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Ubtf upstream binding transcription factor, RNA polymerase I [ Mus musculus (house mouse) ]

Gene ID: 21429, updated on 10-Dec-2022

Summary

Official Symbol
Ubtfprovided by MGI
Official Full Name
upstream binding transcription factor, RNA polymerase Iprovided by MGI
Primary source
MGI:MGI:98512
See related
Ensembl:ENSMUSG00000020923 AllianceGenome:MGI:98512
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
UBF; UBF1; UBF-1; NOR-90; Tcfubf; A930005G04Rik
Summary
Predicted to enable several functions, including RNA polymerase I general transcription initiation factor activity; RNA polymerase I transcription regulatory region sequence-specific DNA binding activity; and scaffold protein binding activity. Involved in positive regulation of transcription by RNA polymerase I. Acts upstream of or within cellular response to leukemia inhibitory factor; rDNA heterochromatin assembly; and transcription elongation from RNA polymerase I promoter. Located in nucleolus. Is expressed in several structures, including brain; branchial arch; early conceptus; genitourinary system; and limb. Orthologous to human UBTF (upstream binding transcription factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 28.0), liver E14 (RPKM 15.9) and 28 other tissues See more
Orthologs
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Genomic context

See Ubtf in Genome Data Viewer
Location:
11; 11 D
Exon count:
25
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (102195386..102214738, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (102304560..102323649, complement)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene transmembrane and ubiquitin-like domain containing 2 Neighboring gene ataxin 7-like 3 Neighboring gene predicted gene, 33851 Neighboring gene solute carrier family 4 (anion exchanger), member 1 Neighboring gene Bloodlinc, erythroid developmental long intergenic non-protein coding transcript Neighboring gene predicted gene, 34253

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (5)  1 citation
  • Endonuclease-mediated (3) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Component Evidence Code Pubs
located_in fibrillar center ISO
Inferred from Sequence Orthology
more info
 
located_in nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
nucleolar transcription factor 1
Names
transcription factor UBF
upstream-binding factor 1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001044383.4NP_001037848.1  nucleolar transcription factor 1 isoform 2

    See identical proteins and their annotated locations for NP_001037848.1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS36343.1
    UniProtKB/TrEMBL
    A0A8C6IAV0, A2AWT6
    Related
    ENSMUSP00000102736.3, ENSMUST00000107119.9
    Conserved Domains (2) summary
    cd01390
    Location:112177
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:442525
    HMG_box_5; HMG (high mobility group) box 5
  2. NM_001302954.3NP_001289883.1  nucleolar transcription factor 1 isoform 2

    See identical proteins and their annotated locations for NP_001289883.1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS36343.1
    UniProtKB/TrEMBL
    A0A8C6IAV0, A2AWT6
    Related
    ENSMUSP00000136310.2, ENSMUST00000178839.8
    Conserved Domains (2) summary
    cd01390
    Location:112177
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:442525
    HMG_box_5; HMG (high mobility group) box 5
  3. NM_001302955.3NP_001289884.1  nucleolar transcription factor 1 isoform 3

    See identical proteins and their annotated locations for NP_001289884.1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS79056.1
    UniProtKB/TrEMBL
    A2AWT7, Q9DBH1
    Related
    ENSMUSP00000006754.8, ENSMUST00000006754.14
    Conserved Domains (3) summary
    COG5648
    Location:311510
    NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
    cd01390
    Location:112177
    HMGB-UBF_HMG-box; HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone ...
    pfam14887
    Location:442525
    HMG_box_5; HMG (high mobility group) box 5
  4. NM_001362544.2NP_001349473.1  nucleolar transcription factor 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS25495.1
    UniProtKB/TrEMBL
    A0A8C6IC56, A2AWT5
    Related
    ENSMUSP00000133611.2, ENSMUST00000173870.8
    Conserved Domains (3) summary
    cd01390
    Location:407470
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:479562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112179
    HMG_box; HMG (high mobility group) box
  5. NM_001362545.2NP_001349474.1  nucleolar transcription factor 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS25495.1
    UniProtKB/TrEMBL
    A0A8C6IC56, A2AWT5
    Related
    ENSMUSP00000078539.5, ENSMUST00000079589.11
    Conserved Domains (3) summary
    cd01390
    Location:407470
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:479562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112179
    HMG_box; HMG (high mobility group) box
  6. NM_001362547.2NP_001349476.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS36343.1
    UniProtKB/TrEMBL
    A0A8C6IAV0, A2AWT6
    Conserved Domains (2) summary
    cd01390
    Location:112177
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:442525
    HMG_box_5; HMG (high mobility group) box 5
  7. NM_001362548.2NP_001349477.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS36343.1
    UniProtKB/TrEMBL
    A0A8C6IAV0, A2AWT6
    Related
    ENSMUSP00000102734.3, ENSMUST00000107117.9
    Conserved Domains (2) summary
    cd01390
    Location:112177
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:442525
    HMG_box_5; HMG (high mobility group) box 5
  8. NM_001362549.2NP_001349478.1  nucleolar transcription factor 1 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Conserved Domains (2) summary
    cd01390
    Location:308371
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:380464
    HMG_box_5; HMG (high mobility group) box 5
  9. NM_001362552.2NP_001349481.1  nucleolar transcription factor 1 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS88262.1
    UniProtKB/TrEMBL
    E9Q4A8
    Related
    ENSMUSP00000131930.2, ENSMUST00000128016.2
    Conserved Domains (1) summary
    cd01390
    Location:112158
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
  10. NM_001404620.1NP_001391549.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A0A8C6IAV0, A2AWT6
  11. NM_001404621.1NP_001391550.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A0A8C6IAV0, A2AWT6
  12. NM_001404622.1NP_001391551.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A0A8C6IAV0, A2AWT6
  13. NM_001404623.1NP_001391552.1  nucleolar transcription factor 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A0A8C6IC56, A2AWT5
  14. NM_001404624.1NP_001391553.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A0A8C6IAV0, A2AWT6
  15. NM_001404625.1NP_001391554.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A0A8C6IAV0, A2AWT6
  16. NM_001404626.1NP_001391555.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A0A8C6IAV0, A2AWT6
  17. NM_001404627.1NP_001391556.1  nucleolar transcription factor 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A0A8C6IC56, A2AWT5
  18. NM_001404628.1NP_001391557.1  nucleolar transcription factor 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A0A8C6IC56, A2AWT5
  19. NM_001404629.1NP_001391558.1  nucleolar transcription factor 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT7
  20. NM_001404630.1NP_001391559.1  nucleolar transcription factor 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT7
  21. NM_001404633.1NP_001391562.1  nucleolar transcription factor 1 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AL954730
  22. NM_011551.8NP_035681.2  nucleolar transcription factor 1 isoform 1

    See identical proteins and their annotated locations for NP_035681.2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS25495.1
    UniProtKB/TrEMBL
    A0A8C6IC56, A2AWT5
    Related
    ENSMUSP00000133844.2, ENSMUST00000174302.8
    Conserved Domains (3) summary
    cd01390
    Location:407470
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:479562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112179
    HMG_box; HMG (high mobility group) box

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    102195386..102214738 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017314430.3XP_017169919.1  nucleolar transcription factor 1 isoform X2

    UniProtKB/TrEMBL
    A2AWT6
    Conserved Domains (2) summary
    cd01390
    Location:112177
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:442525
    HMG_box_5; HMG (high mobility group) box 5
  2. XM_036156510.1XP_036012403.1  nucleolar transcription factor 1 isoform X1

    UniProtKB/TrEMBL
    A0A8C6IC56, A2AWT5
    Conserved Domains (3) summary
    cd01390
    Location:407470
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:479562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112179
    HMG_box; HMG (high mobility group) box
  3. XM_030245777.2XP_030101637.1  nucleolar transcription factor 1 isoform X1

    UniProtKB/TrEMBL
    A0A8C6IC56, A2AWT5
    Conserved Domains (3) summary
    cd01390
    Location:407470
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:479562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112179
    HMG_box; HMG (high mobility group) box
  4. XM_011248888.4XP_011247190.1  nucleolar transcription factor 1 isoform X1

    UniProtKB/TrEMBL
    A2AWT5
    Related
    ENSMUSP00000102740.4, ENSMUST00000107123.10
    Conserved Domains (3) summary
    cd01390
    Location:407470
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:479562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112179
    HMG_box; HMG (high mobility group) box
  5. XM_030245778.1XP_030101638.1  nucleolar transcription factor 1 isoform X1

    Conserved Domains (3) summary
    cd01390
    Location:407470
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam14887
    Location:479562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112179
    HMG_box; HMG (high mobility group) box

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001362550.1: Suppressed sequence

    Description
    NM_001362550.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.
  2. NM_001362551.1: Suppressed sequence

    Description
    NM_001362551.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.