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    NODAL nodal growth differentiation factor [ Homo sapiens (human) ]

    Gene ID: 4838, updated on 16-Apr-2024

    Summary

    Official Symbol
    NODALprovided by HGNC
    Official Full Name
    nodal growth differentiation factorprovided by HGNC
    Primary source
    HGNC:HGNC:7865
    See related
    Ensembl:ENSG00000156574 MIM:601265; AllianceGenome:HGNC:7865
    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
    HTX5
    Summary
    This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate the mature protein, which regulates early embryonic development. This protein is required for maintenance of human embryonic stem cell pluripotency and may play a role in human placental development. Mutations in this gene are associated with heterotaxy, a condition characterized by random orientation of visceral organs with respect to the left-right axis. [provided by RefSeq, Aug 2016]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    10q22.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (70431936..70447951, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (71301367..71317383, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (72191692..72207707, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene centrosomal protein 57 like 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2447 Neighboring gene eukaryotic translation initiation factor 4E binding protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72194899-72195400 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72197102-72197282 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72199683-72200292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72200293-72200900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72200901-72201510 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72202121-72202730 Neighboring gene Sharpr-MPRA regulatory region 10829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72210316-72210984 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:72214954-72215480 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72215481-72216006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72232724-72233490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2449 Neighboring gene phosphatase domain containing paladin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72239853-72240495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72240496-72241137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72242631-72243178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2450 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72253375-72254035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3508 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72258695-72259456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72259457-72260216 Neighboring gene YY1 transcription factor pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72273197-72273732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72273733-72274267 Neighboring gene Sharpr-MPRA regulatory region 14353 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:72288493-72289410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72297349-72298033 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72298034-72298719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72301641-72302141 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72318935-72319878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72319879-72320822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72344798-72345298 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72345790-72345956 Neighboring gene Sharpr-MPRA regulatory region 12376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72356137-72356637 Neighboring gene perforin 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
    Heterotaxy, visceral, 5, autosomal
    MedGen: C3495537 OMIM: 270100 GeneReviews: Not available
    Compare labs
    Holoprosencephaly sequence
    MedGen: C0079541 GeneReviews: Holoprosencephaly Overview
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2013-08-08)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2013-08-08)

    ClinGen Genome Curation PagePubMed

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC138230

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cytokine activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables growth factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables morphogen activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables type I activin receptor binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in axial mesodermal cell fate specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in brain development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell migration involved in gastrulation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in determination of left/right asymmetry in lateral mesoderm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in digestive tract morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic cranial skeleton morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic pattern specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic placenta development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic process involved in female pregnancy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endodermal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in floor plate morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in formation of anatomical boundary IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in germ cell development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in heart looping IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inhibition of neuroepithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in left lung morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in liver development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in maternal placenta development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in maternal process involved in parturition IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mesendoderm development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of androgen receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of chorionic trophoblast cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of trophoblast cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in neural fold formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nodal signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in placenta development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in polarity specification of proximal/distal axis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of ERK1 and ERK2 cascade IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of SMAD protein signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of activin receptor signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell-cell adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cysteine-type endopeptidase activity involved in apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of epithelial cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of vascular endothelial growth factor production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in primitive streak formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of gastrulation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of stem cell population maintenance TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in somatic stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transforming growth factor beta receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in trophectodermal cellular morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in vasculature development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 

    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_012448.2 RefSeqGene

      Range
      11268..21013
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001329906.2NP_001316835.1  nodal homolog isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream translation start site compared to variant 1. The encoded isoform (2) has a shorter N-terminus, and lacks the signal peptide and a portion of the propeptide compared to isoform 1.
      Source sequence(s)
      AC022532, AI670948, BC039861
      Conserved Domains (1) summary
      smart00204
      Location:114213
      TGFB; Transforming growth factor-beta (TGF-beta) family
    2. NM_018055.5NP_060525.3  nodal homolog isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_060525.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC022532, BC033585, BC104976
      Consensus CDS
      CCDS7304.1
      UniProtKB/Swiss-Prot
      Q2M3A5, Q8N4V3, Q96S42
      UniProtKB/TrEMBL
      H7C0E4
      Related
      ENSP00000287139.3, ENST00000287139.8
      Conserved Domains (2) summary
      smart00204
      Location:247346
      TGFB; Transforming growth factor-beta (TGF-beta) family
      pfam00688
      Location:29166
      TGFb_propeptide; TGF-beta propeptide

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      70431936..70447951 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024448028.2XP_024303796.1  nodal homolog isoform X1

      Conserved Domains (1) summary
      smart00204
      Location:114213
      TGFB; Transforming growth factor-beta (TGF-beta) family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      71301367..71317383 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365958.1XP_054221933.1  nodal homolog isoform X1