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

Gene ID: 499146, updated on 2-May-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
Ensembl: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 transcription, DNA-templated. Predicted to be active in nucleus. Orthologous to human SPIB (Spi-B transcription factor). [provided by Alliance of Genome Resources, Apr 2022]
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

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

  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

  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

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

    UniProtKB/TrEMBL
    A0A140TAD6
    Related
    ENSRNOP00000026599.7, ENSRNOT00000026599.7
    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

  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

  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
    Related
    ENSRNOP00000091947.1
    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
    ENSRNOP00000093406.1
    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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