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    UBP1 upstream binding protein 1 [ Homo sapiens (human) ]

    Gene ID: 7342, updated on 27-Nov-2024

    Summary

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    Official Symbol
    UBP1provided by HGNC
    Official Full Name
    upstream binding protein 1provided by HGNC
    Primary source
    HGNC:HGNC:12507
    See related
    Ensembl:ENSG00000153560 MIM:609784; AllianceGenome:HGNC:12507
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LBP1A; LBP1B; LBP-1B; LBP-1a
    Summary
    Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of viral transcription and positive regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 21.9), appendix (RPKM 18.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See UBP1 in Genome Data Viewer
    Location:
    3p22.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (33388336..33441399, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (33390109..33443172, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (33429828..33481897, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:33194307-33195506 Neighboring gene sushi domain containing 5 Neighboring gene Sharpr-MPRA regulatory region 10469 Neighboring gene uncharacterized LOC124909362 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14185 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:33318889-33319056 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14186 Neighboring gene F-box and leucine rich repeat protein 2 Neighboring gene MPRA-validated peak4597 silencer Neighboring gene MPRA-validated peak4598 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:33467587-33468144 Neighboring gene RNA, U7 small nuclear 110 pseudogene Neighboring gene Sharpr-MPRA regulatory region 11903 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:33480902-33481136 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:33481355-33481854 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19649 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:33487995-33488496 Neighboring gene uncharacterized LOC124909363 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:33489631-33490130 Neighboring gene NANOG hESC enhancer GRCh37_chr3:33504525-33505078 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:33508920-33510119 Neighboring gene RNA, 5S ribosomal pseudogene 128

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Repression of HIV-1 transcription by a cellular protein. Kato H, et al. Science, 1991 Mar 22. PMID 2006421
    2. Identification of the UBP1 locus as a critical blood pressure determinant using a combination of mouse and human genetics. Koutnikova H, et al. PLoS Genet, 2009 Aug. PMID 19662162, Free PMC Article
    3. Transactivation activity of LBP-1 proteins and their dimerization in living cells. Katsura A, et al. Genes Cells, 2009 Oct. PMID 19751393
    4. Characterization of a family of related cellular transcription factors which can modulate human immunodeficiency virus type 1 transcription in vitro. Yoon JB, et al. Mol Cell Biol, 1994 Mar. PMID 8114710, Free PMC Article
    5. Inhibition of HIV-1 TAR RNA-Tat peptide complexation using poly(acrylic acid). Zhao H, et al. Biochem Biophys Res Commun, 2004 Jul 16. PMID 15207707

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Studies reveal that TFCP2, TFCP2L1, UBP1 belong to a transcription factors subfamily and involved in various aspects of cancer types and development as either proto-oncogenes or tumor suppressors. They can directly interact with each other; TFCP2, TFCP2L1 and UBP1 can form heteromeric DNA-binding complexes. In addition, TFCP2L1 can modulate the activity of TFCP2 and UBP1. [review]
      Title: TFCP2/TFCP2L1/UBP1 transcription factors in cancer.
    2. Data revealed that dimers composed of LBP-1a and LBP-1c were re-formed probably by a partner-exchange of LBP-1b-containing heterodimers.
      Title: Transactivation activity of LBP-1 proteins and their dimerization in living cells.
    3. UBP1 is a critical blood pressure determinant using a combination of mouse and human genetics.
      Title: Identification of the UBP1 locus as a critical blood pressure determinant using a combination of mouse and human genetics.
    4. LBP-1b and LBP-9 both stimulate LBP-32/MGR promoter activity.
      Title: LBP-1b, LBP-9, and LBP-32/MGR detected in syncytiotrophoblasts from first-trimester human placental tissue and their transcriptional regulation.
    5. LBP-1b is an important SF1-independent transcriptional activator stimulating P450scc expression in human placental JEG-3 cells, whereas LBP-9 modulates the action of LBP-1b, exerting both positive and negative effects
      Title: LBP proteins modulate SF1-independent expression of P450scc in human placental JEG-3 cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Combination of LBP-1 and Oct1 cellular transcription activators represses transcription initiation at the HIV-1 LTR promoter by HIV-1 Tat PubMed
    tat A novel function of LBP-1, restricting HIV-1 transcription at the level of elongation, is suppressed by HIV-1 Tat PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp686L1745

    Gene Ontology Provided by GOA

    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in angiogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of viral transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    upstream-binding protein 1
    Names
    transcription factor LBP-1

    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_001128160.2 → NP_001121632.1  upstream-binding protein 1 isoform LBP-1a

      See identical proteins and their annotated locations for NP_001121632.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the mid-coding region compared to variant 1. The resulting isoform (LBP-1a) is shorter than isoform a.
      Source sequence(s)
      AC093114, AK023274, AL831847, BC047235
      Consensus CDS
      CCDS46788.1
      UniProtKB/TrEMBL
      A8KAN5
      Related
      ENSP00000395558.2, ENST00000447368.6
      Conserved Domains (2) summary
      cd09588
      Location:333 → 399
      SAM_LBP1; SAM domain of LBP1 (UBP1) transcription factors
      pfam04516
      Location:54 → 254
      CP2; CP2 transcription factor

    2. NM_001128161.2 → NP_001121633.1  upstream-binding protein 1 isoform LBP-1b

      See identical proteins and their annotated locations for NP_001121633.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 encode the same isoform (LBP-1b).
      Source sequence(s)
      AK293100, AL831847, BC047235, DB131031
      Consensus CDS
      CCDS2659.1
      UniProtKB/Swiss-Prot
      Q68CT0, Q86Y57, Q9H8V0, Q9NZI7, Q9UD76, Q9UD78
      UniProtKB/TrEMBL
      A8KAN5
      Related
      ENSP00000283628.5, ENST00000283628.9
      Conserved Domains (2) summary
      cd09588
      Location:369 → 435
      SAM_LBP1; SAM domain of LBP1 (UBP1) transcription factors
      pfam04516
      Location:54 → 254
      CP2; CP2 transcription factor

    3. NM_014517.5 → NP_055332.3  upstream-binding protein 1 isoform LBP-1b

      See identical proteins and their annotated locations for NP_055332.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (LBP-1b). Variants 1 and 3 encode the same isoform.
      Source sequence(s)
      AC093114, AF198487, AK023274, AL831847, BC047235
      Consensus CDS
      CCDS2659.1
      UniProtKB/Swiss-Prot
      Q68CT0, Q86Y57, Q9H8V0, Q9NZI7, Q9UD76, Q9UD78
      UniProtKB/TrEMBL
      A8KAN5
      Related
      ENSP00000283629.3, ENST00000283629.8
      Conserved Domains (2) summary
      cd09588
      Location:369 → 435
      SAM_LBP1; SAM domain of LBP1 (UBP1) transcription factors
      pfam04516
      Location:54 → 254
      CP2; CP2 transcription factor

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      33388336..33441399 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448847.1 → XP_047304803.1  upstream-binding protein 1 isoform X2

    2. XM_047448846.1 → XP_047304802.1  upstream-binding protein 1 isoform X1

    3. XM_047448849.1 → XP_047304805.1  upstream-binding protein 1 isoform X4

    4. XM_047448848.1 → XP_047304804.1  upstream-binding protein 1 isoform X3

    RNA

    1. XR_007095724.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      33390109..33443172 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347741.1 → XP_054203716.1  upstream-binding protein 1 isoform X2

    2. XM_054347740.1 → XP_054203715.1  upstream-binding protein 1 isoform X1

    3. XM_054347743.1 → XP_054203718.1  upstream-binding protein 1 isoform X4

    4. XM_054347742.1 → XP_054203717.1  upstream-binding protein 1 isoform X3

    RNA

    1. XR_008486789.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZI7.1 GenPept UniProtKB/Swiss-Prot:Q9NZI7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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