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Aliases for XRN2 Gene

Aliases for XRN2 Gene

  • 5'-3' Exoribonuclease 2 2
  • 5-3 Exoribonuclease 2 2 3
  • 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 shares similarity with the mouse Dhm1 and the yeast dhp1 gene. The yeast gene is involved in homologous recombination and RNA metabolism, such as RNA synthesis and RNA trafficking. Complementation studies show that Dhm1 has a similar function in mouse as dhp1. The function of the human gene has not yet been determined. Transcript variants encoding different isoforms have been noted for this gene; however, their full-length nature is not known. [provided by RefSeq, Jul 2008]

GeneCards Summary for XRN2 Gene

XRN2 (5'-3' Exoribonuclease 2) is a Protein Coding gene. Among its related pathways are Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein and Protein folding. GO annotations related to this gene include nucleic acid binding and 5-3 exonuclease 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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for XRN2 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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:
    No Data Available
    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 Lys172, Lys517, and Lys533
  • Modification sites at PhosphoSitePlus

Other Protein References for XRN2 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for XRN2 (XRN2)

Domains for XRN2 Gene

Suggested Antigen Peptide Sequences for XRN2 Gene

Graphical View of Domain Structure for InterPro Entry

Q9H0D6

UniProtKB/Swiss-Prot:

XRN2_HUMAN :
  • Q9H0D6
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:0001147 transcription termination site sequence-specific DNA binding IDA 21700224
GO:0003676 nucleic acid binding --
GO:0004518 nuclease activity TAS 10409438
GO:0004527 exonuclease activity --
GO:0004534 5-3 exoribonuclease activity TAS 10409438
genes like me logo Genes that share ontologies with XRN2: view

Animal Model Products

CRISPR Products

miRNA for XRN2 Gene

miRTarBase miRNAs that target XRN2

No data available for Phenotypes , Animal Models , Transcription Factor Targeting 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 IDA --
GO:0005730 nucleolus IDA --
GO:0016020 membrane IDA 19946888
GO:0016235 aggresome IDA --
genes like me logo Genes that share ontologies with XRN2: view

Pathways 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 --
GO:0006353 DNA-templated transcription, termination IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006396 RNA processing TAS 10409438
genes like me logo Genes that share ontologies with XRN2: view

Transcripts for XRN2 Gene

mRNA/cDNA for XRN2 Gene

Unigene Clusters for XRN2 Gene

5-3 exoribonuclease 2:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for XRN2

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for XRN2

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 for XRN2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression 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 expressions with XRN2: view

In Situ Assay Products

No data available for 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 35
  • 99.79 (n)
  • 99.79 (a)
XRN2 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia XRN2 35
  • 91.93 (n)
  • 95.89 (a)
XRN2 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia XRN2 35
  • 94.53 (n)
  • 98 (a)
XRN2 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Xrn2 35
  • 92.35 (n)
  • 96.11 (a)
Xrn2 16
Xrn2 36
  • 96 (a)
OneToOne
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 idibd1090 35
xrn2 35
  • 68.21 (n)
  • 73.28 (a)
xrn2 36
  • 71 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004090 35
  • 54.89 (n)
  • 59.11 (a)
fruit fly
(Drosophila melanogaster)
Insecta Rat1 35
  • 56.68 (n)
  • 59.82 (a)
Rat1 36
  • 52 (a)
OneToOne
pcm 37
  • 44 (a)
CG10354 37
  • 44 (a)
worm
(Caenorhabditis elegans)
Secernentea xrn-2 35
  • 57.91 (n)
  • 58.96 (a)
xrn-2 36
  • 51 (a)
OneToOne
Y48B6A.3 37
  • 54 (a)
Y39G8C.1 37
  • 36 (a)
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

Selected 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 MAF
rs14953 -- 21,389,636(-) GAATA(A/C)ACTGT utr-variant-3-prime
rs202823 -- 21,308,173(+) ctcaa(A/G)tatct intron-variant
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

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

No disorders were found for XRN2 Gene.

No data available for UniProtKB/Swiss-Prot 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
  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 23
  3. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S. … Poustka A. (Genome Res. 2001) 3 4
  4. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P. … Rogers J. (Nature 2001) 3 4
  5. Functional proteomic analysis of human nucleolus. (PMID: 12429849) Scherl A. … Diaz J.-J. (Mol. Biol. Cell 2002) 3 4

Products for XRN2 Gene

Sources for XRN2 Gene

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