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Chrd chordin [ Rattus norvegicus (Norway rat) ]

Gene ID: 117275, updated on 6-Jun-2024

Summary

Symbol
Chrdprovided by RGD
Full Name
chordinprovided by RGD
Primary source
RGD:620181
See related
Ensembl:ENSRNOG00000001750 AllianceGenome:RGD:620181
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable heparin binding activity and syndecan binding activity. Predicted to be involved in several processes, including BMP signaling pathway involved in spinal cord dorsal/ventral patterning; negative regulation of cell migration; and positive regulation of mesenchymal cell proliferation. Predicted to act upstream of or within several processes, including gastrulation; negative regulation of BMP signaling pathway; and negative regulation of osteoblast differentiation. Predicted to be located in extracellular space. Orthologous to human CHRD (chordin). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Kidney (RPKM 50.6), Uterus (RPKM 49.3) and 7 other tissues See more
Orthologs
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Genomic context

See Chrd in Genome Data Viewer
Location:
11q23
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (93676400..93685584, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (80171994..80181166, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (83858503..83867543, complement)

Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene U1 spliceosomal RNA Neighboring gene ribosomal protein L12 like 2 Neighboring gene thrombopoietin like 1 Neighboring gene RNA polymerase II, I and III subunit H

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

General gene information

Markers

Gene Ontology Provided by RGD

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

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_057134.1NP_476475.1  chordin precursor

    See identical proteins and their annotated locations for NP_476475.1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000011
    UniProtKB/Swiss-Prot
    Q63148
    UniProtKB/TrEMBL
    A6JS78
    Conserved Domains (3) summary
    smart00214
    Location:779845
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:530642
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:51125
    VWC; von Willebrand factor type C domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086029.1 Reference GRCr8

    Range
    93676400..93685584 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063270249.1XP_063126319.1  chordin isoform X3

    UniProtKB/Swiss-Prot
    Q63148
  2. XM_063270248.1XP_063126318.1  chordin isoform X2

    UniProtKB/Swiss-Prot
    Q63148
  3. XM_006248556.4XP_006248618.1  chordin isoform X1

    UniProtKB/Swiss-Prot
    Q63148
    Conserved Domains (3) summary
    smart00214
    Location:793859
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:544656
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:65139
    VWC; von Willebrand factor type C domain
  4. XM_006248557.4XP_006248619.1  chordin isoform X7

    UniProtKB/Swiss-Prot
    Q63148
    UniProtKB/TrEMBL
    A0A140TA94
    Related
    ENSRNOP00000002394.8
    Conserved Domains (3) summary
    smart00214
    Location:801867
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:552664
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:73147
    VWC; von Willebrand factor type C domain
  5. XM_039087914.2XP_038943842.1  chordin isoform X5

    Conserved Domains (3) summary
    smart00214
    Location:413479
    VWC; von Willebrand factor (vWF) type C domain
    smart00754
    Location:164276
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    cl17735
    Location:501561
    VWC; von Willebrand factor type C domain
  6. XM_017597850.3XP_017453339.1  chordin isoform X4

  7. XM_039087915.2XP_038943843.1  chordin isoform X6

    Conserved Domains (3) summary
    smart00754
    Location:184287
    CHRD; A domain in the BMP inhibitor chordin and in microbial proteins
    pfam00093
    Location:65139
    VWC; von Willebrand factor type C domain
    cl06473
    Location:414481
    CHRD; CHRD domain

RNA

  1. XR_005490963.2 RNA Sequence

  2. XR_005490964.2 RNA Sequence