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Aliases for NUDT21 Gene

Aliases for NUDT21 Gene

  • Nudix Hydrolase 21 2 3 5
  • Cleavage And Polyadenylation Specificity Factor 25 KDa Subunit 3 4
  • Cleavage And Polyadenylation Specific Factor 5, 25 KD Subunit 2 3
  • Nudix (Nucleoside Diphosphate Linked Moiety X)-Type Motif 21 2 3
  • Cleavage And Polyadenylation Specific Factor 5, 25 KDa 2 3
  • Nucleoside Diphosphate-Linked Moiety X Motif 21 3 4
  • Pre-MRNA Cleavage Factor Im 25 KDa Subunit 3 4
  • Cleavage Factor Im Complex 25 KDa Subunit 2 3
  • CPSF 25 KDa Subunit 3 4
  • Nudix Motif 21 3 4
  • CFIM25 3 4
  • CPSF5 3 4
  • Cleavage And Polyadenylation Specificity Factor Subunit 5 3
  • Pre-MRNA Cleavage Factor Im, 25kD Subunit 3
  • Pre-MRNA Cleavage Factor Im (25kD) 3
  • CPSF25 4

External Ids for NUDT21 Gene

Previous HGNC Symbols for NUDT21 Gene

  • CPSF5

Previous GeneCards Identifiers for NUDT21 Gene

  • GC16M055021
  • GC16M042333

Summaries for NUDT21 Gene

Entrez Gene Summary for NUDT21 Gene

  • The protein encoded by this gene is one subunit of a cleavage factor required for 3' RNA cleavage and polyadenylation processing. The interaction of the protein with the RNA is one of the earliest steps in the assembly of the 3' end processing complex and facilitates the recruitment of other processing factors. This gene encodes the 25kD subunit of the protein complex, which is composed of four polypeptides. [provided by RefSeq, Jul 2008]

GeneCards Summary for NUDT21 Gene

NUDT21 (Nudix Hydrolase 21) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include poly(A) RNA binding and RNA binding.

UniProtKB/Swiss-Prot for NUDT21 Gene

  • Component of the cleavage factor Im (CFIm) complex that plays a key role in pre-mRNA 3-processing. Involved in association with CPSF6 or CPSF7 in pre-MRNA 3-end poly(A) site cleavage and poly(A) addition. NUDT21/CPSF5 binds to cleavage and polyadenylation RNA substrates. The homodimer mediates simultaneous sequence-specific recognition of two 5-UGUA-3 elements within the pre-mRNA. Binds to, but does not hydrolyze mono- and di-adenosine nucleotides. May have a role in mRNA export.

Gene Wiki entry for NUDT21 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NUDT21 Gene

Genomics for NUDT21 Gene

Regulatory Elements for NUDT21 Gene

Enhancers for NUDT21 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
GH16G057315 1.7 FANTOM5 Ensembl ENCODE dbSUPER 22.9 -864.2 -864240 2.1 TBP HDGF YBX1 PLRG1 ZBTB40 ZNF366 GATA2 ETV6 FOS RELB NUDT21 ENSG00000260545 RPL23AP91 TRL-CAG2-2
GH16G056450 1.1 ENCODE 34.2 +0.7 685 3.0 HDGF PKNOX1 FOXA2 CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 BBS2 NUDT21 OGFOD1 RSPRY1 NUP93 MT4
GH16G056930 1.4 ENCODE dbSUPER 24.6 -483.3 -483320 10.1 CREB3L1 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF416 ZNF143 SP3 RSPRY1 NUP93 NUDT21 POLR2C CETP SLC12A3 ENSG00000261270 NLRC5 ENSG00000272372 ARL2BP
GH16G057132 1.3 Ensembl ENCODE dbSUPER 24 -682.1 -682121 4.6 CTCF PKNOX1 PLRG1 EBF1 RAD21 ZNF316 ZNF366 ZNF143 SMC3 IKZF2 FAM192A NUDT21 CPNE2 RSPRY1 PLLP LOC105371289 GC16P057096
GH16G057101 0.8 dbSUPER 24 -651.5 -651466 5.2 BCOR ESRRA ETV1 ZMYM3 PLRG1 ZIC2 ZNF121 ZNF366 SCRT2 NR2F6 NUDT21 FAM192A RSPRY1 CPNE2 CIAPIN1 BBS2 GC16P057096 LOC105371289
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NUDT21 on UCSC Golden Path with GeneCards custom track

Promoters for NUDT21 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000086279 699 2201 HDGF PKNOX1 FOXA2 CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2

Genomic Location for NUDT21 Gene

Chromosome:
16
Start:
56,429,133 bp from pter
End:
56,452,199 bp from pter
Size:
23,067 bases
Orientation:
Minus strand

Genomic View for NUDT21 Gene

Genes around NUDT21 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NUDT21 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NUDT21 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NUDT21 Gene

Proteins for NUDT21 Gene

  • Protein details for NUDT21 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43809-CPSF5_HUMAN
    Recommended name:
    Cleavage and polyadenylation specificity factor subunit 5
    Protein Accession:
    O43809
    Secondary Accessions:
    • Q6IB85
    • Q6NE84

    Protein attributes for NUDT21 Gene

    Size:
    227 amino acids
    Molecular mass:
    26227 Da
    Quaternary structure:
    • Homodimer. Component of the cleavage factor Im (CFIm) complex, composed of, at least, NUDT21/CPSF5 and CPSF6 or CPSF7. Within the cleavage factor Im complex, the NUDT21/CPSF5 homodimer is at the core of a heterotetramer, and is clasped by two additional subunits (CPSF6 or CPSF7). Interacts with CPSF6, CPSF7, PABPN1 and SNRNP70. Interacts with PAPOLA; the interaction is diminished by acetylation.

    Three dimensional structures from OCA and Proteopedia for NUDT21 Gene

neXtProt entry for NUDT21 Gene

Post-translational modifications for NUDT21 Gene

  • Acetylated mainly by p300/CBP, recruited to the complex by CPSF6. Acetylation decreases interaction with PAPAO. Deacetylated by the class I/II HDACs, HDAC1, HDAC3 and HDAC10, and by the class III HDACs, SIRT1 AND SIRT2.
  • Ubiquitination at posLast=5656 and Lys182
  • Modification sites at PhosphoSitePlus

Other Protein References for NUDT21 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NUDT21 Gene

Domains & Families for NUDT21 Gene

Gene Families for NUDT21 Gene

Protein Domains for NUDT21 Gene

Suggested Antigen Peptide Sequences for NUDT21 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O43809

UniProtKB/Swiss-Prot:

CPSF5_HUMAN :
  • Belongs to the Nudix hydrolase family. CPSF5 subfamily.
Family:
  • Belongs to the Nudix hydrolase family. CPSF5 subfamily.
genes like me logo Genes that share domains with NUDT21: view

Function for NUDT21 Gene

Molecular function for NUDT21 Gene

UniProtKB/Swiss-Prot Function:
Component of the cleavage factor Im (CFIm) complex that plays a key role in pre-mRNA 3-processing. Involved in association with CPSF6 or CPSF7 in pre-MRNA 3-end poly(A) site cleavage and poly(A) addition. NUDT21/CPSF5 binds to cleavage and polyadenylation RNA substrates. The homodimer mediates simultaneous sequence-specific recognition of two 5-UGUA-3 elements within the pre-mRNA. Binds to, but does not hydrolyze mono- and di-adenosine nucleotides. May have a role in mRNA export.

Gene Ontology (GO) - Molecular Function for NUDT21 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 contributes_to RNA binding IDA,IEA 8626397
GO:0003729 mRNA binding IEA,IDA 21295486
GO:0005515 protein binding IPI 11716503
GO:0016787 hydrolase activity IEA --
GO:0017091 AU-rich element binding IDA 20479262
genes like me logo Genes that share ontologies with NUDT21: view
genes like me logo Genes that share phenotypes with NUDT21: view

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NUDT21 Gene

Localization for NUDT21 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NUDT21 Gene

Nucleus. Note=In punctate subnuclear structures localized adjacent to nuclear speckles, called paraspeckles.

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 NUDT21 gene
Compartment Confidence
nucleus 5
cytoskeleton 4
mitochondrion 2
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for NUDT21 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 20695905
GO:0005654 nucleoplasm TAS --
GO:0005813 centrosome IDA --
GO:0005815 microtubule organizing center IDA --
GO:0005849 mRNA cleavage factor complex IEA,IDA 20695905
genes like me logo Genes that share ontologies with NUDT21: view

Pathways & Interactions for NUDT21 Gene

genes like me logo Genes that share pathways with NUDT21: view

Pathways by source for NUDT21 Gene

Gene Ontology (GO) - Biological Process for NUDT21 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006378 mRNA polyadenylation IEA,IMP 20695905
GO:0006397 mRNA processing IDA,IEA 8626397
GO:0031124 mRNA 3-end processing TAS --
genes like me logo Genes that share ontologies with NUDT21: view

No data available for SIGNOR curated interactions for NUDT21 Gene

Transcripts for NUDT21 Gene

Unigene Clusters for NUDT21 Gene

Nudix (nucleoside diphosphate linked moiety X)-type motif 21:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NUDT21 Gene

No ASD Table

Relevant External Links for NUDT21 Gene

GeneLoc Exon Structure for
NUDT21
ECgene alternative splicing isoforms for
NUDT21

Expression for NUDT21 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NUDT21 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NUDT21 Gene



Protein tissue co-expression partners for NUDT21 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NUDT21 Gene:

NUDT21

SOURCE GeneReport for Unigene cluster for NUDT21 Gene:

Hs.528834

Evidence on tissue expression from TISSUES for NUDT21 Gene

  • Nervous system(4.8)
  • Eye(4.2)
  • Liver(4.2)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with NUDT21: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NUDT21 Gene

Orthologs for NUDT21 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NUDT21 Gene

Organism Taxonomy Gene Similarity Type Details
oppossum
(Monodelphis domestica)
Mammalia NUDT21 35
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia NUDT21 34 35
  • 99.85 (n)
dog
(Canis familiaris)
Mammalia NUDT21 34 35
  • 95.3 (n)
cow
(Bos Taurus)
Mammalia NUDT21 34 35
  • 94.42 (n)
mouse
(Mus musculus)
Mammalia Nudt21 34 16 35
  • 93.69 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NUDT21 35
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nudt21 34
  • 92.07 (n)
chicken
(Gallus gallus)
Aves NUDT21 34 35
  • 85.32 (n)
lizard
(Anolis carolinensis)
Reptilia NUDT21 35
  • 98 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nudt21 34
  • 81.35 (n)
Str.6398 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.3893 34
zebrafish
(Danio rerio)
Actinopterygii cpsf5 34 35
  • 79.15 (n)
zgc63966 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8490 34
fruit fly
(Drosophila melanogaster)
Insecta CG3689 34 35
  • 70.03 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007242 34
  • 67.41 (n)
worm
(Caenorhabditis elegans)
Secernentea cfim-1 34 35
  • 64.94 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G25550 34
  • 59.97 (n)
soybean
(Glycine max)
eudicotyledons Gma.4672 34
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.8939 34
rice
(Oryza sativa)
Liliopsida Os04g0683100 34
  • 58.96 (n)
Os.12933 34
barley
(Hordeum vulgare)
Liliopsida Hv.9029 34
wheat
(Triticum aestivum)
Liliopsida Ta.7293 34
corn
(Zea mays)
Liliopsida Zm.4316 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4504 35
  • 76 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU09014 34
  • 54.5 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13848 34
Species where no ortholog for NUDT21 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for NUDT21 Gene

ENSEMBL:
Gene Tree for NUDT21 (if available)
TreeFam:
Gene Tree for NUDT21 (if available)

Paralogs for NUDT21 Gene

(1) SIMAP similar genes for NUDT21 Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for NUDT21 Gene

genes like me logo Genes that share paralogs with NUDT21: view

No data available for Paralogs for NUDT21 Gene

Variants for NUDT21 Gene

Sequence variations from dbSNP and Humsavar for NUDT21 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs1000562495 -- 56,441,385(+) GTGCC(C/T)GCCAC intron-variant
rs1000838469 -- 56,432,980(+) AATTT(G/T)ATTAA intron-variant
rs1001794402 -- 56,442,645(+) AGAGG(C/T)AAGGC intron-variant
rs1002322328 -- 56,447,699(+) AAATG(A/C)ATGAC intron-variant
rs1002723474 -- 56,432,495(+) AGTAT(C/G)AGCAG utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for NUDT21 Gene

Variant ID Type Subtype PubMed ID
esv3638695 CNV gain 21293372
nsv833242 CNV loss 17160897
nsv833243 CNV gain 17160897
nsv978153 CNV duplication 23825009

Variation tolerance for NUDT21 Gene

Residual Variation Intolerance Score: 41.4% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NUDT21 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NUDT21

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NUDT21 Gene

Disorders for NUDT21 Gene

Relevant External Links for NUDT21

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NUDT21

No disorders were found for NUDT21 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NUDT21 Gene

Publications for NUDT21 Gene

  1. Human pre-mRNA cleavage factor Im is related to spliceosomal SR proteins and can be reconstituted in vitro from recombinant subunits. (PMID: 9659921) Rueegsegger U. … Keller W. (Mol. Cell 1998) 2 3 4 64
  2. Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping. (PMID: 21295486) Yang Q. … Doublie S. (Structure 2011) 3 4 64
  3. Evidence that cleavage factor Im is a heterotetrameric protein complex controlling alternative polyadenylation. (PMID: 20695905) Kim S. … Yamaguchi Y. (Genes Cells 2010) 3 4 64
  4. Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing. (PMID: 20479262) Yang Q. … Doublie S. (Proc. Natl. Acad. Sci. U.S.A. 2010) 3 4 64
  5. Crystal structure of the 25 kDa subunit of human cleavage factor Im. (PMID: 18445629) Coseno M. … Doublie S. (Nucleic Acids Res. 2008) 3 4 64

Products for NUDT21 Gene

Sources for NUDT21 Gene

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