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

    Gene ID: 65110, updated on 2-Nov-2024

    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
    NEW
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    Try the new Transcript table

    Genomic context

    See UPF3A in Genome Data Viewer
    Location:
    13q34
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (114281601..114305817)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (113490661..113514877)
    RS_2024_09 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 ATAC-STARR-seq lymphoblastoid active region 8062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5559 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:115047057-115047744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5561 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:115049711-115049907 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:115057299-115057800 Neighboring gene uncharacterized LOC124903222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:115057801-115058300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:115060371-115060872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8066 Neighboring gene Sharpr-MPRA regulatory region 14980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5563 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 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

    General gene information

    Clone Names

    • FLJ35267, FLJ57970

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables mRNA binding PubMed 
    enables protein binding PubMed 
    enables telomeric DNA binding  
    enables telomeric DNA binding PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm  
    located_in cytoplasm PubMed 
    located_in cytosol  
    located_in cytosol  
    part_of exon-exon junction complex PubMed 
    part_of exon-exon junction complex PubMed 
    located_in intracellular membrane-bounded organelle  
    located_in neuron projection  
    is_active_in nucleolus  
    located_in nucleoplasm  
    located_in nucleus 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)

    NEW Try the new Transcript table

    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
      UniProtKB/TrEMBL
      B3KUE7
      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
      UniProtKB/TrEMBL
      B3KUE7
      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
      UniProtKB/TrEMBL
      B3KUE7
      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
      UniProtKB/TrEMBL
      B3KUE7
      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
      UniProtKB/TrEMBL
      B3KUE7
      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
      A2A366, Q5T8C3, Q5T8C9, Q7Z6N3, Q86YK1, Q9BZI8, 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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      114281601..114305817
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011534844.2XP_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_047430546.1XP_047286502.1  regulator of nonsense transcripts 3A isoform X4

    3. XM_047430549.1XP_047286505.1  regulator of nonsense transcripts 3A isoform X8

    4. XM_011534846.2XP_011533148.1  regulator of nonsense transcripts 3A isoform X3

      Conserved Domains (1) summary
      pfam03467
      Location:65225
      Smg4_UPF3; Smg-4/UPF3 family
    5. XM_024449402.2XP_024305170.1  regulator of nonsense transcripts 3A isoform X7

      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)
    6. XM_024449403.2XP_024305171.1  regulator of nonsense transcripts 3A isoform X9

      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_047430547.1XP_047286503.1  regulator of nonsense transcripts 3A isoform X5

    8. XM_011534845.3XP_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
    9. XM_047430548.1XP_047286504.1  regulator of nonsense transcripts 3A isoform X6

      UniProtKB/TrEMBL
      B3KUE7
    10. XM_024449401.2XP_024305169.1  regulator of nonsense transcripts 3A isoform X6

      UniProtKB/TrEMBL
      B3KUE7
      Conserved Domains (1) summary
      cl28310
      Location:89257
      Rho; Transcription termination factor Rho [Transcription]

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      113490661..113514877
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374866.1XP_054230841.1  regulator of nonsense transcripts 3A isoform X1

    2. XM_054374869.1XP_054230844.1  regulator of nonsense transcripts 3A isoform X4

    3. XM_054374873.1XP_054230848.1  regulator of nonsense transcripts 3A isoform X8

    4. XM_054374868.1XP_054230843.1  regulator of nonsense transcripts 3A isoform X3

    5. XM_054374872.1XP_054230847.1  regulator of nonsense transcripts 3A isoform X7

    6. XM_054374874.1XP_054230849.1  regulator of nonsense transcripts 3A isoform X10

    7. XM_054374875.1XP_054230850.1  regulator of nonsense transcripts 3A isoform X9

    8. XM_054374870.1XP_054230845.1  regulator of nonsense transcripts 3A isoform X5

    9. XM_054374867.1XP_054230842.1  regulator of nonsense transcripts 3A isoform X2

    10. XM_054374871.1XP_054230846.1  regulator of nonsense transcripts 3A isoform X6

      UniProtKB/TrEMBL
      B3KUE7
    11. XM_054374876.1XP_054230851.1  regulator of nonsense transcripts 3A isoform X6

      UniProtKB/TrEMBL
      B3KUE7
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