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] See more...

Aliases for SPIB Gene

Aliases for SPIB Gene

  • Spi-B Transcription Factor 2 3 5
  • Spi-B Transcription Factor (Spi-1/PU.1 Related) 2 3
  • Transcription Factor Spi-B 3 4
  • SPI-B 3

External Ids for SPIB Gene

Previous GeneCards Identifiers for SPIB Gene

  • GC19P051551
  • GC19P051283
  • GC19P055598
  • GC19P055614
  • GC19P050922
  • GC19P047261

Summaries for SPIB Gene

Entrez Gene Summary for SPIB Gene

  • 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]

GeneCards Summary for SPIB Gene

SPIB (Spi-B Transcription Factor) is a Protein Coding gene. Diseases associated with SPIB include Primary Biliary Cirrhosis and Pitt-Hopkins Syndrome. Among its related pathways are Dendritic Cells Developmental Lineage Pathway and NF-kappaB Signaling. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and DNA-binding transcription factor activity, RNA polymerase II-specific. An important paralog of this gene is ENSG00000142539.

UniProtKB/Swiss-Prot Summary for SPIB Gene

  • Sequence specific transcriptional activator which binds to the PU-box, a purine-rich DNA sequence (5'-GAGGAA-3') that can act as a lymphoid-specific enhancer. Promotes development of plasmacytoid dendritic cells (pDCs), also known as type 2 DC precursors (pre-DC2) or natural interferon (IFN)-producing cells. These cells have the capacity to produce large amounts of interferon and block viral replication. May be required for B-cell receptor (BCR) signaling, which is necessary for normal B-cell development and antigenic stimulation.

Gene Wiki entry for SPIB Gene

Additional gene information for SPIB Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPIB Gene

Genomics for SPIB Gene

GeneHancer (GH) Regulatory Elements for SPIB Gene

Promoters and enhancers for SPIB Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J050414 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 500.7 -1.2 -1226 7.1 CTCF ZSCAN5C SIN3A NRF1 TCF12 MYC USF1 SP1 POLR2A ZBTB10 ENSG00000142539 SPIB POLD1 NAPSB KLK3
GH19J050427 Promoter/Enhancer 1.2 EPDnew ENCODE dbSUPER 500.4 +9.6 9649 2.2 HDAC2 POLR2A ZBTB17 SPI1 EBF1 IKZF1 NR2F1 REST ZBTB33 ZMYM3 SPIB ASPDH lnc-FAM71E1-3 piR-54261 ENSG00000142539
GH19J050430 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 0.4 +13.4 13389 4.5 ZBTB40 NRF1 SP1 PHF8 ZIC2 ZBTB10 GABPA ZBTB26 HES1 TOE1 MYBPC2 lnc-FAM71E1-3 ASPDH piR-54261 SPIB
GH19J050421 Enhancer 0.5 dbSUPER 0.7 +3.6 3555 1.2 POU2F2 NR2F1 GLIS1 ESRRA ZNF48 ZNF217 BHLHE40 EBF1 RUNX3 piR-54261 NAPSB KCNC3 SPIB ENSG00000142539
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPIB on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPIB

Top Transcription factor binding sites by QIAGEN in the SPIB gene promoter:
  • AhR
  • AML1a
  • Arnt
  • ARP-1
  • GATA-3
  • GR
  • GR-alpha
  • NF-kappaB1
  • STAT5A

Genomic Locations for SPIB Gene

Genomic Locations for SPIB Gene
chr19:50,418,938-50,431,314
(GRCh38/hg38)
Size:
12,377 bases
Orientation:
Plus strand
chr19:50,922,195-50,934,570
(GRCh37/hg19)
Size:
12,376 bases
Orientation:
Plus strand

Genomic View for SPIB Gene

Genes around SPIB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPIB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPIB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPIB Gene

Proteins for SPIB Gene

  • Protein details for SPIB Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q01892-SPIB_HUMAN
    Recommended name:
    Transcription factor Spi-B
    Protein Accession:
    Q01892
    Secondary Accessions:
    • A8K9C9
    • B4DUG6
    • Q15359

    Protein attributes for SPIB Gene

    Size:
    262 amino acids
    Molecular mass:
    28819 Da
    Quaternary structure:
    • Can form homotypic interactions. Interacts with IRF4. May also interact with CREBBP, EP300, SPI1/PU.1 related, JUN and TBP.

    Alternative splice isoforms for SPIB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPIB Gene

Post-translational modifications for SPIB Gene

No Post-translational modifications

Antibody Products

  • Abcam antibodies for SPIB
  • Boster Bio Antibodies for SPIB
  • Santa Cruz Biotechnology (SCBT) Antibodies for SPIB

No data available for DME Specific Peptides for SPIB Gene

Domains & Families for SPIB Gene

Gene Families for SPIB Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SPIB Gene

Suggested Antigen Peptide Sequences for SPIB Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57438, highly similar to Transcription factor Spi-B (B4DUG6_HUMAN)
  • Transcription factor Spi-B (SPIB_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q01892

UniProtKB/Swiss-Prot:

SPIB_HUMAN :
  • The protein contains a weakly acidic N-terminal transactivation domain (TAD) followed by a second TAD rich in proline, serine and threonine. Each of these domains may be required for transcriptional activation of a subset of target genes.
  • Belongs to the ETS family.
Domain:
  • The protein contains a weakly acidic N-terminal transactivation domain (TAD) followed by a second TAD rich in proline, serine and threonine. Each of these domains may be required for transcriptional activation of a subset of target genes.
Family:
  • Belongs to the ETS family.
genes like me logo Genes that share domains with SPIB: view

Function for SPIB Gene

Molecular function for SPIB Gene

UniProtKB/Swiss-Prot Function:
Sequence specific transcriptional activator which binds to the PU-box, a purine-rich DNA sequence (5'-GAGGAA-3') that can act as a lymphoid-specific enhancer. Promotes development of plasmacytoid dendritic cells (pDCs), also known as type 2 DC precursors (pre-DC2) or natural interferon (IFN)-producing cells. These cells have the capacity to produce large amounts of interferon and block viral replication. May be required for B-cell receptor (BCR) signaling, which is necessary for normal B-cell development and antigenic stimulation.
GENATLAS Biochemistry:
transcription factor SPI-B,homolog to Spi-1/PU.1 putative oncogene,expressed in various hematopoietic cell lines

Phenotypes From GWAS Catalog for SPIB Gene

Gene Ontology (GO) - Molecular Function for SPIB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding IMP 10196196
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IMP 10196196
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IEA --
genes like me logo Genes that share ontologies with SPIB: view
genes like me logo Genes that share phenotypes with SPIB: view

Human Phenotype Ontology for SPIB Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SPIB Gene

MGI Knock Outs for SPIB:

Animal Model Products

CRISPR Products

miRNA for SPIB Gene

miRTarBase miRNAs that target SPIB
Targeted motifs for SPIB Gene
HOMER Transcription Factor Regulatory Elements motif SPIB
  • Consensus sequence: AAAGRGGAAGTG Submotif: canonical Cell Type: OCILY3 GEO ID: GSE56857

Clone Products

  • Addgene plasmids for SPIB

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for SPIB Gene

Localization for SPIB Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPIB Gene

[Isoform 1]: Nucleus.
[Isoform 2]: Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPIB gene
Compartment Confidence
nucleus 4
plasma membrane 2
extracellular 2
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SPIB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA 21873635
GO:0005737 cytoplasm TAS 8670269
genes like me logo Genes that share ontologies with SPIB: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SPIB Gene

Pathways & Interactions for SPIB Gene

genes like me logo Genes that share pathways with SPIB: view

Pathways by source for SPIB Gene

1 R&D Systems pathway for SPIB Gene
1 Cell Signaling Technology pathway for SPIB Gene

SIGNOR curated interactions for SPIB Gene

Is inactivated by:
Other effect:

Gene Ontology (GO) - Biological Process for SPIB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II TAS,IBA 21873635
GO:0030154 cell differentiation IBA 21873635
GO:0045944 positive regulation of transcription by RNA polymerase II IMP 10196196
genes like me logo Genes that share ontologies with SPIB: view

Drugs & Compounds for SPIB Gene

(1) Drugs for SPIB Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SPIB: view

Transcripts for SPIB Gene

mRNA/cDNA for SPIB Gene

4 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for SPIB

Alternative Splicing Database (ASD) splice patterns (SP) for SPIB Gene

No ASD Table

Relevant External Links for SPIB Gene

GeneLoc Exon Structure for
SPIB

Expression for SPIB Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPIB Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SPIB Gene

This gene is overexpressed in Blymphocyte (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SPIB Gene



Protein tissue co-expression partners for SPIB Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPIB

SOURCE GeneReport for Unigene cluster for SPIB Gene:

Hs.437905

mRNA Expression by UniProt/SwissProt for SPIB Gene:

Q01892-SPIB_HUMAN
Tissue specificity: Expressed in plasmacytoid dendritic cells (pDCs) and B-cells, not expressed in T-cells or granulocytes. May also be enriched in stem cell populations of the liver.

Evidence on tissue expression from TISSUES for SPIB Gene

  • Intestine(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SPIB Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • lymphatic
Regions:
Abdomen:
  • biliary tract
  • liver
  • spleen
General:
  • blood
  • coagulation system
  • skin
genes like me logo Genes that share expression patterns with SPIB: view

No data available for mRNA differential expression in normal tissues for SPIB Gene

Orthologs for SPIB Gene

This gene was present in the common ancestor of chordates.

Orthologs for SPIB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia -- 31
  • 100 (a)
OneToMany
dog
(Canis familiaris)
Mammalia SPIB 30
  • 87.53 (n)
-- 31
  • 86 (a)
OneToMany
cow
(Bos Taurus)
Mammalia SPIB 30
  • 87.48 (n)
-- 31
  • 87 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Spib 30
  • 84.48 (n)
mouse
(Mus musculus)
Mammalia Spib 17 31 30
  • 83.72 (n)
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 36 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia spib 30
  • 59.81 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC53020 30
zebrafish
(Danio rerio)
Actinopterygii spi1a 31
  • 36 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 17 (a)
OneToMany
Species where no ortholog for SPIB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SPIB Gene

ENSEMBL:
Gene Tree for SPIB (if available)
TreeFam:
Gene Tree for SPIB (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPIB: view image

Paralogs for SPIB Gene

(2) SIMAP similar genes for SPIB Gene using alignment to 4 proteins:

  • SPIB_HUMAN
  • M0QXA8_HUMAN
  • M0R037_HUMAN
  • M0R2J9_HUMAN
genes like me logo Genes that share paralogs with SPIB: view

Variants for SPIB Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPIB Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
727050 Likely Benign: not provided 50,419,955(+) G/A SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
736583 Benign: not provided 50,419,939(+) C/T INTRON_VARIANT
750599 Likely Benign: not provided 50,419,983(+) G/A INTRON_VARIANT
753149 Likely Benign: not provided 50,423,712(+) T/C SYNONYMOUS_VARIANT
769042 Benign: not provided 50,423,008(+) G/C MISSENSE_VARIANT,SYNONYMOUS_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for SPIB Gene

Structural Variations from Database of Genomic Variants (DGV) for SPIB Gene

Variant ID Type Subtype PubMed ID
esv2661463 CNV deletion 23128226
nsv1066389 CNV gain 25217958
nsv1133010 OTHER inversion 24896259
nsv1140251 OTHER inversion 24896259
nsv1152956 OTHER inversion 26484159

Variation tolerance for SPIB Gene

Residual Variation Intolerance Score: 89% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.04; 60.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPIB Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPIB

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPIB Gene

Disorders for SPIB Gene

MalaCards: The human disease database

(3) MalaCards diseases for SPIB Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
primary biliary cirrhosis
  • pbc
pitt-hopkins syndrome
  • phs
burkitt lymphoma
  • bl
- elite association - COSMIC cancer census association via MalaCards
Search SPIB in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SPIB

genes like me logo Genes that share disorders with SPIB: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SPIB Gene

Publications for SPIB Gene

  1. Characterization of Spi-B, a transcription factor related to the putative oncoprotein Spi-1/PU.1. (PMID: 1406622) Ray D … Moreau-Gachelin F (Molecular and cellular biology 1992) 2 3 4 23 54
  2. The ETS transcription factor Spi-B is required for human plasmacytoid dendritic cell development. (PMID: 15583020) Schotte R … Blom B (The Journal of experimental medicine 2004) 3 4 23 54
  3. The transcription factor Spi-B is expressed in plasmacytoid DC precursors and inhibits T-, B-, and NK-cell development. (PMID: 12393575) Schotte R … Spits H (Blood 2003) 3 4 23 54
  4. Interaction between the hematopoietic Ets transcription factor Spi-B and the coactivator CREB-binding protein associated with negative cross-talk with c-Myb. (PMID: 11864910) Yamamoto H … Oikawa T (Cell growth & differentiation : the molecular biology journal of the American Association for Cancer Research 2002) 3 4 23 54
  5. Expression of transcription factors Pu.1, Spi-B, Blimp-1, BSAP and oct-2 in normal human plasma cells and in multiple myeloma cells. (PMID: 11841448) Nagy M … Matthes T (British journal of haematology 2002) 3 4 23 54

Products for SPIB Gene

Sources for SPIB Gene