ZBED3 zinc finger BED-type containing 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZBED3provided by HGNC
Official Full Name: zinc finger BED-type containing 3provided by HGNC
Primary source: HGNC:HGNC:20711
See related: Ensembl:ENSG00000132846 MIM:615250; AllianceGenome:HGNC:20711
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
Summary: This gene belongs to a class of genes that arose through hAT DNA transposition and that encode regulatory proteins. This gene is upregulated in lung cancer tissues, where the encoded protein causes an accumulation of beta-catenin and enhanced lung cancer cell invasion. In addition, the encoded protein can be secreted and be involved in resistance to insulin. [provided by RefSeq, Jul 2016]
Expression: Ubiquitous expression in fat (RPKM 5.0), kidney (RPKM 4.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q13.3

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (77072072..77087285, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (77553725..77568916, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (76367897..76383110, complement)

Chromosome 5 - NC_000005.10 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RNA 5-methylcytosine writer NSUN5 promotes hepatocellular carcinoma cell proliferation via a ZBED3-dependent mechanism.
Title: RNA 5-methylcytosine writer NSUN5 promotes hepatocellular carcinoma cell proliferation via a ZBED3-dependent mechanism.
Circular RNA hsa_circ_0119412 contributes to tumorigenesis of gastric cancer via the regulation of the miR-1298-5p/zinc finger BED-type containing 3 (ZBED3) axis.
Title: Circular RNA hsa_circ_0119412 contributes to tumorigenesis of gastric cancer via the regulation of the miR-1298-5p/zinc finger BED-type containing 3 (ZBED3) axis.
Long noncoding RNA ZBED3-AS1 restrains breast cancer progression by targeting the microRNA-513a-5p/KLF6 axis.
Title: Long noncoding RNA ZBED3-AS1 restrains breast cancer progression by targeting the microRNA-513a-5p/KLF6 axis.
The function of BED finger domain of Zbed3 in regulating lung cancer cell proliferation.
Title: The function of BED finger domain of Zbed3 in regulating lung cancer cell proliferation.
Zbed3 enhances lung cancer cell proliferation.
Title: Zbed3 promotes proliferation and invasion of lung cancer partly through regulating the function of Axin-Gsk3β complex.
Zbed3 concentrations were significantly higher in metabolic syndrome patients compared with healthy subjects. Circulating Zbed3 concentrations were associated with glucose and lipid parameters, markers of adiposity, and blood pressure.
Title: Circulating Zbed3 Levels in Subjects With and Without Metabolic Syndrome.
Finally, the wnt-inhibitor DKK1 could reverse the stimulatory effect of ZBED3-AS1 on chondrogenesis. These findings demonstrate the role of a new lncRNA, ZBED3-AS1, in SFMSC chondrogenesis and may improve osteoarthritis treatment.
Title: The LncRNA ZBED3-AS1 induces chondrogenesis of human synovial fluid mesenchymal stem cells.
results suggest that Zbed3 may contribute to lung cancer cell invasion through regulating beta-catenin and p120ctn-1 and may be a promissing cancer marker in non-small cell lung cancer
Title: Zbed3 contributes to malignant phenotype of lung cancer via regulating β-catenin and P120-catenin 1.
results suggest that the Zbed3 protein may be a cytokine associated with insulin resistance in humans that is influenced by glucose and insulin levels.
Title: Zinc-finger BED domain-containing 3 (Zbed3) is a novel secreted protein associated with insulin resistance in humans.
Observational study of gene-disease association, gene-gene interaction, and gene-environment interaction. (HuGE Navigator)
Title: Genetic risk reclassification for type 2 diabetes by age below or above 50 years using 40 type 2 diabetes risk single nucleotide polymorphisms.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

EBI GWAS Catalog

Description
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. 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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in actin filament organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in endoplasmic reticulum localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in establishment of spindle localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in mitochondrion localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of protein phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of canonical Wnt signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of embryonic development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein stabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to glucose	IDA Inferred from Direct Assay more info	PubMed
involved_in response to insulin	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: zinc finger BED domain-containing protein 3

Names: 2610005H11Rik; axin-interacting protein; zinc finger, BED domain containing 3

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.

mRNA and Protein(s)

NM_001329564.2 → NP_001316493.1 zinc finger BED domain-containing protein 3

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.

Source sequence(s)

AC008581, BC007239, BF508552, BY798736, DN998543

Consensus CDS

CCDS4036.1

UniProtKB/Swiss-Prot

Q96IU2

UniProtKB/TrEMBL

Q53EL5

Conserved Domains (1) summary

smart00614
Location:47 → 100

ZnF_BED; BED zinc finger
NM_032367.4 → NP_115743.1 zinc finger BED domain-containing protein 3

See identical proteins and their annotated locations for NP_115743.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 both encode the same protein.

Source sequence(s)

AC008581, BC007239, BF508552, DN998543

Consensus CDS

CCDS4036.1

UniProtKB/Swiss-Prot

Q96IU2

UniProtKB/TrEMBL

Q53EL5

Related

ENSP00000255198.2, ENST00000255198.3

Conserved Domains (1) summary

smart00614
Location:47 → 100

ZnF_BED; BED zinc finger

RNA

NR_138050.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 3' end compared to variant 1. This variant is represented as non-coding because it lacks the entire coding region compared to variant 1.

Source sequence(s)

AC008581