Chrd chordin [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Chrdprovided by RGD
Full Name: chordinprovided by RGD
Primary source: RGD:620181
See related: EnsemblRapid: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: human mouse all
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Genomic context

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_086029.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Chordin and noggin were intensely expressed throughout the trigeminal nuclei. chordin prefers dendritic expression than noggin, suggesting that chordin is involved in the regulation of dendritic morphology and synaptic homeostasis. Furthermore, chordin and noggin were differentially expressed in the neuropil of the trigeminal nuclei.
Title: Chordin and noggin expression in the adult rat trigeminal nuclei.
Data indicate that chordin is more widely expressed throughout the adult CNS than previously reported, and its continued abundant expression in the adult brain strongly supports the idea that chordin plays pivotal roles also in the adult brain
Title: Chordin expression in the adult rat brain.

Submit: New GeneRIF Correction

General gene information

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Markers

Chrd (e-PCR), detects polymorphism
- UniSTS:141338

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

General protein information

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Preferred Names: chordin

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)

NM_057134.1 → NP_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

Related

ENSRNOP00000104165.1, ENSRNOT00000163275.1

Conserved Domains (3) summary

smart00214
Location:779 → 845

VWC; von Willebrand factor (vWF) type C domain

smart00754
Location:530 → 642

CHRD; A domain in the BMP inhibitor chordin and in microbial proteins

cl17735
Location:51 → 125

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

NC_086029.1 Reference GRCr8

Range

93676400..93685584 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063270249.1 → XP_063126319.1 chordin isoform X3

UniProtKB/Swiss-Prot

Q63148
XM_063270248.1 → XP_063126318.1 chordin isoform X2

UniProtKB/Swiss-Prot

Q63148
XM_006248556.4 → XP_006248618.1 chordin isoform X1

UniProtKB/Swiss-Prot

Q63148

Conserved Domains (3) summary

smart00214
Location:793 → 859

VWC; von Willebrand factor (vWF) type C domain

smart00754
Location:544 → 656

CHRD; A domain in the BMP inhibitor chordin and in microbial proteins

cl17735
Location:65 → 139

VWC; von Willebrand factor type C domain
XM_006248557.4 → XP_006248619.1 chordin isoform X7

UniProtKB/Swiss-Prot

Q63148

UniProtKB/TrEMBL

A0A140TA94

Related

ENSRNOP00000002394.8, ENSRNOT00000002394.9

Conserved Domains (3) summary

smart00214
Location:801 → 867

VWC; von Willebrand factor (vWF) type C domain

smart00754
Location:552 → 664

CHRD; A domain in the BMP inhibitor chordin and in microbial proteins

cl17735
Location:73 → 147

VWC; von Willebrand factor type C domain
XM_039087914.2 → XP_038943842.1 chordin isoform X5

Conserved Domains (3) summary

smart00214
Location:413 → 479

VWC; von Willebrand factor (vWF) type C domain

smart00754
Location:164 → 276

CHRD; A domain in the BMP inhibitor chordin and in microbial proteins

cl17735
Location:501 → 561

VWC; von Willebrand factor type C domain
XM_017597850.3 → XP_017453339.1 chordin isoform X4
XM_039087915.2 → XP_038943843.1 chordin isoform X6

Conserved Domains (3) summary

smart00754
Location:184 → 287

CHRD; A domain in the BMP inhibitor chordin and in microbial proteins

pfam00093
Location:65 → 139

VWC; von Willebrand factor type C domain

cl06473
Location:414 → 481

CHRD; CHRD domain