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

Gene ID: 6689, updated on 2-Oct-2018

Summary

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; Vega:OTTHUMG00000183039
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

Genomic context

See SPIB in Genome Data Viewer
Location:
19q13.33
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (50418938..50431053)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (50922195..50934310)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene nuclear receptor subfamily 1 group H member 2 Neighboring gene DNA polymerase delta 1, catalytic subunit Neighboring gene myosin binding protein C, fast type Neighboring gene family with sequence similarity 71 member E1 Neighboring gene ER membrane protein complex subunit 10

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001243998.1NP_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, AK225720, AK300639, GD140573
    Consensus CDS
    CCDS58674.1
    UniProtKB/Swiss-Prot
    Q01892
    Related
    ENSP00000391877.2, ENST00000439922.6
    Conserved Domains (1) summary
    smart00413
    Location:77165
    ETS; erythroblast transformation specific domain
  2. NM_001243999.1NP_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, AK225720, GD140573, X96998
    Consensus CDS
    CCDS59412.1
    UniProtKB/Swiss-Prot
    Q01892
    Related
    ENSP00000270632.7, OTTHUMP00000270694, ENST00000270632.7, OTTHUMT00000464750
  3. NM_001244000.1NP_001230929.1  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, AK225720, DA957263, GD140573, X66079
    UniProtKB/Swiss-Prot
    Q01892
    Conserved Domains (1) summary
    smart00413
    Location:137225
    ETS; erythroblast transformation specific domain
  4. NM_003121.4NP_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, AK225720, GD140573, X66079
    Consensus CDS
    CCDS33080.1
    UniProtKB/Swiss-Prot
    Q01892
    UniProtKB/TrEMBL
    A0A024R4I5
    Related
    ENSP00000471921.1, OTTHUMP00000270690, ENST00000595883.5, OTTHUMT00000464744
    Conserved Domains (1) summary
    smart00413
    Location:168256
    ETS; erythroblast transformation specific domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    50418938..50431053
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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