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

Gene ID: 301038, updated on 10-Oct-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, Apr 2022]
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 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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