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FUBP1 far upstream element binding protein 1 [ Homo sapiens (human) ]

Gene ID: 8880, updated on 10-Jan-2019

Summary

Official Symbol
FUBP1provided by HGNC
Official Full Name
far upstream element binding protein 1provided by HGNC
Primary source
HGNC:HGNC:4004
See related
Ensembl:ENSG00000162613 MIM:603444
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
FBP; FUBP; hDH V
Summary
The protein encoded by this gene is a single stranded DNA-binding protein that binds to multiple DNA elements, including the far upstream element (FUSE) located upstream of c-myc. Binding to FUSE occurs on the non-coding strand, and is important to the regulation of c-myc in undifferentiated cells. This protein contains three domains, an amphipathic helix N-terminal domain, a DNA-binding central domain, and a C-terminal transactivation domain that contains three tyrosine-rich motifs. The N-terminal domain is thought to repress the activity of the C-terminal domain. This protein is also thought to bind RNA, and contains 3'-5' helicase activity with in vitro activity on both DNA-DNA and RNA-RNA duplexes. Aberrant expression of this gene has been found in malignant tissues, and this gene is important to neural system and lung development. Binding of this protein to viral RNA is thought to play a role in several viral diseases, including hepatitis C and hand, foot and mouth disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Expression
Ubiquitous expression in lymph node (RPKM 23.3), bone marrow (RPKM 20.3) and 25 other tissues See more
Orthologs

Genomic context

See FUBP1 in Genome Data Viewer
Location:
1p31.1
Exon count:
26
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (77944051..77979435, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (78409740..78444839, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene mitoguardin 1 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 25 Neighboring gene NEXN antisense RNA 1 Neighboring gene nexilin F-actin binding protein Neighboring gene DnaJ heat shock protein family (Hsp40) member B4 Neighboring gene nitrilase family member 2 pseudogene Neighboring gene GIPC PDZ domain containing family member 2 Neighboring gene RNA, U6 small nuclear 1102, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 downregulates the expression of far upstream element-binding protein in T-cell lines and umbilical cord blood mononuclear cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
PubMed 
RNA binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
single-stranded DNA binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
positive regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
far upstream element-binding protein 1
Names
DNA helicase V
FUSE binding protein 1
epididymis secretory sperm binding protein
far upstream element (FUSE) binding protein 1

NCBI Reference Sequences (RefSeq)

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_033243.2 RefSeqGene

    Range
    4889..35692
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_995

mRNA and Protein(s)

  1. NM_001303433.1NP_001290362.1  far upstream element-binding protein 1 isoform 1

    See identical proteins and their annotated locations for NP_001290362.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK300032, CB133133, DA113820, U05040
    UniProtKB/Swiss-Prot
    Q96AE4
    UniProtKB/TrEMBL
    B4DT31
    Conserved Domains (3) summary
    cd00105
    Location:299360
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam00013
    Location:123187
    KH_1; KH domain
    pfam09005
    Location:623643
    DUF1897; Domain of unknown function (DUF1897)
  2. NM_003902.4NP_003893.2  far upstream element-binding protein 1 isoform 2

    See identical proteins and their annotated locations for NP_003893.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    CB133133, DA113820, U05040
    Consensus CDS
    CCDS683.1
    UniProtKB/Swiss-Prot
    Q96AE4
    Related
    ENSP00000359804.2, ENST00000370768.6
    Conserved Domains (3) summary
    cd00105
    Location:278339
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam00013
    Location:102166
    KH_1; KH domain
    pfam09005
    Location:602622
    DUF1897; Domain of unknown function (DUF1897)

RNA

  1. NR_130152.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate internal exon, uses an alternate splice site in an internal exon, and differs in the 3' terminal region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC017247, DA113820
  2. NR_146539.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate internal exon, uses an alternate splice site in an internal exon, and differs in the 3' terminal region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AW295160, BC017247, BQ934904, DA113820
  3. NR_146540.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate internal exon, and differs in the 3' terminal region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL532525, AW295160, BC017247, BQ934904, DA113820

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    77944051..77979435 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002739.1XP_016858228.1  far upstream element-binding protein 1 isoform X1

    Conserved Domains (3) summary
    cd00105
    Location:299360
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam00013
    Location:123187
    KH_1; KH domain
    pfam09005
    Location:623643
    DUF1897; Domain of unknown function (DUF1897)
  2. XM_024450628.1XP_024306396.1  far upstream element-binding protein 1 isoform X5

    Conserved Domains (3) summary
    cd00105
    Location:277338
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam00013
    Location:101165
    KH_1; KH domain
    pfam09005
    Location:601621
    DUF1897; Domain of unknown function (DUF1897)
  3. XM_017002743.2XP_016858232.1  far upstream element-binding protein 1 isoform X7

    UniProtKB/Swiss-Prot
    Q96AE4
    Related
    ENSP00000294623.4, ENST00000294623.8
    Conserved Domains (3) summary
    cd00105
    Location:277338
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam00013
    Location:101165
    KH_1; KH domain
    pfam09005
    Location:601621
    DUF1897; Domain of unknown function (DUF1897)
  4. XM_017002744.2XP_016858233.1  far upstream element-binding protein 1 isoform X8

    Conserved Domains (3) summary
    cd00105
    Location:277338
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam00013
    Location:101165
    KH_1; KH domain
    pfam09005
    Location:601621
    DUF1897; Domain of unknown function (DUF1897)
  5. XM_011542391.3XP_011540693.1  far upstream element-binding protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011540693.1

    Conserved Domains (3) summary
    cd00105
    Location:299360
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam00013
    Location:123187
    KH_1; KH domain
    pfam09005
    Location:623643
    DUF1897; Domain of unknown function (DUF1897)
  6. XM_017002740.2XP_016858229.1  far upstream element-binding protein 1 isoform X3

    Conserved Domains (3) summary
    cd00105
    Location:299360
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam00013
    Location:123187
    KH_1; KH domain
    pfam09005
    Location:623643
    DUF1897; Domain of unknown function (DUF1897)
  7. XM_011542392.2XP_011540694.1  far upstream element-binding protein 1 isoform X2

    See identical proteins and their annotated locations for XP_011540694.1

    Conserved Domains (3) summary
    cd00105
    Location:298359
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam00013
    Location:122186
    KH_1; KH domain
    pfam09005
    Location:622642
    DUF1897; Domain of unknown function (DUF1897)
  8. XM_017002742.1XP_016858231.1  far upstream element-binding protein 1 isoform X6

    Conserved Domains (3) summary
    cd00105
    Location:298359
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam00013
    Location:122186
    KH_1; KH domain
    pfam09005
    Location:622642
    DUF1897; Domain of unknown function (DUF1897)
  9. XM_011542393.3XP_011540695.1  far upstream element-binding protein 1 isoform X4

    See identical proteins and their annotated locations for XP_011540695.1

    Conserved Domains (3) summary
    cd00105
    Location:278339
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam00013
    Location:102166
    KH_1; KH domain
    pfam09005
    Location:602622
    DUF1897; Domain of unknown function (DUF1897)

RNA

  1. XR_001737521.1 RNA Sequence

  2. XR_946791.2 RNA Sequence

  3. XR_001737524.2 RNA Sequence

  4. XR_946790.3 RNA Sequence

  5. XR_001737519.2 RNA Sequence

  6. XR_001737517.2 RNA Sequence

  7. XR_001737516.2 RNA Sequence

  8. XR_001737518.2 RNA Sequence

  9. XR_001737515.2 RNA Sequence

  10. XR_001737514.2 RNA Sequence

  11. XR_001737520.1 RNA Sequence

  12. XR_001737522.2 RNA Sequence

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