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

Gene ID: 6689, updated on 5-Mar-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
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Genomic context

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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. 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.
  2. Peroxiredoxin2 regulates trophoblast proliferation and migration through SPIB-HDAC2 pathway.
    Title: Peroxiredoxin2 regulates trophoblast proliferation and migration through SPIB-HDAC2 pathway.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. These results show that the mechanism of action of lenalidomide in ABC-DLBCL cells involves downregulation of SPIB transcription by cereblon-induced degradation of IKAROS.
    Title: Lenalidomide modulates gene expression in human ABC-DLBCL cells by regulating IKAROS interaction with an intronic control region of SPIB.
Submit: New GeneRIF Correction See all GeneRIFs (26)

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

    See identical proteins and their annotated locations for NP_001230927.1

    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

    See identical proteins and their annotated locations for NP_001230928.1

    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

    See identical proteins and their annotated locations for NP_003112.2

    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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