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Chrd chordin [ Mus musculus (house mouse) ]

Gene ID: 12667, updated on 6-Jun-2024

Summary

Official Symbol
Chrdprovided by MGI
Official Full Name
chordinprovided by MGI
Primary source
MGI:MGI:1313268
See related
Ensembl:ENSMUSG00000006958 AllianceGenome:MGI:1313268
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Chd
Summary
Enables heparin binding activity and syndecan binding activity. Acts upstream of or within several processes, including gastrulation; negative regulation of BMP signaling pathway; and negative regulation of osteoblast differentiation. Located in extracellular space. Is expressed in several structures, including alimentary system; branchial arch; central nervous system; genitourinary system; and skeletal system. Used to study DiGeorge syndrome and velocardiofacial syndrome. Orthologous to human CHRD (chordin). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in adrenal adult (RPKM 15.3), cortex adult (RPKM 13.6) and 23 other tissues See more
Orthologs
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Genomic context

See Chrd in Genome Data Viewer
Location:
16 B1; 16 12.51 cM
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (20551528..20561132)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (20731425..20742384)

Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 131, member A Neighboring gene STARR-seq mESC enhancer starr_40329 Neighboring gene chloride channel, voltage-sensitive 2 Neighboring gene STARR-positive B cell enhancer ABC_E1489 Neighboring gene polymerase (RNA) II (DNA directed) polypeptide H Neighboring gene STARR-seq mESC enhancer starr_40331 Neighboring gene thrombopoietin Neighboring gene predicted gene, 22741 Neighboring gene STARR-seq mESC enhancer starr_40332 Neighboring gene predicted gene, 46544

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables BMP binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables BMP binding IDA
Inferred from Direct Assay
more info
PubMed 
enables heparan sulfate proteoglycan binding IDA
Inferred from Direct Assay
more info
PubMed 
enables heparin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables syndecan binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in BMP signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in BMP signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in BMP signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in BMP signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in artery morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cell population proliferation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within central nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in chordate pharynx development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cranial skeletal system development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in descending aorta development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in dorsal/ventral pattern formation IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within dorsal/ventral pattern formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in embryonic axis specification IDA
Inferred from Direct Assay
more info
PubMed 
involved_in embryonic heart tube development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in epithelial cell fate commitment IDA
Inferred from Direct Assay
more info
PubMed 
involved_in exploration behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in fibroblast growth factor receptor signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in forebrain development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within forebrain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within gastrulation with mouth forming second IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in in utero embryonic development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in long-term synaptic potentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in maintenance of protein location IDA
Inferred from Direct Assay
more info
PubMed 
involved_in mesenchymal cell fate commitment IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within mesoderm formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of BMP signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within negative regulation of BMP signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of BMP signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of BMP signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of cell migration ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of osteoblast differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of osteoblast differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in neural crest formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in neuron fate commitment IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within osteoblast differentiation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within pattern specification process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of cell adhesion ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of mesenchymal cell proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in presynaptic modulation of chemical synaptic transmission IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in protein import IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of neuronal synaptic plasticity IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in short-term synaptic potentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within skeletal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in smoothened signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in specification of segmental identity, mandibular segment IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in spinal cord dorsal/ventral patterning ISO
Inferred from Sequence Orthology
more info
 
involved_in synapse organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in venous blood vessel morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in visual learning IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
is_active_in cell surface IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in extracellular region IDA
Inferred from Direct Assay
more info
PubMed 
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)

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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.

mRNA and Protein(s)

  1. NM_001278041.2NP_001264970.1  chordin isoform 2 precursor

    See identical proteins and their annotated locations for NP_001264970.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site in the 5' coding region compared to variant 1, which results in a longer isoform (2) containing an internal protein segment not found in isoform 1.
    Source sequence(s)
    CT010490
    Consensus CDS
    CCDS88902.1
    UniProtKB/TrEMBL
    A6H5Z6, Q3UEN0
    Related
    ENSMUSP00000156080.2, ENSMUST00000232646.2
    Conserved Domains (3) summary
    smart00214
    Location:801867
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:422539
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:73147
    VWC; von Willebrand factor type C domain
  2. NM_001354995.2NP_001341924.1  chordin isoform 3

    Status: VALIDATED

    Source sequence(s)
    CT010490
    Conserved Domains (4) summary
    smart00214
    Location:300366
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:51163
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl06473
    Location:238
    CHRD; CHRD domain
    cl17735
    Location:388448
    VWC; von Willebrand factor type C domain
  3. NM_001354996.2NP_001341925.1  chordin isoform 4 precursor

    Status: VALIDATED

    Source sequence(s)
    CT010490
    UniProtKB/TrEMBL
    Q3UEN0
    Conserved Domains (3) summary
    smart00214
    Location:779845
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:400517
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:51125
    VWC; von Willebrand factor type C domain
  4. NM_001416766.1NP_001403695.1  chordin isoform 5 precursor

    Status: VALIDATED

    Source sequence(s)
    CT010490
    UniProtKB/TrEMBL
    Q3UEN0
  5. NM_009893.3NP_034023.1  chordin isoform 1 precursor

    See identical proteins and their annotated locations for NP_034023.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes the shorter isoform (1).
    Source sequence(s)
    CT010490
    Consensus CDS
    CCDS28059.1
    UniProtKB/Swiss-Prot
    Q9Z0E2
    UniProtKB/TrEMBL
    Q3UEN0
    Related
    ENSMUSP00000007171.7, ENSMUST00000007171.13
    Conserved Domains (3) summary
    smart00214
    Location:779845
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:400517
    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_184392.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    CT010490
    Related
    ENSMUST00000153299.8

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000082.7 Reference GRCm39 C57BL/6J

    Range
    20551528..20561132
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011245817.4XP_011244119.1  chordin isoform X6

    UniProtKB/TrEMBL
    Q3UEN0
    Conserved Domains (3) summary
    smart00214
    Location:798864
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:419536
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:51125
    VWC; von Willebrand factor type C domain
  2. XM_030248947.2XP_030104807.1  chordin isoform X7

    UniProtKB/TrEMBL
    Q3UEN0
    Conserved Domains (3) summary
    smart00214
    Location:779845
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:400517
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:51125
    VWC; von Willebrand factor type C domain
  3. XM_011245814.3XP_011244116.1  chordin isoform X1

    UniProtKB/TrEMBL
    Q3UEN0
    Conserved Domains (3) summary
    smart00214
    Location:820886
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:441558
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:73147
    VWC; von Willebrand factor type C domain
  4. XM_011245815.3XP_011244117.1  chordin isoform X2

    UniProtKB/TrEMBL
    Q3UEN0
    Conserved Domains (3) summary
    smart00214
    Location:820886
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:441558
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:73147
    VWC; von Willebrand factor type C domain
  5. XM_011245816.3XP_011244118.1  chordin isoform X3

    UniProtKB/TrEMBL
    Q3UEN0
    Conserved Domains (3) summary
    smart00214
    Location:820886
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:441558
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:73147
    VWC; von Willebrand factor type C domain
  6. XM_036159761.1XP_036015654.1  chordin isoform X4

    UniProtKB/TrEMBL
    Q3UEN0
    Conserved Domains (3) summary
    smart00214
    Location:820886
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:441558
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:73147
    VWC; von Willebrand factor type C domain
  7. XM_006521745.4XP_006521808.1  chordin isoform X5

    UniProtKB/TrEMBL
    Q3UEN0
    Conserved Domains (3) summary
    smart00214
    Location:801867
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:422539
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:73147
    VWC; von Willebrand factor type C domain
  8. XM_036159763.1XP_036015656.1  chordin isoform X10

    Conserved Domains (3) summary
    smart00214
    Location:413479
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:34151
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:501561
    VWC; von Willebrand factor type C domain
  9. XM_036159762.1XP_036015655.1  chordin isoform X10

    Conserved Domains (3) summary
    smart00214
    Location:413479
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:34151
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:501561
    VWC; von Willebrand factor type C domain
  10. XM_030248950.2XP_030104810.1  chordin isoform X11

    Conserved Domains (3) summary
    smart00214
    Location:413479
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:34151
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:501561
    VWC; von Willebrand factor type C domain
  11. XM_017316861.1XP_017172350.1  chordin isoform X9

    Conserved Domains (4) summary
    smart00214
    Location:571637
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:192309
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:659719
    VWC; von Willebrand factor type C domain
    cl06473
    Location:2465
    CHRD; CHRD domain

RNA

  1. XR_004939151.1 RNA Sequence

  2. XR_004939153.1 RNA Sequence

  3. XR_003951745.2 RNA Sequence

  4. XR_875721.4 RNA Sequence

  5. XR_004939152.1 RNA Sequence

  6. XR_001781784.3 RNA Sequence