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NUDT21 nudix hydrolase 21 [ Homo sapiens (human) ]

Gene ID: 11051, updated on 17-Jun-2024

Summary

Official Symbol
NUDT21provided by HGNC
Official Full Name
nudix hydrolase 21provided by HGNC
Primary source
HGNC:HGNC:13870
See related
Ensembl:ENSG00000167005 MIM:604978; AllianceGenome:HGNC:13870
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CPSF5; CFIM25
Summary
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]
Expression
Ubiquitous expression in brain (RPKM 30.7), ovary (RPKM 29.1) and 25 other tissues See more
Orthologs
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Genomic context

See NUDT21 in Genome Data Viewer
Location:
16q13
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (56429133..56451332, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (62224204..62246406, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (56463045..56485244, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene G protein subunit alpha o1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56297649-56298217 Neighboring gene microRNA 3935 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56311207-56311706 Neighboring gene Sharpr-MPRA regulatory region 182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:56316059-56316608 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:56316609-56317156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56318360-56318881 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56322213-56322875 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56337209-56337709 Neighboring gene NANOG hESC enhancer GRCh37_chr16:56339811-56340312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56346109-56347085 Neighboring gene Sharpr-MPRA regulatory region 3823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56379271-56379958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56382339-56382839 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:56389828-56389987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10848 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:56396251-56396424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56396447-56396947 Neighboring gene autocrine motility factor receptor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7508 Neighboring gene 2-oxoglutarate and iron dependent oxygenase domain containing 1 Neighboring gene Sharpr-MPRA regulatory region 6357 Neighboring gene Bardet-Biedl syndrome 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10851 Neighboring gene uncharacterized LOC105371283

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify cleavage and polyadenylation specificity factor 5 (CPSF5; NUDT21), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify cleavage and polyadenylation specificity factor 5 (CPSF5; NUDT21), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify cleavage and polyadenylation specificity factor 5 (CPSF5; NUDT21), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify cleavage and polyadenylation specificity factor 5 (CPSF5; NUDT21), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • DKFZp686H1588

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
contributes_to RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
 
enables histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables identical protein binding IDA
Inferred from Direct Assay
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables mRNA 3'-UTR AU-rich region binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables mRNA 3'-UTR AU-rich region binding IDA
Inferred from Direct Assay
more info
PubMed 
enables mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in mRNA 3'-end processing IDA
Inferred from Direct Assay
more info
PubMed 
involved_in mRNA alternative polyadenylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in mRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in mRNA processing IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of pro-B cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of stem cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in post-transcriptional regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in protein heterotetramerization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein tetramerization IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in centriolar satellite IDA
Inferred from Direct Assay
more info
 
located_in centrosome IDA
Inferred from Direct Assay
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
part_of mRNA cleavage and polyadenylation specificity factor complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of mRNA cleavage factor complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of mRNA cleavage factor complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of mRNA cleavage factor complex IPI
Inferred from Physical Interaction
more info
PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in paraspeckles IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
cleavage and polyadenylation specificity factor subunit 5
Names
CPSF 25 kDa subunit
cleavage and polyadenylation specific factor 5, 25 kD subunit
cleavage and polyadenylation specific factor 5, 25 kDa
cleavage and polyadenylation specificity factor 25 kDa subunit
cleavage factor Im complex 25 kDa subunit
nucleoside diphosphate-linked moiety X motif 21
nudix (nucleoside diphosphate linked moiety X)-type motif 21
nudix motif 21
pre-mRNA cleavage factor Im (25kD)
pre-mRNA cleavage factor Im 25 kDa subunit
pre-mRNA cleavage factor Im 68 kDa subunit
pre-mRNA cleavage factor Im, 25kD subunit

NCBI Reference Sequences (RefSeq)

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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_007006.3NP_008937.1  cleavage and polyadenylation specificity factor subunit 5

    See identical proteins and their annotated locations for NP_008937.1

    Status: REVIEWED

    Source sequence(s)
    AC092140, AL535307, BC001403
    Consensus CDS
    CCDS10760.1
    UniProtKB/Swiss-Prot
    O43809, Q6IB85, Q6NE84
    UniProtKB/TrEMBL
    B2R6U8
    Related
    ENSP00000300291.5, ENST00000300291.10
    Conserved Domains (1) summary
    pfam13869
    Location:35222
    NUDIX_2; Nucleotide hydrolase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    56429133..56451332 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    62224204..62246406 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)