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    SPIB Spi-B transcription factor [ Homo sapiens (human) ]

    Gene ID: 6689, updated on 30-Apr-2024

    Summary

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    Official Symbol
    SPIBprovided by HGNC
    Official Full Name
    Spi-B transcription factorprovided by HGNC
    Primary source
    HGNC:HGNC:11242
    See related
    Ensembl:ENSG00000269404 MIM:606802; AllianceGenome:HGNC:11242
    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
    SPI-B
    Summary
    The protein encoded by this gene is a transcriptional activator that binds to the PU-box (5'-GAGGAA-3') and acts as a lymphoid-specific enhancer. Four transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
    Expression
    Biased expression in lymph node (RPKM 17.1), appendix (RPKM 10.5) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SPIB in Genome Data Viewer
    Location:
    19q13.33
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (50418938..50431314)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (53506494..53518875)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (50922195..50934571)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50879623-50880434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10961 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50888337-50888838 Neighboring gene nuclear receptor subfamily 1 group H member 2 Neighboring gene DNA polymerase delta 1, catalytic subunit Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50918101-50918885 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50918886-50919670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10966 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:50921334-50921502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14987 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50930914-50931487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50931488-50932060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10967 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50935955-50936713 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50937528-50938028 Neighboring gene myosin binding protein C2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50954383-50954951 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:50970469-50970655 Neighboring gene golgi associated RAB2 interactor 5A Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:50979402-50979902 Neighboring gene ER membrane protein complex subunit 10

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Comprehensive pan-cancer analysis reveals the prognostic value and immunological role of SPIB. Ding M, et al. Aging (Albany NY), 2022 Aug 14. PMID 35969172, Free PMC Article
    2. SPI1-related protein inhibits cervical cancer cell progression and prevents macrophage cell migration. Jin J, et al. J Obstet Gynaecol Res, 2022 Sep. PMID 35770729
    3. SPIB acts as a tumor suppressor by activating the NFkB and JNK signaling pathways through MAP4K1 in colorectal cancer cells. Zhao X, et al. Cell Signal, 2021 Dec. PMID 34530056
    4. SPIB promotes anoikis resistance via elevated autolysosomal process in lung cancer cells. Zhang H, et al. FEBS J, 2020 Nov. PMID 32129936
    5. ETV6-RUNX1 interacts with a region in SPIB intron 1 to regulate gene expression in pre-B-cell acute lymphoblastic leukemia. Xu LS, et al. Exp Hematol, 2019 May. PMID 30986496

    See all (46) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. IGSF10 inhibits the metastasis of lung adenocarcinoma via the Spi-B/Integrin-beta1 signaling pathway.
      Title: IGSF10 inhibits the metastasis of lung adenocarcinoma via the Spi-B/Integrin-β1 signaling pathway.
    2. SPIB Knockdown Inhibits the Immune Escape of Ovarian Cancer Cells by Reducing PD-L1 (CD274) Expression and Inactivating the JAK/STAT Pathway.
      Title: SPIB Knockdown Inhibits the Immune Escape of Ovarian Cancer Cells by Reducing PD-L1 (CD274) Expression and Inactivating the JAK/STAT Pathway.
    3. Peroxiredoxin2 regulates trophoblast proliferation and migration through SPIB-HDAC2 pathway.
      Title: Peroxiredoxin2 regulates trophoblast proliferation and migration through SPIB-HDAC2 pathway.
    4. SPI1-related protein inhibits cervical cancer cell progression and prevents macrophage cell migration.
      Title: SPI1-related protein inhibits cervical cancer cell progression and prevents macrophage cell migration.
    5. Comprehensive pan-cancer analysis reveals the prognostic value and immunological role of SPIB.
      Title: Comprehensive pan-cancer analysis reveals the prognostic value and immunological role of SPIB.
    6. Integrated transcriptomic and regulatory network analyses uncovers the role of let-7b-5p, SPIB, and HLA-DPB1 in sepsis.
      Title: Integrated transcriptomic and regulatory network analyses uncovers the role of let-7b-5p, SPIB, and HLA-DPB1 in sepsis.
    7. SPIB acts as a tumor suppressor by activating the NFkB and JNK signaling pathways through MAP4K1 in colorectal cancer cells.
      Title: SPIB acts as a tumor suppressor by activating the NFkB and JNK signaling pathways through MAP4K1 in colorectal cancer cells.
    8. SPIB promotes anoikis resistance via elevated autolysosomal process in lung cancer cells.
      Title: SPIB promotes anoikis resistance via elevated autolysosomal process in lung cancer cells.
    9. Taken together, this study identifies SPIB as an important target of ETV6-RUNX1 in regulation of B-cell gene expression in t(12;21) leukemia.
      Title: ETV6-RUNX1 interacts with a region in SPIB intron 1 to regulate gene expression in pre-B-cell acute lymphoblastic leukemia.
    10. Results provide evidence that SPIB is a specific transcription factor that participates in pH-mediated regulation of AQP1 gene expression.
      Title: pH-mediated upregulation of AQP1 gene expression through the Spi-B transcription factor.
    Submit: New GeneRIF Correction See all GeneRIFs (27)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.
    EBI GWAS Catalog
    Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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 GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in cytoplasm TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    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_001243998.2 → NP_001230927.1  transcription factor Spi-B isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC020909
      Consensus CDS
      CCDS58674.1
      UniProtKB/Swiss-Prot
      Q01892
      Related
      ENSP00000391877.2, ENST00000439922.6
      Conserved Domains (1) summary
      smart00413
      Location:77 → 165
      ETS; erythroblast transformation specific domain

    2. NM_001243999.2 → NP_001230928.1  transcription factor Spi-B isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3, also known as DeltaSpi-B) uses an alternate splice junction at the 3' end of a coding exon compared to variant 1, that causes a frameshift. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1. This isoform is found in the cytoplasm instead of the nucleus.
      Source sequence(s)
      AC020909
      Consensus CDS
      CCDS59412.1
      UniProtKB/Swiss-Prot
      Q01892
      Related
      ENSP00000270632.7, ENST00000270632.7

    3. NM_001244000.2 → NP_001230929.2  transcription factor Spi-B isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice junction at the 5' end of a coding exon compared to variant 1, that causes a frameshift. The resulting isoform (4) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC020909
      Conserved Domains (1) summary
      smart00413
      Location:137 → 225
      ETS; erythroblast transformation specific domain

    4. NM_003121.5 → NP_003112.2  transcription factor Spi-B isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC020909
      Consensus CDS
      CCDS33080.1
      UniProtKB/Swiss-Prot
      A8K9C9, B4DUG6, Q01892, Q15359
      Related
      ENSP00000471921.1, ENST00000595883.6
      Conserved Domains (1) summary
      smart00413
      Location:168 → 256
      ETS; erythroblast transformation specific domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      50418938..50431314
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      53506494..53518875
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q01892.1 GenPept UniProtKB/Swiss-Prot:Q01892

    Gene LinkOut

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