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UPF3A UPF3A regulator of nonsense mediated mRNA decay [ Homo sapiens (human) ]

Gene ID: 65110, updated on 25-Jan-2022

Summary

Official Symbol
UPF3Aprovided by HGNC
Official Full Name
UPF3A regulator of nonsense mediated mRNA decayprovided by HGNC
Primary source
HGNC:HGNC:20332
See related
Ensembl:ENSG00000169062 MIM:605530; AllianceGenome:HGNC:20332
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
UPF3; HUPF3A; RENT3A
Summary
This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome 13. Several splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]
Expression
Ubiquitous expression in testis (RPKM 21.9), thyroid (RPKM 13.7) and 25 other tissues See more
Orthologs
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Genomic context

See UPF3A in Genome Data Viewer
Location:
13q34
Exon count:
14
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (114281598..114305817)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (115047076..115071292)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene cell division cycle 16 Neighboring gene microRNA 548ar Neighboring gene uncharacterized LOC105370384 Neighboring gene microRNA 4502 Neighboring gene Charcot-Leyden crystal protein pseudogene 2 Neighboring gene chromosome alignment maintaining phosphoprotein 1

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ35267, FLJ57970

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables structural constituent of nuclear pore NAS
Non-traceable Author Statement
more info
PubMed 
enables telomeric DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables telomeric DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytoplasm NAS
Non-traceable Author Statement
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
part_of exon-exon junction complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of exon-exon junction complex TAS
Traceable Author Statement
more info
PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
regulator of nonsense transcripts 3A
Names
UPF3 regulator of nonsense transcripts homolog A
hUpf3
nonsense mRNA reducing factor 3A
up-frameshift suppressor 3 homolog A

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.

Genomic

  1. NG_029528.1 RefSeqGene

    Range
    5018..29234
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001353644.2NP_001340573.1  regulator of nonsense transcripts 3A isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), as well as variants 4-7, encodes isoform c.
    Source sequence(s)
    AL160396
    Conserved Domains (1) summary
    cl28310
    Location:89257
    Rho; Transcription termination factor Rho [Transcription]
  2. NM_001353645.1NP_001340574.1  regulator of nonsense transcripts 3A isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), as well as variants 3 and 5-7, encodes isoform c.
    Source sequence(s)
    AL160396
    Conserved Domains (1) summary
    cl28310
    Location:89257
    Rho; Transcription termination factor Rho [Transcription]
  3. NM_001353646.1NP_001340575.1  regulator of nonsense transcripts 3A isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5), as well as variants 3, 4, 6, and 7, encodes isoform c.
    Source sequence(s)
    AL160396
    Conserved Domains (1) summary
    cl28310
    Location:89257
    Rho; Transcription termination factor Rho [Transcription]
  4. NM_001353647.1NP_001340576.1  regulator of nonsense transcripts 3A isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6), as well as variants 3-5 and 7, encodes isoform c.
    Source sequence(s)
    AL160396
    Conserved Domains (1) summary
    cl28310
    Location:89257
    Rho; Transcription termination factor Rho [Transcription]
  5. NM_001353648.2NP_001340577.1  regulator of nonsense transcripts 3A isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7), as well as variants 3-6, encodes isoform c.
    Source sequence(s)
    AL160396
    Conserved Domains (1) summary
    cl28310
    Location:89257
    Rho; Transcription termination factor Rho [Transcription]
  6. NM_001353649.1NP_001340578.1  regulator of nonsense transcripts 3A isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8), as well as variant 9, encodes isoform d.
    Source sequence(s)
    AL160396
    Conserved Domains (1) summary
    cl28310
    Location:85253
    Rho; Transcription termination factor Rho [Transcription]
  7. NM_001353650.1NP_001340579.1  regulator of nonsense transcripts 3A isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9), as well as variant 8, encodes isoform d.
    Source sequence(s)
    AL160396
    Conserved Domains (1) summary
    cl28310
    Location:85253
    Rho; Transcription termination factor Rho [Transcription]
  8. NM_001353651.2NP_001340580.1  regulator of nonsense transcripts 3A isoform e

    Status: REVIEWED

    Source sequence(s)
    AL160396
    Conserved Domains (1) summary
    cd12727
    Location:66149
    RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)
  9. NM_001353652.2NP_001340581.1  regulator of nonsense transcripts 3A isoform f

    Status: REVIEWED

    Source sequence(s)
    AL160396
    Conserved Domains (1) summary
    cd12727
    Location:66152
    RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)
  10. NM_023011.4NP_075387.1  regulator of nonsense transcripts 3A isoform hUpf3p

    See identical proteins and their annotated locations for NP_075387.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (Upf3p).
    Source sequence(s)
    AY013250, BC008694, BQ008047
    Consensus CDS
    CCDS9543.1
    UniProtKB/Swiss-Prot
    Q9H1J1
    Related
    ENSP00000364448.3, ENST00000375299.8
    Conserved Domains (1) summary
    pfam03467
    Location:65225
    Smg4_UPF3; Smg-4/UPF3 family
  11. NM_080687.3NP_542418.1  regulator of nonsense transcripts 3A isoform hUpf3pdelta

    See identical proteins and their annotated locations for NP_542418.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to transcript variant 1. The resulting isoform (hUpf3pdelta) lacks an internal segment, compared to isoform hUpf3p.
    Source sequence(s)
    AY013250, BC023569, BQ008047
    Consensus CDS
    CCDS9544.1
    UniProtKB/Swiss-Prot
    Q9H1J1
    Related
    ENSP00000329592.5, ENST00000351487.5
    Conserved Domains (2) summary
    cd12727
    Location:66149
    RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)
    cl28310
    Location:257440
    Rho; Transcription termination factor Rho [Transcription]

RNA

  1. NR_148482.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396, BC047735
  2. NR_148483.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  3. NR_148484.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  4. NR_148485.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  5. NR_148486.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  6. NR_148487.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  7. NR_148488.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  8. NR_148489.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  9. NR_148490.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  10. NR_148491.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  11. NR_148492.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  12. NR_148493.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
    Related
    ENST00000475218.2
  13. NR_148494.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  14. NR_148495.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396
  15. NR_148496.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160396

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    114281598..114305817
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534844.1XP_011533146.1  regulator of nonsense transcripts 3A isoform X1

    Conserved Domains (1) summary
    cd12727
    Location:66150
    RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)
  2. XM_017020709.1XP_016876198.1  regulator of nonsense transcripts 3A isoform X2

    Conserved Domains (1) summary
    cl17169
    Location:1095
    RRM_SF; RNA recognition motif (RRM) superfamily
  3. XM_011534845.2XP_011533147.1  regulator of nonsense transcripts 3A isoform X2

    See identical proteins and their annotated locations for XP_011533147.1

    Conserved Domains (1) summary
    cl17169
    Location:1095
    RRM_SF; RNA recognition motif (RRM) superfamily
  4. XM_011534848.2XP_011533150.1  regulator of nonsense transcripts 3A isoform X4

    See identical proteins and their annotated locations for XP_011533150.1

    UniProtKB/TrEMBL
    B3KUE7
    Conserved Domains (1) summary
    cl28310
    Location:89257
    Rho; Transcription termination factor Rho [Transcription]
  5. XM_011534846.1XP_011533148.1  regulator of nonsense transcripts 3A isoform X3

    Conserved Domains (1) summary
    pfam03467
    Location:65225
    Smg4_UPF3; Smg-4/UPF3 family
  6. XM_024449402.1XP_024305170.1  regulator of nonsense transcripts 3A isoform X5

    Conserved Domains (1) summary
    cd12727
    Location:66152
    RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)
  7. XM_024449403.1XP_024305171.1  regulator of nonsense transcripts 3A isoform X6

    Conserved Domains (1) summary
    cd12727
    Location:66152
    RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)
  8. XM_017020711.1XP_016876200.1  regulator of nonsense transcripts 3A isoform X4

    UniProtKB/TrEMBL
    B3KUE7
    Conserved Domains (1) summary
    cl28310
    Location:89257
    Rho; Transcription termination factor Rho [Transcription]
  9. XM_005266202.4XP_005266259.1  regulator of nonsense transcripts 3A isoform X4

    See identical proteins and their annotated locations for XP_005266259.1

    UniProtKB/TrEMBL
    B3KUE7
    Conserved Domains (1) summary
    cl28310
    Location:89257
    Rho; Transcription termination factor Rho [Transcription]
  10. XM_006719991.4XP_006720054.1  regulator of nonsense transcripts 3A isoform X2

    See identical proteins and their annotated locations for XP_006720054.1

    Conserved Domains (1) summary
    cl17169
    Location:1095
    RRM_SF; RNA recognition motif (RRM) superfamily
  11. XM_011534847.2XP_011533149.1  regulator of nonsense transcripts 3A isoform X4

    See identical proteins and their annotated locations for XP_011533149.1

    UniProtKB/TrEMBL
    B3KUE7
    Conserved Domains (1) summary
    cl28310
    Location:89257
    Rho; Transcription termination factor Rho [Transcription]
  12. XM_024449400.1XP_024305168.1  regulator of nonsense transcripts 3A isoform X4

    Conserved Domains (1) summary
    cl28310
    Location:89257
    Rho; Transcription termination factor Rho [Transcription]
  13. XM_024449401.1XP_024305169.1  regulator of nonsense transcripts 3A isoform X4

    Conserved Domains (1) summary
    cl28310
    Location:89257
    Rho; Transcription termination factor Rho [Transcription]

RNA

  1. XR_001749647.2 RNA Sequence

  2. XR_001749644.2 RNA Sequence

  3. XR_941422.3 RNA Sequence

  4. XR_001749646.2 RNA Sequence

  5. XR_001749649.2 RNA Sequence

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