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CHRD chordin [ Homo sapiens (human) ]

Gene ID: 8646, updated on 1-Jun-2020

Summary

Official Symbol
CHRDprovided by HGNC
Official Full Name
chordinprovided by HGNC
Primary source
HGNC:HGNC:1949
See related
Ensembl:ENSG00000090539 MIM:603475
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

Genomic context

See CHRD in Genome Data Viewer
Location:
3q27.1
Exon count:
24
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (184380073..184390739)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (184097861..184107617)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene RNA polymerase II, I and III subunit H Neighboring gene thrombopoietin Neighboring gene long intergenic non-protein coding RNA 2054 Neighboring gene transmembrane epididymal protein 1 pseudogene

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

NHGRI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC133038

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cytokine binding NAS
Non-traceable Author Statement
more info
PubMed 
heparin binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
syndecan binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
BMP signaling pathway involved in spinal cord dorsal/ventral patterning IMP
Inferred from Mutant Phenotype
more info
PubMed 
floor plate development TAS
Traceable Author Statement
more info
PubMed 
forebrain development IEA
Inferred from Electronic Annotation
more info
 
gastrulation with mouth forming second IEA
Inferred from Electronic Annotation
more info
 
mesoderm formation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of BMP signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of osteoblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
osteoblast differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of mesenchymal cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
skeletal system development TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
extracellular space NAS
Non-traceable Author Statement
more info
PubMed 

NCBI Reference Sequences (RefSeq)

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
    5001..14763
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001304472.1NP_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)
    AF209928, AY358926, BC029879, BC112345
    Consensus CDS
    CCDS77868.1
    UniProtKB/Swiss-Prot
    Q9H2X0
    UniProtKB/TrEMBL
    E7ESX1, Q8N2W7
    Related
    ENSP00000408972.1, ENST00000450923.5
    Conserved Domains (3) summary
    smart00214
    Location:784850
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:532646
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:51125
    VWC; von Willebrand factor type C domain
  2. NM_001304473.2NP_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/Swiss-Prot
    Q9H2X0
    UniProtKB/TrEMBL
    Q8N2W7
    Conserved Domains (3) summary
    smart00214
    Location:414480
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:162276
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:335392
    VWC; von Willebrand factor type C domain
  3. NM_001304474.2NP_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/Swiss-Prot
    Q9H2X0
    UniProtKB/TrEMBL
    Q8N2W7
    Conserved Domains (3) summary
    smart00214
    Location:414480
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:162276
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:335392
    VWC; von Willebrand factor type C domain
  4. NM_003741.3NP_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)
    AF209928, BC029879, BC112345
    Consensus CDS
    CCDS3266.1
    UniProtKB/Swiss-Prot
    Q9H2X0
    UniProtKB/TrEMBL
    Q8N2W7
    Related
    ENSP00000204604.1, ENST00000204604.5
    Conserved Domains (3) summary
    smart00214
    Location:784850
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:532646
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:51125
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    184380073..184390739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007388.1XP_016862877.1  chordin isoform X1

  2. XM_017007389.1XP_016862878.1  chordin isoform X2

  3. XM_017007390.1XP_016862879.1  chordin isoform X3

  4. XM_017007391.1XP_016862880.1  chordin isoform X4

  5. XM_011513254.1XP_011511556.1  chordin isoform X5

    Conserved Domains (3) summary
    smart00214
    Location:696762
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:532644
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:51125
    VWC; von Willebrand factor type C domain
  6. XM_017007392.1XP_016862881.1  chordin isoform X6

  7. XM_017007393.1XP_016862882.1  chordin isoform X7

  8. XM_017007394.1XP_016862883.1  chordin isoform X8

  9. XM_024453803.1XP_024309571.1  chordin isoform X9

    Conserved Domains (3) summary
    smart00214
    Location:414480
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:162276
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:335392
    VWC; von Willebrand factor type C domain

RNA

  1. XR_002959603.1 RNA Sequence

  2. XR_001740334.1 RNA Sequence

  3. XR_001740335.1 RNA Sequence

  4. XR_001740336.1 RNA Sequence

  5. XR_001740337.1 RNA Sequence

    Related
    ENST00000420973.5

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.
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