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

    Gene ID: 21429, updated on 27-Nov-2024

    Summary

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    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 and transcription elongation by RNA polymerase I. Located in nucleolus. Is expressed in several structures, including brain; branchial arch; early conceptus; genitourinary system; and limb. Human ortholog(s) of this gene implicated in childhood-onset neurodegeneration with brain atrophy. Orthologous to human UBTF (upstream binding transcription factor). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 28.0), liver E14 (RPKM 15.9) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ubtf in Genome Data Viewer
    Location:
    11 66.29 cM; 11 D
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (102195393..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 STARR-positive B cell enhancer ABC_E1432 Neighboring gene transmembrane and ubiquitin-like domain containing 2 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:102156604-102156807 Neighboring gene ataxin 7-like 3 Neighboring gene STARR-positive B cell enhancer ABC_E469 Neighboring gene predicted gene, 33851 Neighboring gene STARR-positive B cell enhancer ABC_E5281 Neighboring gene STARR-seq mESC enhancer starr_30800 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. The splice variants of UBF differentially regulate RNA polymerase I transcription elongation in response to ERK phosphorylation. Stefanovsky VY, et al. Nucleic Acids Res, 2008 Sep. PMID 18676449, Free PMC Article
    2. Cloning and structural analysis of cDNA and the gene for mouse transcription factor UBF. Hisatake K, et al. Nucleic Acids Res, 1991 Sep 11. PMID 1891354, Free PMC Article
    3. Polymerase I pathway inhibitor ameliorates experimental autoimmune encephalomyelitis. Achiron A, et al. J Neuroimmunol, 2013 Oct 15. PMID 23998422
    4. Cardiac hypertrophy in vivo is associated with increased expression of the ribosomal gene transcription factor UBF. Brandenburger Y, et al. FEBS Lett, 2003 Jul 31. PMID 12885411
    5. The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development. Nakagawa S, et al. Stem Cell Reports, 2024 May 14. PMID 38701778, Free PMC Article

    See all (78) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. UBF and Nopp140 dynamic redistribution between the two-cell and blastocyst stages (time of implantation) is correlated with morphological and structural modifications that occur in embryonic nucleolar compartments.
      Title: Three-Dimensional Distribution of UBF and Nopp140 in Relationship to Ribosomal DNA Transcription During Mouse Preimplantation Development.
    2. inhibition of UBF function is a major factor in the cytotoxicity of cisplatin; its depletion selectively induces p53-independent apoptotic death in transformed cells
      Title: Depletion of the cisplatin targeted HMGB-box factor UBF selectively induces p53-independent apoptotic death in transformed cells.
    3. Loss of UBF also unexpectedly induced the formation in cells of a large sub-nuclear structure resembling the nucleolar precursor body (NPB) of oocytes and early embryos.
      Title: Conditional inactivation of Upstream Binding Factor reveals its epigenetic functions and the existence of a somatic nucleolar precursor body.
    4. we have uncovered a novel role for UBTF1 and UBTF2 in maintaining genome stability through coordinating the expression of highly transcribed Pol I (UBTF1 activity) and Pol II genes (UBTF2 activity).
      Title: A novel role for the Pol I transcription factor UBTF in maintaining genome stability through the regulation of highly transcribed Pol II genes.
    5. Inhibition of the POL1 pathway delays and suppresses the development of experimental autoimmune encephalomyelitis and ameliorates the disease in mice with persistent clinical signs.
      Title: Polymerase I pathway inhibitor ameliorates experimental autoimmune encephalomyelitis.
    6. UBF1 mutation (K352A, K352Q, and K352R) decreased rDNA transcriptional activity.
      Title: Dysregulation of upstream binding factor-1 acetylation at K352 is linked to impaired ribosomal DNA transcription in Huntington's disease.
    7. augmented ribosome biogenesis occurs in UBF-dependent manner during increased protein synthesis induced by high glucose in glomerular epithelial cells that correlates with UBF activation and renal hypertrophy in rodents with type 1 and type 2 diabetes.
      Title: Ribosomal biogenesis induction by high glucose requires activation of upstream binding factor in kidney glomerular epithelial cells.
    8. Myeloid cell IGF-1 receptor-mediated regulation of UBF-1 levels involves IRS-1 and ERK pathways.
      Title: Dual regulation of upstream binding factor 1 levels by IRS-1 and ERKs in IGF-1-receptor signaling.
    9. Phosphatidylinositol 3-kinase subunit directly phosphorylates and activates UBF1, an exclusively nucleolar protein.
      Title: Control of cell size through phosphorylation of upstream binding factor 1 by nuclear phosphatidylinositol 3-kinase.
    10. increased UBF levels correlate with elevated pressure load and increased cardiac growth rates
      Title: Cardiac hypertrophy in vivo is associated with increased expression of the ribosomal gene transcription factor UBF.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    Variation

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    Alleles

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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase I cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase I core promoter sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase I core promoter sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase I general transcription initiation factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase I general transcription initiation factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables scaffold protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase I IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase I IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in transcription by RNA polymerase I IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription by RNA polymerase I ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within transcription elongation by RNA polymerase I IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in transcription initiation at RNA polymerase I promoter ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in transcription initiation at RNA polymerase I promoter ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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

    NCBI Reference Sequences (RefSeq)

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    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_001044383.4 → NP_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/Swiss-Prot
      P25976
      UniProtKB/TrEMBL
      A2AWT6
      Related
      ENSMUSP00000102736.3, ENSMUST00000107119.9
      Conserved Domains (2) summary
      cd01390
      Location:112 → 177
      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:442 → 525
      HMG_box_5; HMG (high mobility group) box 5

    2. NM_001302954.3 → NP_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/Swiss-Prot
      P25976
      UniProtKB/TrEMBL
      A2AWT6
      Related
      ENSMUSP00000136310.2, ENSMUST00000178839.8
      Conserved Domains (2) summary
      cd01390
      Location:112 → 177
      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:442 → 525
      HMG_box_5; HMG (high mobility group) box 5

    3. NM_001302955.3 → NP_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:311 → 510
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01390
      Location:112 → 177
      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:442 → 525
      HMG_box_5; HMG (high mobility group) box 5

    4. NM_001362544.2 → NP_001349473.1  nucleolar transcription factor 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL954730
      Consensus CDS
      CCDS25495.1
      UniProtKB/Swiss-Prot
      P25976
      UniProtKB/TrEMBL
      A2AWT5
      Related
      ENSMUSP00000133611.2, ENSMUST00000173870.8
      Conserved Domains (3) summary
      cd01390
      Location:407 → 470
      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:479 → 562
      HMG_box_5; HMG (high mobility group) box 5
      pfam00505
      Location:112 → 179
      HMG_box; HMG (high mobility group) box

    5. NM_001362545.2 → NP_001349474.1  nucleolar transcription factor 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL954730
      Consensus CDS
      CCDS25495.1
      UniProtKB/Swiss-Prot
      P25976
      UniProtKB/TrEMBL
      A2AWT5
      Related
      ENSMUSP00000078539.5, ENSMUST00000079589.11
      Conserved Domains (3) summary
      cd01390
      Location:407 → 470
      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:479 → 562
      HMG_box_5; HMG (high mobility group) box 5
      pfam00505
      Location:112 → 179
      HMG_box; HMG (high mobility group) box

    6. NM_001362547.2 → NP_001349476.1  nucleolar transcription factor 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL954730
      Consensus CDS
      CCDS36343.1
      UniProtKB/Swiss-Prot
      P25976
      UniProtKB/TrEMBL
      A2AWT6
      Conserved Domains (2) summary
      cd01390
      Location:112 → 177
      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:442 → 525
      HMG_box_5; HMG (high mobility group) box 5

    7. NM_001362548.2 → NP_001349477.1  nucleolar transcription factor 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL954730
      Consensus CDS
      CCDS36343.1
      UniProtKB/Swiss-Prot
      P25976
      UniProtKB/TrEMBL
      A2AWT6
      Related
      ENSMUSP00000102734.3, ENSMUST00000107117.9
      Conserved Domains (2) summary
      cd01390
      Location:112 → 177
      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:442 → 525
      HMG_box_5; HMG (high mobility group) box 5

    8. NM_001362549.2 → NP_001349478.1  nucleolar transcription factor 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL954730
      Conserved Domains (2) summary
      cd01390
      Location:308 → 371
      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:380 → 464
      HMG_box_5; HMG (high mobility group) box 5

    9. NM_001362552.2 → NP_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:112 → 158
      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_001404620.1 → NP_001391549.1  nucleolar transcription factor 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL954730
      UniProtKB/TrEMBL
      A2AWT6

    11. NM_001404621.1 → NP_001391550.1  nucleolar transcription factor 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL954730
      UniProtKB/TrEMBL
      A2AWT6

    12. NM_001404622.1 → NP_001391551.1  nucleolar transcription factor 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL954730
      UniProtKB/TrEMBL
      A2AWT6

    13. NM_001404623.1 → NP_001391552.1  nucleolar transcription factor 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL954730
      UniProtKB/TrEMBL
      A2AWT5

    14. NM_001404624.1 → NP_001391553.1  nucleolar transcription factor 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL954730
      UniProtKB/TrEMBL
      A2AWT6

    15. NM_001404625.1 → NP_001391554.1  nucleolar transcription factor 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL954730
      UniProtKB/TrEMBL
      A2AWT6

    16. NM_001404626.1 → NP_001391555.1  nucleolar transcription factor 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL954730
      UniProtKB/TrEMBL
      A2AWT6
      Related
      ENSMUSP00000102732.2, ENSMUST00000107115.8

    17. NM_001404627.1 → NP_001391556.1  nucleolar transcription factor 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL954730
      UniProtKB/TrEMBL
      A2AWT5
      Related
      ENSMUSP00000102740.4, ENSMUST00000107123.10

    18. NM_001404628.1 → NP_001391557.1  nucleolar transcription factor 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL954730
      UniProtKB/TrEMBL
      A2AWT5

    19. NM_001404629.1 → NP_001391558.1  nucleolar transcription factor 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL954730
      UniProtKB/TrEMBL
      A2AWT7

    20. NM_001404630.1 → NP_001391559.1  nucleolar transcription factor 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL954730
      UniProtKB/TrEMBL
      A2AWT7

    21. NM_001404633.1 → NP_001391562.1  nucleolar transcription factor 1 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AL954730

    22. NM_011551.8 → NP_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/Swiss-Prot
      P25976
      UniProtKB/TrEMBL
      A2AWT5
      Related
      ENSMUSP00000133844.2, ENSMUST00000174302.8
      Conserved Domains (3) summary
      cd01390
      Location:407 → 470
      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:479 → 562
      HMG_box_5; HMG (high mobility group) box 5
      pfam00505
      Location:112 → 179
      HMG_box; HMG (high mobility group) box

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    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
      102195393..102214738 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036156510.1 → XP_036012403.1  nucleolar transcription factor 1 isoform X1

      UniProtKB/Swiss-Prot
      P25976
      UniProtKB/TrEMBL
      A2AWT5
      Conserved Domains (3) summary
      cd01390
      Location:407 → 470
      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:479 → 562
      HMG_box_5; HMG (high mobility group) box 5
      pfam00505
      Location:112 → 179
      HMG_box; HMG (high mobility group) box

    2. XM_030245777.2 → XP_030101637.1  nucleolar transcription factor 1 isoform X1

      UniProtKB/Swiss-Prot
      P25976
      UniProtKB/TrEMBL
      A2AWT5
      Conserved Domains (3) summary
      cd01390
      Location:407 → 470
      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:479 → 562
      HMG_box_5; HMG (high mobility group) box 5
      pfam00505
      Location:112 → 179
      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.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P25976.1 GenPept UniProtKB/Swiss-Prot:P25976

    Gene LinkOut

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

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