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    Chrd chordin [ Mus musculus (house mouse) ]

    Gene ID: 12667, updated on 3-Dec-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 BMP binding activity; heparin binding activity; and proteoglycan binding activity. Involved in several processes, including cell surface receptor signaling pathway; circulatory system development; and modulation of chemical synaptic transmission. Acts upstream of or within several processes, including gastrulation; negative regulation of osteoblast differentiation; and osteoblast differentiation. Located in extracellular space. Is active in cell surface and extracellular region. 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, Nov 2024]
    Expression
    Broad expression in adrenal adult (RPKM 15.3), cortex adult (RPKM 13.6) and 23 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    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 
    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 
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
     

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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