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ZEB2 zinc finger E-box binding homeobox 2 [ Homo sapiens (human) ]

Gene ID: 9839, updated on 30-Dec-2018

Summary

Official Symbol
ZEB2provided by HGNC
Official Full Name
zinc finger E-box binding homeobox 2provided by HGNC
Primary source
HGNC:HGNC:14881
See related
Ensembl:ENSG00000169554 MIM:605802
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
SIP1; SIP-1; ZFHX1B; HSPC082; SMADIP1
Summary
The protein encoded by this gene is a member of the Zfh1 family of 2-handed zinc finger/homeodomain proteins. It is located in the nucleus and functions as a DNA-binding transcriptional repressor that interacts with activated SMADs. Mutations in this gene are associated with Hirschsprung disease/Mowat-Wilson syndrome. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Jan 2010]
Expression
Ubiquitous expression in brain (RPKM 13.4), appendix (RPKM 10.2) and 23 other tissues See more
Orthologs

Genomic context

See ZEB2 in Genome Data Viewer
Location:
2q22.3
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (144384375..144520391, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (145141942..145277958, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Rho GTPase activating protein 15 Neighboring gene uncharacterized LOC105373654 Neighboring gene uncharacterized LOC101928386 Neighboring gene glycosyltransferase like domain containing 1 Neighboring gene skeletal muscle cis-regulatory module overlapping ZEB2 Neighboring gene VISTA enhancer hs407 Neighboring gene uncharacterized LOC105373656 Neighboring gene VISTA enhancer hs1802 Neighboring gene long intergenic non-protein coding RNA 1412 Neighboring gene ZEB2 antisense RNA 1

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mowat-Wilson syndrome
MedGen: C1856113 OMIM: 235730 GeneReviews: Mowat-Wilson Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2011-10-06)

ClinGen Genome Curation PagePubMed
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2011-10-06)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Common variation at 2q22.3 (ZEB2) influences the risk of renal cancer.
NHGRI GWA Catalog
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
NHGRI GWA Catalog
Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32
NHGRI GWA Catalog
Genome-wide association study identifies ZFHX1B as a susceptibility locus for severe myopia.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Pathways from BioSystems

  • MicroRNAs in cancer, organism-specific biosystem (from KEGG)
    MicroRNAs in cancer, organism-specific biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • MicroRNAs in cancer, conserved biosystem (from KEGG)
    MicroRNAs in cancer, conserved biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • TGF-beta Receptor Signaling, organism-specific biosystem (from WikiPathways)
    TGF-beta Receptor Signaling, organism-specific biosystemThe Transforming growth factor beta (TGFβ) signaling pathway is involved in many cellular processes in both the adult organism and the developing embryo including cell growth, cell differentiat...
  • TGF-beta Signaling Pathway, organism-specific biosystem (from WikiPathways)
    TGF-beta Signaling Pathway, organism-specific biosystemThe signal transduction mechanisms underlying the pathophysiological activities of transforming growth factor-? (TGF-?) have been extensively studied since its discovery nearly 30 years ago. TGF-? li...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ42816, KIAA0569

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cell proliferation in forebrain IEA
Inferred from Electronic Annotation
more info
 
collateral sprouting IEA
Inferred from Electronic Annotation
more info
 
corpus callosum morphogenesis IEA
Inferred from Electronic Annotation
more info
 
corticospinal tract morphogenesis IEA
Inferred from Electronic Annotation
more info
 
developmental pigmentation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
hippocampus development IEA
Inferred from Electronic Annotation
more info
 
mammillary axonal complex development IEA
Inferred from Electronic Annotation
more info
 
melanocyte migration ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
nervous system development NAS
Non-traceable Author Statement
more info
PubMed 
neural crest cell migration IEA
Inferred from Electronic Annotation
more info
 
neural tube closure IEA
Inferred from Electronic Annotation
more info
 
positive regulation of JUN kinase activity IEA
Inferred from Electronic Annotation
more info
 
positive regulation of Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of axonogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of lens fiber cell differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of melanin biosynthetic process IC
Inferred by Curator
more info
PubMed 
positive regulation of melanocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of melanosome organization ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
somitogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
zinc finger E-box-binding homeobox 2
Names
SMAD interacting protein 1
Smad-interacting protein 1
zinc finger homeobox 1b

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.

Genomic

  1. NG_016431.1 RefSeqGene

    Range
    5001..141017
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001171653.1NP_001165124.1  zinc finger E-box-binding homeobox 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is missing an in-frame coding exon compared to variant 1, resulting in a shorter isoform (2) lacking an internal protein segment compared to isoform 1.
    Source sequence(s)
    AB056507, AC010130, AI341193, AK294928, BP218652, DA305985
    Consensus CDS
    CCDS54403.1
    UniProtKB/Swiss-Prot
    O60315
    Related
    ENSP00000443792.2, ENST00000539609.7
    Conserved Domains (6) summary
    COG5048
    Location:10001101
    COG5048; FOG: Zn-finger [General function prediction only]
    COG5576
    Location:570702
    COG5576; Homeodomain-containing transcription factor [Transcription]
    cd00086
    Location:629671
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    sd00017
    Location:977997
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:258280
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:272295
    zf-H2C2_2; Zinc-finger double domain
  2. NM_014795.4NP_055610.1  zinc finger E-box-binding homeobox 2 isoform 1

    See identical proteins and their annotated locations for NP_055610.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AB056507, AC010130, AI341193, DA305985
    Consensus CDS
    CCDS2186.1
    UniProtKB/Swiss-Prot
    O60315
    Related
    ENSP00000487174.1, ENST00000627532.2
    Conserved Domains (6) summary
    COG5048
    Location:10241125
    COG5048; FOG: Zn-finger [General function prediction only]
    COG5576
    Location:594726
    COG5576; Homeodomain-containing transcription factor [Transcription]
    cd00086
    Location:653695
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    sd00017
    Location:10011021
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:282304
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:296319
    zf-H2C2_2; Zinc-finger double domain

RNA

  1. NR_033258.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) is missing many exons from the 3' end and contains an alternate 3' terminal exon compared to variant 1. It is represented as non-coding because it has transcript support but lacks a large portion of the coding region.
    Source sequence(s)
    BC025696, BC025730, BP218652, BU688017
    Related
    ENST00000465070.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    144384375..144520391 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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