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CHRD chordin [ Homo sapiens (human) ]

Gene ID: 8646, updated on 2-Nov-2024

Summary

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Official Symbol
CHRDprovided by HGNC
Official Full Name
chordinprovided by HGNC
Primary source
HGNC:HGNC:1949
See related
Ensembl:ENSG00000090539 MIM:603475; AllianceGenome:HGNC:1949
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 encodes a secreted protein that dorsalizes early vertebrate embryonic tissues by binding to ventralizing TGF-beta-like bone morphogenetic proteins and sequestering them in latent complexes. The encoded protein may also have roles in organogenesis and during adulthood. It has been suggested that this gene could be a candidate gene for Cornelia de Lange syndrome. Reduced expression of this gene results in enhanced bone regeneration. Alternative splicing results in multiple transcript variants. Other alternative splice variants have been described but their full length sequence has not been determined. [provided by RefSeq, Jan 2015]
Expression
Broad expression in endometrium (RPKM 10.5), liver (RPKM 6.4) and 23 other tissues See more
Orthologs
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Genomic context

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See CHRD in Genome Data Viewer
Location:
3q27.1
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (184380054..184390739)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (187189309..187199979)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (184097842..184108527)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20911 Neighboring gene RNA polymerase II, I and III subunit H Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184103787-184104288 Neighboring gene thrombopoietin Neighboring gene long intergenic non-protein coding RNA 2054 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184134067-184134568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184183685-184184186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184184187-184184686 Neighboring gene long intergenic non-protein coding RNA 1839 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:184208759-184209703 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:184209704-184210647 Neighboring gene transmembrane epididymal protein 3, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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?
  1. Data suggest CHRD (chordin) cleavage by tolloid-like metalloproteinases is insufficient to regulate BMP(bone morphogenetic protein)/BMPR signaling; CHRD fragments and TSG (twisted gastrulation protein) contribute to inhibition of BMP/BMPR signaling.
    Title: The role of chordin fragments generated by partial tolloid cleavage in regulating BMP activity.
  2. C-terminal chordin domains play an important role in Bone morphogenetic protein regulation.
    Title: Nanoscale structure of the BMP antagonist chordin supports cooperative BMP binding.
  3. chordin silencing increased osteogenic differentiation without supplemented BMP-2.
    Title: Gene silencing of chordin improves BMP-2 effects on osteogenic differentiation of human adipose tissue-derived stromal cells.
  4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  5. Noggin and chordin were also expressed most intensely in areas of cartilage formation and there was no difference in their expression between the non-hypertrophic and hypertrophic chondrocytes.
    Title: Regional and cellular localisation of BMPs and their inhibitors' expression in human fractures.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  7. there was no difference in the expression of the noggin and chordin between healing and nonhealing fractures
    Title: Altered relative expression of BMPs and BMP inhibitors in cartilaginous areas of human fractures progressing towards nonunion.
  8. Bone morphogenetic protein (BMP) chordin is produced endogenously during osteogenic differentiation of human mesenchymal stem cells (MSCs); blockade of bone morphogenetic inhibitor chordin increases the rate of osteogenic differentiation of MSCs in vitro.
    Title: Chordin knockdown enhances the osteogenic differentiation of human mesenchymal stem cells.
  9. results suggest that CHRD could participate in regulating BMP activity in normal ovarian surface epithelium physiology, and that its mis-expression in ovarian surface epithelium may facilitate cancer incidence and/or progression
    Title: Chordin is underexpressed in ovarian tumors and reduces tumor cell motility.
  10. Alternatively spliced variants have different patterns of expression to influence BMP activity in varying physiolgical situations.
    Title: The human chordin gene encodes several differentially expressed spliced variants with distinct BMP opposing activities.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of hematological and biochemical traits in a Japanese population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC133038

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables BMP binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cytokine binding 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 BMP signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in dorsal/ventral pattern formation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in floor plate development TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of BMP signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of BMP signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cell migration IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of osteoblast differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell adhesion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of mesenchymal cell proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in skeletal system development TAS
Traceable Author Statement
more info
 PubMed 
involved_in spinal cord dorsal/ventral patterning IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
chordin

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_029559.1 RefSeqGene

    Range
    4982..14757
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001304472.2 → NP_001291401.1  chordin isoform 2 precursor

    See identical proteins and their annotated locations for NP_001291401.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1 The encoded isoform (2) is one amino acid shorter than isoform 1.
    Source sequence(s)
    AC078797
    Consensus CDS
    CCDS77868.1
    UniProtKB/TrEMBL
    B7Z1H7, E7ESX1
    Related
    ENSP00000408972.1, ENST00000450923.5
    Conserved Domains (3) summary
    smart00214
    Location:784 → 850
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:532 → 646
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:51 → 125
    VWC; von Willebrand factor type C domain

  2. NM_001304473.2 → NP_001291402.1  chordin isoform 3

    See identical proteins and their annotated locations for NP_001291402.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon and uses an alternate splice site in its 5' UTR, compared to variant 1. These differences cause translation initiation at a downstream start codon and result in an isoform (3) with a shorter N-terminus, compared to isoform 1. Variants 3 and 4 encode the same protein.
    Source sequence(s)
    AC078797, AF209928, AF209930, AY358926, BC029879, BC112345
    UniProtKB/TrEMBL
    B7Z6K6
    Conserved Domains (3) summary
    smart00214
    Location:414 → 480
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:162 → 276
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:335 → 392
    VWC; von Willebrand factor type C domain

  3. NM_001304474.2 → NP_001291403.1  chordin isoform 3

    See identical proteins and their annotated locations for NP_001291403.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in its 5' UTR, compared to variant 1. This differences causes translation initiation at a downstream start codon and result in an isoform (3) with a shorter N-terminus, compared to isoform 1. Variants 3 and 4 encode the same protein.
    Source sequence(s)
    AC078797, AF209928, AF283325, AY358926, BC029879, BC112345
    UniProtKB/TrEMBL
    B7Z6K6
    Conserved Domains (3) summary
    smart00214
    Location:414 → 480
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:162 → 276
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:335 → 392
    VWC; von Willebrand factor type C domain

  4. NM_003741.4 → NP_003732.2  chordin isoform 1 precursor

    See identical proteins and their annotated locations for NP_003732.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC078797
    Consensus CDS
    CCDS3266.1
    UniProtKB/Swiss-Prot
    O95254, Q2M1I8, Q6UW83, Q9H2D3, Q9H2W8, Q9H2W9, Q9H2X0, Q9P0Z2, Q9P0Z3, Q9P0Z4, Q9P0Z5
    UniProtKB/TrEMBL
    B7Z1H7
    Related
    ENSP00000204604.1, ENST00000204604.6
    Conserved Domains (3) summary
    smart00214
    Location:784 → 850
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:532 → 646
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:51 → 125
    VWC; von Willebrand factor type C domain

RNA

  1. NR_130747.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate splice structure and lacks an alternate exon at internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC078797, AF209928, AK074147, BC029879, BC112345
    Related
    ENST00000470150.5

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    184380054..184390739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007388.2 → XP_016862877.1  chordin isoform X1

    UniProtKB/TrEMBL
    B7Z1H7

  2. XM_017007390.2 → XP_016862879.1  chordin isoform X3

    UniProtKB/TrEMBL
    B7Z1H7

  3. XM_011513254.2 → XP_011511556.1  chordin isoform X5

    UniProtKB/TrEMBL
    B7Z1H7
    Conserved Domains (3) summary
    smart00214
    Location:696 → 762
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:532 → 644
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:51 → 125
    VWC; von Willebrand factor type C domain

  4. XM_017007389.2 → XP_016862878.1  chordin isoform X2

    UniProtKB/TrEMBL
    B7Z1H7

  5. XM_017007391.2 → XP_016862880.1  chordin isoform X4

    UniProtKB/TrEMBL
    B7Z1H7

  6. XM_017007392.2 → XP_016862881.1  chordin isoform X6

    UniProtKB/TrEMBL
    B7Z1H7

  7. XM_047449110.1 → XP_047305066.1  chordin isoform X7

  8. XM_047449111.1 → XP_047305067.1  chordin isoform X8

  9. XM_017007393.2 → XP_016862882.1  chordin isoform X9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    187189309..187199979
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348216.1 → XP_054204191.1  chordin isoform X1

  2. XM_054348218.1 → XP_054204193.1  chordin isoform X3

  3. XM_054348220.1 → XP_054204195.1  chordin isoform X5

  4. XM_054348217.1 → XP_054204192.1  chordin isoform X2

  5. XM_054348219.1 → XP_054204194.1  chordin isoform X4

  6. XM_054348221.1 → XP_054204196.1  chordin isoform X6

  7. XM_054348222.1 → XP_054204197.1  chordin isoform X7

  8. XM_054348223.1 → XP_054204198.1  chordin isoform X8

  9. XM_054348224.1 → XP_054204199.1  chordin isoform X9

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_177978.1: Suppressed sequence

    Description
    NM_177978.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  2. NM_177979.1: Suppressed sequence

    Description
    NM_177979.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H2X0.2 GenPept UniProtKB/Swiss-Prot:Q9H2X0

Gene LinkOut

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