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    Spib Spi-B transcription factor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 499146, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Spibprovided by RGD
    Official Full Name
    Spi-B transcription factorprovided by RGD
    Primary source
    RGD:1565899
    See related
    EnsemblRapid:ENSRNOG00000019660 AllianceGenome:RGD:1565899
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in immature B cell differentiation and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within macrophage differentiation and regulation of DNA-templated transcription. Predicted to be active in nucleus. Orthologous to human SPIB (Spi-B transcription factor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 195.2), Thymus (RPKM 45.0) and 1 other tissue See more
    Orthologs
    human mouse all
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    Genomic context

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    See Spib in Genome Data Viewer
    Location:
    1q22
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (104155456..104161311, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (95018939..95024804, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (100531538..100537397, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene golgi associated RAB2 interactor 5A Neighboring gene myosin binding protein C2 Neighboring gene DNA polymerase delta 1, catalytic subunit Neighboring gene nuclear receptor subfamily 1, group H, member 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Spi-B can functionally replace PU.1 in myeloid but not lymphoid development. Dahl R, et al. EMBO J, 2002 May 1. PMID 11980719, Free PMC Article
    2. SPI-B activates transcription via a unique proline, serine, and threonine domain and exhibits DNA binding affinity differences from PU.1. Rao S, et al. J Biol Chem, 1999 Apr 16. PMID 10196196
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Clone Names

    • MGC109046

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in immature B cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within macrophage differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    transcription factor Spi-B
    Names
    Spi-B transcription factor (Spi-1/PU.1 related)

    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_001024286.1 → NP_001019457.1  transcription factor Spi-B

      See identical proteins and their annotated locations for NP_001019457.1

      Status: PROVISIONAL

      Source sequence(s)
      BC089881
      UniProtKB/Swiss-Prot
      Q5EBA3
      UniProtKB/TrEMBL
      A0A140TAD6
      Conserved Domains (1) summary
      smart00413
      Location:175 → 263
      ETS; erythroblast transformation specific domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      104155456..104161311 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063270969.1 → XP_063127039.1  transcription factor Spi-B isoform X10

      UniProtKB/TrEMBL
      A0A140TAD6

    2. XM_063270971.1 → XP_063127041.1  transcription factor Spi-B isoform X13

      UniProtKB/TrEMBL
      A0A140TAD6

    3. XM_063270973.1 → XP_063127043.1  transcription factor Spi-B isoform X16

    4. XM_063270975.1 → XP_063127045.1  transcription factor Spi-B isoform X19

    5. XM_063270972.1 → XP_063127042.1  transcription factor Spi-B isoform X14

      UniProtKB/TrEMBL
      A0A140TAD6

    6. XM_039087406.2 → XP_038943334.1  transcription factor Spi-B isoform X17

    7. XM_006229115.5 → XP_006229177.1  transcription factor Spi-B isoform X7

      UniProtKB/TrEMBL
      A0A140TAD6
      Conserved Domains (1) summary
      smart00413
      Location:174 → 262
      ETS; erythroblast transformation specific domain

    8. XM_063270967.1 → XP_063127037.1  transcription factor Spi-B isoform X8

      UniProtKB/TrEMBL
      A0A140TAD6

    9. XM_006229112.4 → XP_006229174.1  transcription factor Spi-B isoform X2

      UniProtKB/TrEMBL
      A0A140TAD6
      Related
      ENSRNOP00000026599.7, ENSRNOT00000026599.8
      Conserved Domains (1) summary
      smart00413
      Location:192 → 280
      ETS; erythroblast transformation specific domain

    10. XM_039087403.2 → XP_038943331.1  transcription factor Spi-B isoform X11

      UniProtKB/TrEMBL
      A0A140TAD6
      Conserved Domains (1) summary
      smart00413
      Location:165 → 253
      ETS; erythroblast transformation specific domain

    11. XM_039087412.1 → XP_038943340.1  transcription factor Spi-B isoform X18

    12. XM_039087388.1 → XP_038943316.1  transcription factor Spi-B isoform X3

      UniProtKB/TrEMBL
      A0A140TAD6
      Conserved Domains (1) summary
      smart00413
      Location:183 → 271
      ETS; erythroblast transformation specific domain

    13. XM_039087404.1 → XP_038943332.1  transcription factor Spi-B isoform X15

    14. XM_063270968.1 → XP_063127038.1  transcription factor Spi-B isoform X9

      UniProtKB/TrEMBL
      A0A140TAD6

    15. XM_006229113.4 → XP_006229175.1  transcription factor Spi-B isoform X6

      UniProtKB/TrEMBL
      A0A140TAD6
      Conserved Domains (1) summary
      smart00413
      Location:175 → 263
      ETS; erythroblast transformation specific domain

    16. XM_063270970.1 → XP_063127040.1  transcription factor Spi-B isoform X12

      UniProtKB/TrEMBL
      A0A140TAD6

    17. XM_006229111.4 → XP_006229173.1  transcription factor Spi-B isoform X1

      UniProtKB/TrEMBL
      A0A140TAD6
      Conserved Domains (1) summary
      smart00413
      Location:193 → 281
      ETS; erythroblast transformation specific domain

    18. XM_008759404.4 → XP_008757626.1  transcription factor Spi-B isoform X4

      UniProtKB/TrEMBL
      A0A140TAD6
      Conserved Domains (1) summary
      smart00413
      Location:176 → 264
      ETS; erythroblast transformation specific domain

    19. XM_006229114.5 → XP_006229176.1  transcription factor Spi-B isoform X5

      UniProtKB/TrEMBL
      A0A140TAD6, A0A8I6AKC1
      Related
      ENSRNOP00000091947.1, ENSRNOT00000102341.2
      Conserved Domains (1) summary
      smart00413
      Location:175 → 263
      ETS; erythroblast transformation specific domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5EBA3.1 GenPept UniProtKB/Swiss-Prot:Q5EBA3

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