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    CHRD chordin [ Homo sapiens (human) ]

    Gene ID: 8646, updated on 10-Dec-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
    mouse all
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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
    • 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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    Related articles in PubMed

    1. Opponent activities of Shh and BMP signaling during floor plate induction in vivo. Patten I, et al. Curr Biol, 2002 Jan 8. PMID 11790302
    2. BMP-binding modules in chordin: a model for signalling regulation in the extracellular space. Larraín J, et al. Development, 2000 Feb. PMID 10648240, Free PMC Article
    3. Gene silencing of chordin improves BMP-2 effects on osteogenic differentiation of human adipose tissue-derived stromal cells. Schneider H, et al. Tissue Eng Part A, 2014 Jan. PMID 23931154
    4. Nanoscale structure of the BMP antagonist chordin supports cooperative BMP binding. Troilo H, et al. Proc Natl Acad Sci U S A, 2014 Sep 9. PMID 25157165, Free PMC Article
    5. Chordin knockdown enhances the osteogenic differentiation of human mesenchymal stem cells. Kwong FN, et al. Arthritis Res Ther, 2008. PMID 18533030, Free PMC Article

    See all (38) citations in PubMed

    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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    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
    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

      UniProtKB/TrEMBL
      B7Z1H7

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

      UniProtKB/TrEMBL
      B7Z1H7

    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

      UniProtKB/TrEMBL
      B7Z1H7

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

      UniProtKB/TrEMBL
      B7Z1H7

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

      UniProtKB/TrEMBL
      B7Z1H7

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

      UniProtKB/TrEMBL
      B7Z1H7

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

      UniProtKB/TrEMBL
      B7Z1H7

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

      UniProtKB/TrEMBL
      B7Z1H7

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

      UniProtKB/TrEMBL
      B7Z1H7

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

      UniProtKB/TrEMBL
      B7Z1H7

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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