U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

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

    Gene ID: 9839, updated on 5-May-2024

    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; AllianceGenome:HGNC:14881
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See ZEB2 in Genome Data Viewer
    Location:
    2q22.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (144384081..144520119, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (144832138..144968126, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (145141648..145277686, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Rho GTPase activating protein 15 Neighboring gene ARHGAP15 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:144419424-144419959 Neighboring gene NANOG hESC enhancer GRCh37_chr2:144486483-144487103 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:144537063-144537656 Neighboring gene MPRA-validated peak3890 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:144649008-144649513 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:144649514-144650018 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:144664226-144664784 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:144694058-144694741 Neighboring gene uncharacterized LOC101928386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11990 Neighboring gene glycosyltransferase like domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16601 Neighboring gene MPRA-validated peak3893 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:145025446-145026228 Neighboring gene Sharpr-MPRA regulatory region 4867 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:145045189-145045690 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:145048337-145048837 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11992 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:145090135-145090712 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:145114539-145115052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16603 Neighboring gene skeletal muscle cis-regulatory module overlapping ZEB2 Neighboring gene Sharpr-MPRA regulatory region 3137 Neighboring gene VISTA enhancer hs407 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:145236544-145237256 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:145267859-145268774 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:145274915-145275416 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:145324978-145325484 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:145325485-145325991 Neighboring gene VISTA enhancer hs1802 Neighboring gene long intergenic non-protein coding RNA 1412 Neighboring gene long intergenic non-protein coding RNA 2993 Neighboring gene NANOG hESC enhancer GRCh37_chr2:145366588-145367089 Neighboring gene ZEB2 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:145469568-145470218 Neighboring gene testis expressed 41 Neighboring gene SGCE pseudogene 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 Functions

    What'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 2020-06-24)

    ClinGen Genome Curation PagePubMed
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-06-24)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ42816, KIAA0569

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in anatomical structure development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in astrocyte activation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in developmental pigmentation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in endothelial cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endothelial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in fibroblast activation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in melanocyte migration ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in myofibroblast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of fibroblast migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nervous system development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of melanin biosynthetic process IC
    Inferred by Curator
    more info
    PubMed 
    involved_in positive regulation of melanocyte differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of myofibroblast contraction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transforming growth factor beta receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in pyroptosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of blood-brain barrier permeability IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of melanosome organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in regulation of myofibroblast cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to oxygen-glucose deprivation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stress fiber assembly IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in 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)

    NEW Try the new Transcript table

    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
      5273..141311
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001171653.2NP_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, DA305985
      Consensus CDS
      CCDS54403.1
      UniProtKB/TrEMBL
      A0JP08
      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
      A0JP09, B7Z2P2, F5H814, O60315, Q9UED1
      UniProtKB/TrEMBL
      A0JP08
      Related
      ENSP00000487174.1, ENST00000627532.3
      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_033258.2 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, BU688017
      Related
      ENST00000465070.5

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      144384081..144520119 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      144832138..144968126 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)