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

Gene ID: 7342, updated on 3-Apr-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, Apr 2022]
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_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (33388336..33441399, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (33390109..33443172, complement)
105.20220307 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. Transactivation activity of LBP-1 proteins and their dimerization in living cells. Katsura A, et al. Genes Cells, 2009 Oct. PMID 19751393
  3. 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
  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. TFCP2/TFCP2L1/UBP1 transcription factors in cancer. Kotarba G, et al. Cancer Lett, 2018 Apr 28. PMID 29410248

See all (50) 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)

Genotypes

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
part_of 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_2023_10

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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