UPF1 Gene
protein-coding GIFtS: 60
GCID: GC19P018942
|
|
UPF1 regulator of nonsense transcripts homolog (yeast)(Previous name: regulator of nonsense transcripts 1 )
(Previous symbol: RENT1)
| |
Aliases
for UPF1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| UPF1 Regulator Of Nonsense Transcripts Homolog (Yeast)1 2 | | ATP-Dependent Helicase RENT12 3 | | RENT11 2 3 5 | | Delta Helicase2 | | NORF11 2 3 | | Smg-2 Homolog, Nonsense Mediated MRNA Decay Factor2 | | HUPF11 2 | | UP Frameshift 12 | | PNORF11 | | Up-Frameshift Mutation 1 Homolog2 | | Regulator Of Nonsense Transcripts 11 2 | | Yeast Upf1p Homolog2 | | Smg-21 | | EC 3.6.4.-3 | | KIAA02211 3 | | HUpf11 | | Nonsense MRNA Reducing Factor 12 3 | | EC 3.6.18 | | Up-Frameshift Suppressor 1 Homolog2 3 | | |
Export aliases for UPF1 gene to outside databasesPrevious GC identifers: GC19P018804 GC19P018507 |
Summaries
for UPF1 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for UPF1:
This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear exportand mRNA surveillance. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiatesnonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMDto degrade mRNAs containing premature stop codons. This protein is located only in the cytoplasm. When translationends, it interacts with the protein that is a functional homolog of yeast Upf2p to trigger mRNA decapping. Use ofmultiple polyadenylation sites has been noted for this gene. (provided by RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: RENT1_HUMAN, Q92900Function: RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing prematurestop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation anddephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalledribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. InEJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotidesdownstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complexwhich is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought toprovide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serveas adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling ofNMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJCindicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end ofphase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiationof NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. TheATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability
Gene Wiki entry for UPF1
|
Genomic Views
for UPF1 gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000019.9 NC_018930.1 NT_011295.11
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the UPF1 gene promoter:
Nkx2-5
Other transcription factors
Search SABiosciences Chromatin IP Primers for UPF1
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat UPF1 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 19p13.2-p13.11 Ensembl cytogenetic band: 19p13.11 HGNC cytogenetic band: 19p13.2-p13.11UPF1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 19 GeneLoc Exon Structure GeneLoc location for GC19P018942: view genomic region
(about GC identifiers)
Start:
|
18,942,744 bp from pter |
End:
|
18,979,039 bp from pter |
Size:
|
36,296 bases |
Orientation:
|
plus strand |
|
Proteins
for UPF1 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: RENT1_HUMAN, Q92900 (See
protein sequence)Recommended Name: Regulator of nonsense transcripts 1 Size: 1129 amino acids; 124345 Da
Subunit: Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex(EJC). Associates with the SGM1C complex; is phosphorylated by the complex kinase component SGM1. Interacts with UPF2,UPF3A and UPF3B. Interacts with EST1A and SLBP. Interacts (when hyperphosphorylated) with PNRC2. Interacts withEIF2C1, EIF2C2 and GSPT2. Interacts with isoform 1 and isoform 5 of ADAR/ADAR1
Subcellular location: Cytoplasm. Cytoplasm, P-body. Nucleus. Note=Hyperphosphorylated form is targeted to the P-body,while unphosphorylated protein is distributed throughout the cytoplasm
Sequence caution: Sequence=BAA19664.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
6/8 PDB 3D structures from  and Proteopedia  for UPF1 (see all 8):2GJK (3D)
2GK6 (3D)
2GK7 (3D)
2IYK (3D)
2WJV (3D)
2WJY (3D)
Secondary accessions: O00239 O43343 Q86Z25 Q92842Alternative splicing: 2 isoforms: Q92900-1 Q92900-2 Explore the universe of human proteins at neXtProt for UPF1: NX_Q92900
Post-translational modifications:
Phosphorylated by SMG1; required for formation of mRNA surveillance complexes1
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q92900
4/17 DME Specific Peptides for UPF1 (Q92900) (see all 17)
UPF1 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_002902.2
ENSEMBL proteins: ENSP00000262803 Reactome Protein details: Q92900
Human Recombinant Protein Products for UPF1:
Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7): About this table
UPF1 for ontologies About GeneDecksing
UPF1 Antibody Products:
Assay Products for UPF1: |
Protein
Domains /
Families
for UPF1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
UPF1 for domains About GeneDecksing
1 InterPro domain/family:Graphical View of Domain Structure for InterPro Entry Q92900ProtoNet protein and cluster: Q92900 UniProtKB/Swiss-Prot: RENT1_HUMAN, Q92900Domain: The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase familySimilarity: Belongs to the DNA2/NAM7 helicase familySimilarity: Contains 1 UPF1-type zinc finger |
Function
for UPF1 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Sirion Biotech,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Molecular Function:
UniProtKB/Swiss-Prot Summary: RENT1_HUMAN, Q92900Function: RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing prematurestop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation anddephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalledribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. InEJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotidesdownstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complexwhich is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought toprovide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serveas adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling ofNMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJCindicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end ofphase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiationof NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. TheATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability Enzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.4.-1
Gene Ontology (GO): 5/8 molecular function terms (GO ID links to tree view) (see all 8): About this table
UPF1 for ontologies About GeneDecksing
Phenotypes:
2 GenomeRNAi human phenotypes for UPF1:
4 MGI mutant phenotypes (inferred from 1 allele ) (MGI details for Upf1):
UPF1 for phenotypes About GeneDecksing
Animal Models:
Mouse knock-out Upf1tm1Hcd for UPF1
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for UPF1 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for UPF1 (see all 2)
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: UPF1 (NM_002911) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for UPF1 | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat UPF1 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UPF1 |
|
Pathways & Interactions
for UPF1 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
|
Unified GeneCards pathways - 5/7 super-pathways (see all 7) About this table
See pathways by source
| Super-pathway | contained gene-specific pathways |
|---|
| 1 | Synthesis of PB1-F2 | | | 2 | Metabolism of mRNA | | | 3 | Decay of mRNA in SMG6:SMG5:SMG7:mRNA Complex | | | 4 | mRNA surveillance pathway | | | 5 | RNA transport | |
Pathway sources
See GeneCards unified pathways
Show all pathways
1 
Cell Signaling Technology (CST) Pathway for UPF1
5/9 
Reactome Pathways for UPF1 (see all 9)
2 
Kegg Pathways (Kegg details for UPF1):
UPF1 for pathways About GeneDecksing
Interactions:
SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for UPF1
STRING Interaction
Network Preview (showing 5 interactants - click image to see 25)
5/952 Interacting proteins for UPF1 (Q929001, 2, 3 ENSP000002628034) via UniProtKB, MINT, STRING, and/or I2D (see all 952)| Interactant | Interaction Details |
|---|
| GeneCard | External ID(s) |
|---|
| UPF2 | Q9HAU51, 2, 3, ENSP000003487084 | EBI-373471,EBI-372073 MINT-6539840 MINT-7904432 MINT-6539908 MINT-7904445 MINT-7945693 MINT-7904564 MINT-4791496 MINT-7904530 MINT-6539883 MINT-7904547 MINT-7904417 MINT-7904495 MINT-7904598 MINT-7947479 MINT-6539859 MINT-7904478 MINT-7904581 MINT-7904403 MINT-7904512 MINT-7904458 I2D:
score=9 STRING: ENSP00000348708 | | GSPT1 | P151702, 3, ENSP000003981314 | MINT-6539771 MINT-6539822 MINT-7945693 MINT-6539753 I2D:
score=1 STRING: ENSP00000398131 | | ETF1 | P624952, 3, ENSP000003537414 | MINT-7945693 MINT-6539753 MINT-7947479 I2D:
score=3 STRING: ENSP00000353741 | | TERT | O147462, 3, ENSP000003095724 | MINT-8286561 MINT-8286551 MINT-8286579 I2D:
score=1 STRING: ENSP00000309572 | | PSMD12 | O002322, 3, ENSP000003484424 | MINT-7945693 MINT-7947479 I2D:
score=5 STRING: ENSP00000348442 |
About this table
Gene Ontology (GO): 5/11 biological process terms (GO ID links to tree view) (see all 11): About this table
UPF1 for ontologies About GeneDecksing
|
Drugs & Compounds
for UPF1 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
UPF1 for compounds About GeneDecksing
 Browse Tocris compounds for UPF1
4 Novoseek chemical compound relationships for UPF1 gene About this table
Search CenterWatch for drugs/clinical trials and news about UPF1 / RENT1
|
Transcripts
for UPF1 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
Sirion Biotech,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for UPF1 gene: NM_002911.3 Unigene Cluster for UPF1: UPF1 regulator of nonsense transcripts homolog (yeast) Hs.515266 [show with all ESTs]Unigene Representative Sequence: NM_0029111 Ensembl transcript including schematic representation, and UCSC links where relevant: ENST00000262803(uc002nkf.3 uc002nkg.3 uc002nkh.3)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for UPF1 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for UPF1 (see all 2)
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: UPF1 (NM_002911) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for UPF1 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat UPF1 |
Additional cDNA sequence: AF074016.1 AK125797.1 AK128727.1 BC034291.1 BC039817.1 D86988.1 U59323.1 U65533.1 23 DOTS entries: DT.100822434 DT.456245 DT.97802108 DT.100801983 DT.92441421 DT.40289544 DT.121468677 DT.95190426 DT.100822424 DT.100822429 DT.100822431 DT.102828678 DT.121468685 DT.121468688 DT.121468701 DT.121468708 DT.121468718 DT.91947800 DT.91968174 DT.92441407 DT.97801452 DT.100822428 DT.92441406 24/431 AceView cDNA sequences (see all 431): D86988 BM742246 BG288234 BX384942 BU431219 BQ439866 BU727281 BQ271175 BM016503 AA412091 AK125797 AA705513 AW009890 BI050221 CA946823 BF508927 CD364377 BM764737 CR614589 AW272624 BQ950083 BM693677 NM_002911 AI569472
GeneLoc Exon Structure
5/13 Alternative Splicing Database (ASD) splice patterns (SP) for UPF1 (see all 13) About this scheme
| ExUns: | 1a | · | 1b | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12a | · | 12b | · | 12c | · | 12d | · | 12e | ^ | 13a | · | 13b | · | 13c | ^ | 14 | ^ | 15 | ^ | 16 | ^ | 17a | · | 17b | ^ | 18 | ^ |
|---|
|
| SP1: | | | | | - | | | | | | - | | - | | - | | - | | | | | | - | | | | | | | | | | | | | | | | - | | | | | | | | | | | | | | |
| SP2: | | | | | - | | | | | | - | | - | | - | | - | | | | | | - | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP3: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP4: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| ExUns: | 19 | ^ | 20 | ^ | 21 | ^ | 22a | · | 22b | ^ | 23a | · | 23b | ^ | 24 | ^ | 25a | · | 25b | ^ | 26a | · | 26b | ^ | 27 | ^ | 28 | ^ | 29 | ^ | 30 | ^ | 31 |
|---|
|
| SP1: | | | | | | | - | | | | - | | | | | | | | | | - | | | | | | | | | | | | | | |
| SP2: | | | | | | | - | | | | - | | | | | | | | | | - | | | | | | | | | | | | | | |
| SP3: | | | | | | | | | | | - | | | | | | | | | | - | | | | | | | | | | | | | | |
| SP4: | | | | | | | - | | | | - | | | | | | | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
ECgene alternative splicing isoforms for UPF1
|
Expression
for UPF1 gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| UPF1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: CACCGGGTAG
About this image
See UPF1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for UPF1
SOURCE GeneReport for Unigene cluster: Hs.515266
UniProtKB/Swiss-Prot: RENT1_HUMAN, Q92900Tissue specificity: Ubiquitous
SABiosciences Custom PCR Arrays for UPF1
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for UPF1
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat UPF1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat UPF1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat UPF1 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UPF1 |
Orthologs
for UPF1 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of eukaryotes.
Orthologs for UPF1 gene from 9/37 species (see all 37) About this table
| Organism |
Taxonomic
classification |
Gene |
Description |
Human
Similarity |
Orthology
Type |
Details |
mouse
(Mus musculus) |
Mammalia |
Upf11 , 5 |
UPF1 regulator of nonsense transcripts homolog (yeast)1, 5 |
88.92(n)1
98.92(a)1 |
|
8 (34.15 cM)5
197041 NM_001122829.11 NP_001116301.11
703315225 |
chicken
(Gallus gallus) |
Aves |
UPF11 |
UPF1 regulator of nonsense transcripts homolog (yeast) |
81.08(n)
97.87(a) |
|
420119 XM_418237.3 XP_418237.3 |
African clawed frog
(Xenopus laevis) |
Amphibia |
Xl.105472 |
Xenopus laevis transcribed sequence with strong similarity more |
79.67(n) |
|
BU914294.1 |
zebrafish
(Danio rerio) |
Actinopterygii |
Dr.135942 |
Danio rerio mRNA similar to regulator of nonsense transcripts more |
82.95(n) |
|
BC045353.1 |
fruit fly
(Drosophila melanogaster) |
Insecta |
Upf11 |
CG1559-PA |
68.46(n)
71.44(a) |
|
32153 NM_132539.2 NP_572767.1 |
worm
(Caenorhabditis elegans) |
Secernentea |
smg-21 |
Protein SMG-2 |
54.6(n)
52.86(a) |
|
171696 NM_058428.3 NP_490829.1 |
baker's yeast
(Saccharomyces cerevisiae) |
Saccharomycetes |
NAM7(YMR080C)4
NAM71 |
ATP-dependent RNA helicase of the SFI superfamily involved more4
Nam7p1 |
53.86(n)1
56.88(a)1 |
|
13(429627-426712)4
8551041, 4 NP_013797.11, 4 |
thale cress
(Arabidopsis thaliana) |
eudicotyledons |
LBA11 |
Regulator of nonsense transcripts 1-like protein |
58.41(n)
63.94(a) |
|
834747 NM_124072.2 NP_199512.2 |
rice
(Oryza sativa) |
Liliopsida |
Os.188372 |
Oryza sativa (japonica cultivar-group) cDNA cloneJ more |
72.8(n) |
|
AK067729.1 |
ENSEMBL Gene Tree for UPF1 (if available)
TreeFam Gene Tree for UPF1 (if available) |
Paralogs
for UPF1 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for UPF1 gene
- ZNFX12 AQR2 C4orf212
UPF1 for paralogs About GeneDecksing
|
Genomic Variants
for UPF1 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
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|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 19 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for UPF1 (18942744 - 18979039 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for UPF1: -- | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing UPF1 |
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Disorders
/ Diseases
for UPF1 gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
UPF1 for disorders About GeneDecksing
OMIM gene information: 601430
OMIM disorders: --
13  diseases for UPF1: About MalaCardsullrich congenital muscular dystrophy amyotrophic lateral sclerosis (als) amyotrophic lateral sclerosis congenital muscular dystrophy
long qt syndrome muscular dystrophy lateral sclerosis colon cancer
gastric cancer colorectal cancer prostate cancer prostatitis
malaria
1 disease from the University of Copenhagen DISEASES database for UPF1:Ullrich congenital muscular dystrophy Export disorders for UPF1 gene to outside databases
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Publications
for UPF1 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for UPF1 gene, integrated from 9 sources (see all 124):
(articles sorted by number of sources associating them with UPF1) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Cloning and characterization of HUPF1, a human homolog of the Saccharomyces cerevisiae nonsense mRNA-reducing UPF1 protein. (PubMed id 9064659)1, 2, 3, 9 Applequist S.E.... Jaeck H.-M. (1997)
- Mammalian orthologues of a yeast regulator of nonsense transcript stability. (PubMed id 8855285)1, 2, 3, 9 Perlick H.A....Dietz H.C. (1996)
- Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1. (PubMed id 12554878)1, 2, 9 Chiu S.-Y.... Maquat L.E. (2003)
- Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay. (PubMed id 16452507)1, 2, 9 Kashima I....Ohno S. (2006)
- SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway. (PubMed id 15721257)1, 2, 9 Fukuhara N....Conti E. (2005)
- SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay. (PubMed id 19417104)1, 2, 9 Yamashita A....Ohno S. (2009)
- Characterization of the biochemical properties of the human Upf1 gene product that is involved in nonsense-mediated mRNA decay. (PubMed id 10999600)1, 2, 9 Bhattacharya A....Peltz S.W. (2000)
- Human proline-rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex. (PubMed id 19150429)1, 2, 9 Cho H.... Kim Y.K. (2009)
- Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1. (PubMed id 16086026)1, 2, 9 Kaygun H. and Marzluff W.F. (2005)
- Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein. (PubMed id 11331269)1, 2, 9 Denning G.... Fields A.P. (2001)
|
External Searches for UPF1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
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|
|
Genome Databases showing UPF1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
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|
|
Other Databases showing UPF1 gene
(According to HUGE)
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| |
Specialized Databases showing UPF1 gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for UPF1 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for UPF1 gene:
Search GeneIP for patents involving UPF1
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for UPF1 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section
|
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 | |
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