Tissue specificity: Expressed in the spleen, thymus, prostate, testis, ovary, small intestine, colon, peripheral blood leukocytes, heart, brain, placenta, lung, liver, skeletal muscle, kidney, and pancreas. Isoform 2 is expressed predominantly in peripheral blood leukocytes.

Evidence on tissue expression from TISSUES for XRN2 Gene

  • Liver(4.4)
  • Intestine(4.3)
  • Nervous system(4.1)
  • Lung(3.1)
  • Spleen(2)
genes like me logo Genes that share expression patterns with XRN2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for XRN2 Gene

Orthologs for XRN2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for XRN2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia XRN2 34 35
  • 99.79 (n)
dog
(Canis familiaris)
Mammalia XRN2 34 35
  • 94.53 (n)
mouse
(Mus musculus)
Mammalia Xrn2 34 16 35
  • 92.35 (n)
cow
(Bos Taurus)
Mammalia XRN2 34 35
  • 91.93 (n)
oppossum
(Monodelphis domestica)
Mammalia XRN2 35
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia XRN2 35
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Xrn2 34
  • 89.94 (n)
chicken
(Gallus gallus)
Aves XRN2 34 35
  • 78.99 (n)
lizard
(Anolis carolinensis)
Reptilia XRN2 35
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia xrn2 34
  • 73.19 (n)
Str.1210 34
zebrafish
(Danio rerio)
Actinopterygii xrn2 34 35
  • 68.21 (n)
idibd1090 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8562 34
fruit fly
(Drosophila melanogaster)
Insecta Rat1 34 35
  • 56.68 (n)
CG10354 36
  • 44 (a)
pcm 36
  • 44 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004090 34
  • 54.89 (n)
worm
(Caenorhabditis elegans)
Secernentea xrn-2 34 35
  • 57.91 (n)
Y48B6A.3 36
  • 54 (a)
Y39G8C.1 36
  • 36 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RAT1 34 35 37
  • 57.22 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F07469g 34
  • 56.25 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR303W 34
  • 51.23 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons XRN3 34
  • 54.79 (n)
rice
(Oryza sativa)
Liliopsida Os01g0872700 34
  • 53.98 (n)
Os.19368 34
wheat
(Triticum aestivum)
Liliopsida Ta.27926 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10503 35
  • 57 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes dhp1 34
  • 55.06 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01643 34
  • 53.91 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2723 34
Species where no ortholog for XRN2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for XRN2 Gene

ENSEMBL:
Gene Tree for XRN2 (if available)
TreeFam:
Gene Tree for XRN2 (if available)

Paralogs for XRN2 Gene

(1) SIMAP similar genes for XRN2 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with XRN2: view

No data available for Paralogs for XRN2 Gene

Variants for XRN2 Gene

Sequence variations from dbSNP and Humsavar for XRN2 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs1000100413 -- 21,382,621(+) TTAAA(C/T)GCAGA intron-variant
rs1000113184 -- 21,319,648(+) ACTTG(C/T)TTAGT intron-variant
rs1000148428 -- 21,373,259(+) CGCCT(C/T)GTTCT intron-variant
rs1000267448 -- 21,363,501(+) CCTTG(C/T)CCTGC intron-variant
rs1000299311 -- 21,337,697(+) ATCCT(A/G)CTGCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for XRN2 Gene

Variant ID Type Subtype PubMed ID
dgv2222n106 CNV deletion 24896259
dgv7517n54 CNV gain 21841781
esv1007546 CNV deletion 20482838
esv1596170 CNV deletion 17803354
esv22449 CNV gain 19812545
esv2276285 CNV deletion 18987734
esv2458583 CNV deletion 19546169
esv2579624 CNV loss 19546169
esv2722286 CNV deletion 23290073
esv3072679 CNV deletion 24192839
esv3556931 CNV deletion 23714750
esv3645493 CNV loss 21293372
esv7933 CNV loss 19470904
nsv1063280 CNV gain 25217958
nsv1070803 CNV deletion 25765185
nsv1125720 CNV tandem duplication 24896259
nsv1151460 CNV deletion 26484159
nsv179550 CNV deletion 16902084
nsv512606 CNV loss 21212237
nsv514936 CNV loss 21397061
nsv585706 CNV loss 21841781
nsv585710 CNV gain 21841781
nsv585711 CNV loss 21841781
nsv585712 CNV loss 21841781
nsv585713 CNV loss 21841781
nsv820835 CNV deletion 20802225
nsv955127 CNV deletion 24416366

Variation tolerance for XRN2 Gene

Residual Variation Intolerance Score: 6.51% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.64; 45.53% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for XRN2 Gene

Human Gene Mutation Database (HGMD)
XRN2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
XRN2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for XRN2 Gene

Disorders for XRN2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for XRN2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
amyotrophic lateral sclerosis 4, juvenile
  • amyotrophic lateral sclerosis type 4
- elite association - COSMIC cancer census association via MalaCards
Search XRN2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for XRN2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
XRN2
genes like me logo Genes that share disorders with XRN2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for XRN2 Gene

Publications for XRN2 Gene

  1. Cloning and mapping of the XRN2 gene to human chromosome 20p11.1- p11.2. (PMID: 10409438) Zhang M. … Zhao S.Y. (Genomics 1999) 2 3 4 22 64
  2. A novel splice variant of human XRN2 gene is mainly expressed in blood leukocyte. (PMID: 16147866) Li J. … Mao Y. (DNA Seq. 2005) 3 4 22 64
  3. SMN and symmetric arginine dimethylation of RNA polymerase II C- terminal domain control termination. (PMID: 26700805) Yanling Zhao D. … Greenblatt J.F. (Nature 2015) 3 4 64
  4. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. (PMID: 21700224) Skourti-Stathaki K. … Gromak N. (Mol. Cell 2011) 3 4 64
  5. Pause sites promote transcriptional termination of mammalian RNA polymerase II. (PMID: 16648491) Gromak N. … Proudfoot N.J. (Mol. Cell. Biol. 2006) 3 4 64

Products for XRN2 Gene

Sources for XRN2 Gene

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