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EDN3 endothelin 3 [ Homo sapiens (human) ]

Gene ID: 1908, updated on 4-Jan-2025

Summary

Official Symbol
EDN3provided by HGNC
Official Full Name
endothelin 3provided by HGNC
Primary source
HGNC:HGNC:3178
See related
Ensembl:ENSG00000124205 MIM:131242; AllianceGenome:HGNC:3178
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
ET3; ET-3; WS4B; HSCR4; PPET3
Summary
The protein encoded by this gene is a member of the endothelin family. Endothelins are endothelium-derived vasoactive peptides involved in a variety of biological functions. The active form of this protein is a 21 amino acid peptide processed from the precursor protein. The active peptide is a ligand for endothelin receptor type B (EDNRB). The interaction of this endothelin with EDNRB is essential for development of neural crest-derived cell lineages, such as melanocytes and enteric neurons. Mutations in this gene and EDNRB have been associated with Hirschsprung disease (HSCR) and Waardenburg syndrome (WS), which are congenital disorders involving neural crest-derived cells. Altered expression of this gene is implicated in tumorigenesis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]
Expression
Biased expression in small intestine (RPKM 16.6), duodenum (RPKM 16.3) and 11 other tissues See more
Orthologs
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Genomic context

See EDN3 in Genome Data Viewer
Location:
20q13.32
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (59300611..59325992)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (61083933..61109315)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (57875666..57901047)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:57697082-57697631 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:57724967-57725189 Neighboring gene mitochondrial ribosomal protein S16 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57734401-57735226 Neighboring gene zinc finger protein 831 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:57770614-57771813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57893004-57893504 Neighboring gene Sharpr-MPRA regulatory region 9189 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57950919-57951420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57979490-57979990 Neighboring gene NANOG hESC enhancer GRCh37_chr20:58013205-58013760 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:58051005-58051166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58070963-58071463 Neighboring gene piezo type mechanosensitive ion channel component 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58089356-58090192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58090193-58091028 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:58133017-58133222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58143003-58143837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58147145-58147686 Neighboring gene MPRA-validated peak4290 silencer Neighboring gene phosphatase and actin regulator 3 Neighboring gene PHACTR3 antisense RNA 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Hirschsprung disease, susceptibility to, 4
MedGen: C3150975 OMIM: 613712 GeneReviews: Not available
Compare labs
Waardenburg syndrome type 4B
MedGen: C2750457 OMIM: 613265 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.
EBI GWAS Catalog
Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.
EBI GWAS Catalog
Genome-wide association study of blood pressure and hypertension.
EBI GWAS Catalog
Genomic association analysis of common variants influencing antihypertensive response to hydrochlorothiazide.
EBI GWAS Catalog

Pathways from PubChem

Interactions

General gene information

Clone Names

  • MGC15067, MGC61498

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables endothelin B receptor binding  
enables endothelin B receptor binding PubMed 
enables hormone activity  
enables hormone activity PubMed 
enables signaling receptor binding PubMed 
Items 1 - 25 of 33
Process Evidence Code Pubs
NOT involved_in artery smooth muscle contraction PubMed 
involved_in axon extension  
involved_in axon guidance  
involved_in blood circulation PubMed 
involved_in cell population proliferation  
involved_in cell surface receptor signaling pathway PubMed 
involved_in cell-cell signaling PubMed 
involved_in establishment of localization in cell  
involved_in intracellular calcium ion homeostasis  
involved_in intracellular magnesium ion homeostasis  
involved_in melanocyte differentiation  
involved_in neural crest cell migration  
involved_in neutrophil chemotaxis PubMed 
involved_in peptide hormone secretion PubMed 
involved_in positive regulation of MAP kinase activity PubMed 
acts_upstream_of_or_within positive regulation of cell differentiation PubMed 
acts_upstream_of_or_within positive regulation of cell population proliferation PubMed 
involved_in positive regulation of heart rate PubMed 
involved_in positive regulation of hormone secretion PubMed 
involved_in positive regulation of leukocyte chemotaxis PubMed 
involved_in positive regulation of mitotic nuclear division PubMed 
involved_in positive regulation of potassium ion transmembrane transport  
involved_in positive regulation of smooth muscle contraction  
involved_in potassium ion transmembrane transport  
involved_in regulation of developmental pigmentation  
acts_upstream_of_or_within regulation of gene expression PubMed 
involved_in regulation of systemic arterial blood pressure by endothelin  
involved_in regulation of systemic arterial blood pressure by endothelin PubMed 
involved_in regulation of vasoconstriction  
involved_in signal transduction PubMed 
involved_in vasoconstriction PubMed 
involved_in vein smooth muscle contraction  
involved_in vein smooth muscle contraction PubMed 
Items 1 - 25 of 33
Component Evidence Code Pubs
located_in extracellular region  
is_active_in extracellular space  
located_in extracellular space PubMed 

General protein information

Preferred Names
endothelin-3
Names
preproendothelin-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.

Genomic

  1. NG_008050.1 RefSeqGene

    Range
    5168..30549
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1381

mRNA and Protein(s)

  1. NM_001302455.2NP_001289384.1  endothelin-3 isoform 4 preproprotein

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in the 3' terminal exon, which results in a frameshift and an early stop codon, compared to variant 4. The encoded isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC008876, BC053866, DN989853
    UniProtKB/TrEMBL
    A0A2R8Y214
    Related
    ENSP00000493472.1, ENST00000644821.1
    Conserved Domains (2) summary
    smart00272
    Location:158179
    END; Endothelin
    pfam00322
    Location:93121
    Endothelin; Endothelin family
  2. NM_001302456.2NP_001289385.1  endothelin-3 isoform 5 preproprotein

    See identical proteins and their annotated locations for NP_001289385.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an exon in the 3' coding region, which results in a frameshift and an early stop codon, compared to variant 4. The encoded isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC008876, BC053866, DQ096281, X52001
    Consensus CDS
    CCDS77597.1
    UniProtKB/TrEMBL
    A0A2R8Y214, Q4FAT2
    Related
    ENSP00000360064.3, ENST00000371025.7
    Conserved Domains (2) summary
    smart00272
    Location:158179
    END; Endothelin
    pfam00322
    Location:93121
    Endothelin; Endothelin family
  3. NM_001424361.1NP_001411290.1  endothelin-3 isoform 6 preproprotein

    Status: REVIEWED

    Source sequence(s)
    AL035250
    UniProtKB/TrEMBL
    A0A2R8Y214
  4. NM_001424362.1NP_001411291.1  endothelin-3 isoform 7 preproprotein

    Status: REVIEWED

    Source sequence(s)
    AL035250
  5. NM_001424363.1NP_001411292.1  endothelin-3 isoform 8 preproprotein

    Status: REVIEWED

    Source sequence(s)
    AL035250
    UniProtKB/TrEMBL
    A0A2R8Y214
  6. NM_207032.3NP_996915.1  endothelin-3 isoform 2 preproprotein

    See identical proteins and their annotated locations for NP_996915.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 4. The encoded isoform (2), is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC008876, BC053866
    Consensus CDS
    CCDS13479.1
    UniProtKB/TrEMBL
    A0A2R8Y214
    Related
    ENSP00000311854.7, ENST00000311585.11
    Conserved Domains (2) summary
    smart00272
    Location:158179
    END; Endothelin
    pfam00322
    Location:93121
    Endothelin; Endothelin family
  7. NM_207033.3NP_996916.1  endothelin-3 isoform 3 preproprotein

    See identical proteins and their annotated locations for NP_996916.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 3' coding region and uses an alternate in-frame splice site in the 3' coding region, compared to variant 4. The encoded isoform (3) is shorter and has two distinct internal amino acids, compared to isoform 1.
    Source sequence(s)
    BC008876, BC053866, X52001
    Consensus CDS
    CCDS13478.1
    UniProtKB/TrEMBL
    A0A2R8Y214
    Related
    ENSP00000379015.3, ENST00000395654.3
    Conserved Domains (2) summary
    smart00272
    Location:158179
    END; Endothelin
    pfam00322
    Location:93121
    Endothelin; Endothelin family
  8. NM_207034.3NP_996917.1  endothelin-3 isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_996917.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (1).
    Source sequence(s)
    BC008876
    Consensus CDS
    CCDS13477.1
    UniProtKB/Swiss-Prot
    E1P5I5, P14138, Q03229, Q7Z6D2, Q9UGT7
    UniProtKB/TrEMBL
    A0A2R8Y214
    Related
    ENSP00000337128.2, ENST00000337938.7
    Conserved Domains (3) summary
    PHA03418
    Location:2487
    PHA03418; hypothetical E4 protein; Provisional
    smart00272
    Location:158179
    END; Endothelin
    pfam00322
    Location:93121
    Endothelin; Endothelin family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    59300611..59325992
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011528655.3XP_011526957.1  endothelin-3 isoform X2

    Conserved Domains (2) summary
    smart00272
    Location:158179
    END; Endothelin
    pfam00322
    Location:93121
    Endothelin; Endothelin family

RNA

  1. XR_936513.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    61083933..61109315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054323135.1XP_054179110.1  endothelin-3 isoform X2

RNA

  1. XR_008485241.1 RNA Sequence

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