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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 63

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 type 4 and setx. Among its related pathways are Gene Expression and Transport to the Golgi and subsequent modification. 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 Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for XRN2 Gene

Genomics for XRN2 Gene

Regulatory Elements for XRN2 Gene

Promoters for XRN2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around XRN2 on UCSC Golden Path with GeneCards custom track

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.
    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

Proteomics data for XRN2 Gene at MOPED

Post-translational modifications for XRN2 Gene

  • Ubiquitination at Lys 172, Lys 517, and Lys 533
  • Modification sites at PhosphoSitePlus

Other Protein References for XRN2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for XRN2 (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.
  • Contains 1 CCHC-type zinc finger.
Family:
  • Belongs to the 5-3 exonuclease family. XRN2/RAT1 subfamily.
Similarity:
  • Contains 1 CCHC-type zinc finger.
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:0003676 nucleic acid binding IEA --
GO:0004518 nuclease activity TAS 10409438
GO:0004527 exonuclease activity IEA --
GO:0004534 5-3 exoribonuclease activity IEA,TAS 10409438
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

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
Jensen Localization Image for XRN2 Gene COMPARTMENTS Subcellular localization image for XRN2 gene
Compartment Confidence
nucleus 5
cytosol 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for XRN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,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

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:0006353 DNA-templated transcription, termination IEA --
GO:0006364 rRNA processing TAS --
GO:0006401 RNA catabolic process TAS 10409438
GO:0016070 RNA metabolic process IEA,ISS --
genes like me logo Genes that share ontologies with XRN2: view

No data available for SIGNOR curated interactions for XRN2 Gene

Drugs & Compounds for XRN2 Gene

No Compound Related Data Available

Transcripts for XRN2 Gene

mRNA/cDNA for XRN2 Gene

Unigene Clusters for XRN2 Gene

5-3 exoribonuclease 2:
Representative Sequences:

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 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, MOPED, and MaxQB for XRN2 Gene



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.
genes like me logo Genes that share expression patterns with XRN2: view

Protein tissue co-expression partners for XRN2 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues 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 36
  • 100 (a)
OneToOne
XRN2 35
  • 99.79 (n)
  • 99.79 (a)
cow
(Bos Taurus)
Mammalia XRN2 35
  • 91.93 (n)
  • 95.89 (a)
XRN2 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia XRN2 36
  • 96 (a)
OneToOne
XRN2 35
  • 94.53 (n)
  • 98 (a)
mouse
(Mus musculus)
Mammalia Xrn2 16
Xrn2 36
  • 96 (a)
OneToOne
Xrn2 35
  • 92.35 (n)
  • 96.11 (a)
oppossum
(Monodelphis domestica)
Mammalia XRN2 36
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia XRN2 36
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Xrn2 35
  • 89.94 (n)
  • 95.36 (a)
chicken
(Gallus gallus)
Aves XRN2 35
  • 78.99 (n)
  • 83.47 (a)
XRN2 36
  • 83 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia XRN2 36
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.1210 35
xrn2 35
  • 73.19 (n)
  • 77.19 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8562 35
zebrafish
(Danio rerio)
Actinopterygii xrn2 36
  • 71 (a)
OneToOne
idibd1090 35
xrn2 35
  • 68.21 (n)
  • 73.28 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004090 35
  • 54.89 (n)
  • 59.11 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG10354 37
  • 44 (a)
pcm 37
  • 44 (a)
Rat1 35
  • 56.68 (n)
  • 59.82 (a)
Rat1 36
  • 52 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea xrn-2 35
  • 57.91 (n)
  • 58.96 (a)
Y39G8C.1 37
  • 36 (a)
Y48B6A.3 37
  • 54 (a)
xrn-2 36
  • 51 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR303W 35
  • 51.23 (n)
  • 48.15 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RAT1 35
  • 57.22 (n)
  • 54.43 (a)
RAT1 36
  • 38 (a)
OneToOne
RAT1 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F07469g 35
  • 56.25 (n)
  • 52 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons XRN3 35
  • 54.79 (n)
  • 48.12 (a)
rice
(Oryza sativa)
Liliopsida Os.19368 35
Os01g0872700 35
  • 53.98 (n)
  • 50.32 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.27926 35
bread mold
(Neurospora crassa)
Ascomycetes NCU01643 35
  • 53.91 (n)
  • 50.97 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes dhp1 35
  • 55.06 (n)
  • 51.54 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2723 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10503 36
  • 57 (a)
OneToOne
Species with no ortholog for XRN2:
  • 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
rs6137324 - 21,357,765(+) GTTAA(A/G)GGATC reference, missense
rs6047420 - 21,386,992(+) ATGAT(C/T)GTGGA reference, missense
rs202824 -- 21,308,674(+) tcttc(A/G)gttgt intron-variant
rs202825 -- 21,309,996(+) gggtt(C/T)aactt intron-variant
rs202826 -- 21,310,784(+) gtgtc(A/G)cccag intron-variant

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

Variant ID Type Subtype PubMed ID
nsv912813 CNV Loss 21882294
esv1007546 CNV Deletion 20482838
esv2458583 CNV Deletion 19546169
esv2579624 CNV Loss 19546169
nsv820835 CNV Deletion 20802225
esv2276285 CNV Deletion 18987734
esv2722286 CNV Deletion 23290073
nsv512606 CNV Loss 21212237
esv7933 CNV Loss 19470904
esv1596170 CNV Deletion 17803354
esv22449 CNV Gain 19812545
nsv514936 CNV Loss 21397061
nsv179550 CNV Loss 16902084

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

HapMap Linkage Disequilibrium report
XRN2
Human Gene Mutation Database (HGMD)
XRN2

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

Disorders for XRN2 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
amyotrophic lateral sclerosis type 4
  • amyotrophic lateral sclerosis 4, juvenile
setx
- 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 23 67
  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 23
  3. Dissecting the roles of the 5' exoribonucleases Xrn1 and Xrn2 in restricting hepatitis C virus replication. (PMID: 25673723) Li Y. … Lemon S.M. (J. Virol. 2015) 3
  4. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3
  5. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3

Products for XRN2 Gene

Sources for XRN2 Gene

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