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CHRD chordin [ Homo sapiens (human) ]

Gene ID: 8646, updated on 1-Mar-2024

Summary

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

See CHRD in Genome Data Viewer
Location:
3q27.1
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (184380054..184390739)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (187189309..187199979)
105.20220307 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

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

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 
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 

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_001304472.2NP_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: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/TrEMBL
    B7Z6K6
    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/TrEMBL
    B7Z6K6
    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_003741.4NP_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: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: 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_000003.12 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017007388.2XP_016862877.1  chordin isoform X1

    UniProtKB/TrEMBL
    B7Z1H7
  2. XM_017007390.2XP_016862879.1  chordin isoform X3

    UniProtKB/TrEMBL
    B7Z1H7
  3. XM_011513254.2XP_011511556.1  chordin isoform X5

    UniProtKB/TrEMBL
    B7Z1H7
    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
  4. XM_017007389.2XP_016862878.1  chordin isoform X2

    UniProtKB/TrEMBL
    B7Z1H7
  5. XM_017007391.2XP_016862880.1  chordin isoform X4

    UniProtKB/TrEMBL
    B7Z1H7
  6. XM_017007392.2XP_016862881.1  chordin isoform X6

    UniProtKB/TrEMBL
    B7Z1H7
  7. XM_047449110.1XP_047305066.1  chordin isoform X7

    UniProtKB/TrEMBL
    B7Z1H7
  8. XM_047449111.1XP_047305067.1  chordin isoform X8

    UniProtKB/TrEMBL
    B7Z1H7
  9. XM_017007393.2XP_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_054348216.1XP_054204191.1  chordin isoform X1

    UniProtKB/TrEMBL
    B7Z1H7
  2. XM_054348218.1XP_054204193.1  chordin isoform X3

    UniProtKB/TrEMBL
    B7Z1H7
  3. XM_054348220.1XP_054204195.1  chordin isoform X5

    UniProtKB/TrEMBL
    B7Z1H7
  4. XM_054348217.1XP_054204192.1  chordin isoform X2

    UniProtKB/TrEMBL
    B7Z1H7
  5. XM_054348219.1XP_054204194.1  chordin isoform X4

    UniProtKB/TrEMBL
    B7Z1H7
  6. XM_054348221.1XP_054204196.1  chordin isoform X6

    UniProtKB/TrEMBL
    B7Z1H7
  7. XM_054348222.1XP_054204197.1  chordin isoform X7

    UniProtKB/TrEMBL
    B7Z1H7
  8. XM_054348223.1XP_054204198.1  chordin isoform X8

    UniProtKB/TrEMBL
    B7Z1H7
  9. XM_054348224.1XP_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.