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    Ubp1 upstream binding protein 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 301038, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Ubp1provided by RGD
    Official Full Name
    upstream binding protein 1provided by RGD
    Primary source
    RGD:1564700
    See related
    EnsemblRapid:ENSRNOG00000009729 AllianceGenome:RGD:1564700
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1564700
    Summary
    Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of viral transcription and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within angiogenesis. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Orthologous to human UBP1 (upstream binding protein 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 133.2), Lung (RPKM 112.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ubp1 in Genome Data Viewer
    Location:
    8q32
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (122748005..122793824)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (113869771..113915625)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (122196576..122241368)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene cytoplasmic linker associated protein 2 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene uncharacterized LOC120094275 Neighboring gene F-box and leucine-rich repeat protein 2 Neighboring gene COP9 signalosome subunit 7B, pseudogene 1 Neighboring gene U6 spliceosomal RNA Neighboring gene sushi domain containing 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Defective extraembryonic angiogenesis in mice lacking LBP-1a, a member of the grainyhead family of transcription factors. Parekh V, et al. Mol Cell Biol, 2004 Aug. PMID 15282311, Free PMC Article
    2. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within angiogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of viral transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    upstream-binding protein 1
    Names
    upstream binding protein 1 (LBP-1a)

    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_001191819.2 → NP_001178748.1  upstream-binding protein 1

      Status: VALIDATED

      Source sequence(s)
      BQ780402, FM039161, FM064075, FN798828, JAXUCZ010000008
      UniProtKB/TrEMBL
      A0A8I6GFC7
      Related
      ENSRNOP00000086807.1, ENSRNOT00000112819.2
      Conserved Domains (2) summary
      cd09588
      Location:369 → 435
      SAM_LBP1; SAM domain of LBP1 (UBP1) transcription factors
      pfam04516
      Location:50 → 254
      CP2; CP2 transcription factor

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086026.1 Reference GRCr8

      Range
      122748005..122793824
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039081289.2 → XP_038937217.1  upstream-binding protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6GFC7
      Related
      ENSRNOP00000102156.1, ENSRNOT00000151156.1
      Conserved Domains (2) summary
      cd09588
      Location:369 → 435
      SAM_LBP1; SAM domain of LBP1 (UBP1) transcription factors
      pfam04516
      Location:50 → 254
      CP2; CP2 transcription factor

    2. XM_063265297.1 → XP_063121367.1  upstream-binding protein 1 isoform X5

      UniProtKB/TrEMBL
      D4A030

    3. XM_039081290.2 → XP_038937218.1  upstream-binding protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6GFC7
      Conserved Domains (2) summary
      cd09588
      Location:369 → 435
      SAM_LBP1; SAM domain of LBP1 (UBP1) transcription factors
      pfam04516
      Location:50 → 254
      CP2; CP2 transcription factor

    4. XM_063265298.1 → XP_063121368.1  upstream-binding protein 1 isoform X5

      UniProtKB/TrEMBL
      D4A030

    5. XM_039081291.2 → XP_038937219.1  upstream-binding protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6GFC7
      Conserved Domains (2) summary
      cd09588
      Location:369 → 435
      SAM_LBP1; SAM domain of LBP1 (UBP1) transcription factors
      pfam04516
      Location:50 → 254
      CP2; CP2 transcription factor

    6. XM_063265299.1 → XP_063121369.1  upstream-binding protein 1 isoform X5

      UniProtKB/TrEMBL
      D4A030

    7. XM_006243962.3 → XP_006244024.2  upstream-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6GFC7
      Related
      ENSRNOP00000013050.7, ENSRNOT00000013050.8
      Conserved Domains (2) summary
      cd09588
      Location:422 → 488
      SAM_LBP1; SAM domain of LBP1 (UBP1) transcription factors
      pfam04516
      Location:139 → 343
      CP2; CP2 transcription factor

    8. XM_039081288.2 → XP_038937216.1  upstream-binding protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6GFC7
      Conserved Domains (2) summary
      pfam04516
      Location:139 → 343
      CP2; CP2 transcription factor
      cl15755
      Location:458 → 514
      SAM_superfamily; SAM (Sterile alpha motif )

    9. XM_039081292.2 → XP_038937220.1  upstream-binding protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A8I6GFC7
      Conserved Domains (2) summary
      pfam04516
      Location:139 → 343
      CP2; CP2 transcription factor
      cl15755
      Location:458 → 512
      SAM_superfamily; SAM (Sterile alpha motif )

    10. XM_039081293.2 → XP_038937221.1  upstream-binding protein 1 isoform X6

      Conserved Domains (2) summary
      cd09588
      Location:217 → 283
      SAM_LBP1; SAM domain of LBP1 (UBP1) transcription factors
      pfam04516
      Location:2 → 102
      CP2; CP2 transcription factor

    RNA

    1. XR_005487800.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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