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

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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ABCs begin with ZEB2.
Title: ABCs begin with ZEB2.
Age-associated CD4[+] T cells with B cell-promoting functions are regulated by ZEB2 in autoimmunity.
Title: Age-associated CD4(+) T cells with B cell-promoting functions are regulated by ZEB2 in autoimmunity.
Zeb2 drives the formation of CD11c[+] atypical B cells to sustain germinal centers that control persistent infection.
Title: Zeb2 drives the formation of CD11c(+) atypical B cells to sustain germinal centers that control persistent infection.
The transcription factor ZEB2 drives the formation of age-associated B cells.
Title: The transcription factor ZEB2 drives the formation of age-associated B cells.
The mesodermal and myogenic specification of hESCs depend on ZEB1 and are inhibited by ZEB2.
Title: The mesodermal and myogenic specification of hESCs depend on ZEB1 and are inhibited by ZEB2.
The SNTB1 and ZFHX1B gene have susceptibility in northern Han Chinese populations with high myopia.
Title: The SNTB1 and ZFHX1B gene have susceptibility in northern Han Chinese populations with high myopia.
Mowat-Wilson syndrome factor ZEB2 controls early formation of human neural crest through BMP signaling modulation.
Title: Mowat-Wilson syndrome factor ZEB2 controls early formation of human neural crest through BMP signaling modulation.
MOF-mediated acetylation of SIRT6 disrupts SIRT6-FOXA2 interaction and represses SIRT6 tumor-suppressive function by upregulating ZEB2 in NSCLC.
Title: MOF-mediated acetylation of SIRT6 disrupts SIRT6-FOXA2 interaction and represses SIRT6 tumor-suppressive function by upregulating ZEB2 in NSCLC.
miR-147a targets ZEB2 to regulate ox-LDL-induced monocyte adherence to HUVECs, atherosclerotic plaque formation, and stability in atherosclerosis.
Title: miR-147a targets ZEB2 to regulate ox-LDL-induced monocyte adherence to HUVECs, atherosclerotic plaque formation, and stability in atherosclerosis.
Lnc NR2F1-AS1 Promotes Breast Cancer Metastasis by Targeting the MiR-25-3p/ZEB2 Axis.
Title: Lnc NR2F1-AS1 Promotes Breast Cancer Metastasis by Targeting the MiR-25-3p/ZEB2 Axis.

Submit: New GeneRIF Correction See all GeneRIFs (273)

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

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Zeb2 (e-PCR), detects polymorphism
- UniSTS:546057

D11S2921 (e-PCR)
- UniSTS:152074

PMC156606P1 (e-PCR)
- UniSTS:271408

PMC156606P2 (e-PCR)
- UniSTS:271409

PMC156606P3 (e-PCR)
- UniSTS:271410

D8S2278 (e-PCR)
- UniSTS:473906

PMC156606P4 (e-PCR)
- UniSTS:271411

D8S2279 (e-PCR)
- UniSTS:473907

sY3084 (e-PCR)
- UniSTS:515126

RH69384 (e-PCR)
- UniSTS:68407

SHGC-32856 (e-PCR)
- UniSTS:23101

RH68819 (e-PCR)
- UniSTS:23373

SHGC-32375 (e-PCR)
- UniSTS:16722

L18426 (e-PCR)
- UniSTS:34648

RH16638 (e-PCR)
- UniSTS:11878

SHGC-79910 (e-PCR)
- UniSTS:101479

STS-T23699 (e-PCR)
- UniSTS:4201

RH98161 (e-PCR)
- UniSTS:87935

WI-17978 (e-PCR)
- UniSTS:8328

RH119637 (e-PCR)
- UniSTS:133006

D11S3114 (e-PCR)
- UniSTS:152207

SHGC-35092 (e-PCR)
- UniSTS:35732

Zeb2 (e-PCR), detects polymorphism
- UniSTS:275880

RH16338 (e-PCR)
- UniSTS:9146

SHGC-82424 (e-PCR)
- UniSTS:104407

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables phosphatase regulator activity	NAS Non-traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

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

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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)

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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.

Genomic

NG_016431.1 RefSeqGene

Range

5273..141311

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001171653.2 → NP_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:1000 → 1101

COG5048; FOG: Zn-finger [General function prediction only]

COG5576
Location:570 → 702

COG5576; Homeodomain-containing transcription factor [Transcription]

cd00086
Location:629 → 671

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:977 → 997

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:258 → 280

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:272 → 295

zf-H2C2_2; Zinc-finger double domain
NM_014795.4 → NP_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:1024 → 1125

COG5048; FOG: Zn-finger [General function prediction only]

COG5576
Location:594 → 726

COG5576; Homeodomain-containing transcription factor [Transcription]

cd00086
Location:653 → 695

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:1001 → 1021

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:282 → 304

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:296 → 319

zf-H2C2_2; Zinc-finger double domain

RNA

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