Human Gene CHRD (ENST00000448472.5) from GENCODE V44
  Description: Dorsalizing factor. Key developmental protein that dorsalizes early vertebrate embryonic tissues by binding to ventralizing TGF-beta family bone morphogenetic proteins (BMPs) and sequestering them in latent complexes (By similarity). (from UniProt Q9H2X0)
RefSeq Summary (NM_003741): 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].
Gencode Transcript: ENST00000448472.5
Gencode Gene: ENSG00000090539.16
Transcript (Including UTRs)
   Position: hg38 chr3:184,380,073-184,389,829 Size: 9,757 Total Exon Count: 24 Strand: +
Coding Region
   Position: hg38 chr3:184,380,319-184,381,108 Size: 790 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:184,380,073-184,389,829)mRNA (may differ from genome)Protein (94 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
PubMedUniProtKB

-  Comments and Description Text from UniProtKB
  ID: CHRD_HUMAN
DESCRIPTION: RecName: Full=Chordin; Flags: Precursor;
FUNCTION: Dorsalizing factor. Key developmental protein that dorsalizes early vertebrate embryonic tissues by binding to ventralizing TGF-beta family bone morphogenetic proteins (BMPs) and sequestering them in latent complexes (By similarity).
SUBUNIT: Interacts with TWSG1 and/or BMP4 (By similarity).
INTERACTION: P84022:SMAD3; NbExp=2; IntAct=EBI-947551, EBI-347161;
SUBCELLULAR LOCATION: Secreted (By similarity).
TISSUE SPECIFICITY: Expressed at the highest level in liver.
PTM: Cleaved by tolloid proteases; cleavage participates in dorsoventral patterning during early development (By similarity).
SIMILARITY: Belongs to the chordin family.
SIMILARITY: Contains 4 CHRD domains.
SIMILARITY: Contains 4 VWFC domains.

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CHRD
Diseases sorted by gene-association score: cornelia de lange syndrome (11)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 101.45 RPKM in Brain - Cerebellum
Total median expression: 717.28 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -78.20246-0.318 Picture PostScript Text
3' UTR -1430.303016-0.474 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016353 - Chordin
IPR010895 - CHRD
IPR001007 - VWF_C

Pfam Domains:
PF07452 - CHRD domain
PF00093 - von Willebrand factor type C domain

ModBase Predicted Comparative 3D Structure on Q9H2X0
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008201 heparin binding
GO:0019955 cytokine binding
GO:0045545 syndecan binding

Biological Process:
GO:0001501 skeletal system development
GO:0001649 osteoblast differentiation
GO:0001702 gastrulation with mouth forming second
GO:0001707 mesoderm formation
GO:0002053 positive regulation of mesenchymal cell proliferation
GO:0007275 multicellular organism development
GO:0007389 pattern specification process
GO:0007417 central nervous system development
GO:0009953 dorsal/ventral pattern formation
GO:0021919 BMP signaling pathway involved in spinal cord dorsal/ventral patterning
GO:0030336 negative regulation of cell migration
GO:0030514 negative regulation of BMP signaling pathway
GO:0030900 forebrain development
GO:0033504 floor plate development
GO:0045668 negative regulation of osteoblast differentiation
GO:0045785 positive regulation of cell adhesion

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space


-  Descriptions from all associated GenBank mRNAs
  LF213803 - JP 2014500723-A/21306: Polycomb-Associated Non-Coding RNAs.
MA449380 - JP 2018138019-A/21306: Polycomb-Associated Non-Coding RNAs.
LF212670 - JP 2014500723-A/20173: Polycomb-Associated Non-Coding RNAs.
MA448247 - JP 2018138019-A/20173: Polycomb-Associated Non-Coding RNAs.
LF212672 - JP 2014500723-A/20175: Polycomb-Associated Non-Coding RNAs.
MA448249 - JP 2018138019-A/20175: Polycomb-Associated Non-Coding RNAs.
AF209929 - Homo sapiens chordin variant 1 (CHRD) mRNA, complete cds, alternatively spliced.
AF209928 - Homo sapiens chordin (CHRD) mRNA, complete cds, alternatively spliced.
AF209930 - Homo sapiens chordin variant 2 (CHRD) mRNA, complete cds, alternatively spliced.
AF283325 - Homo sapiens chordin variant 3 (CHRD) mRNA, complete cds, alternatively spliced.
AY358926 - Homo sapiens clone DNA35917 chordin (UNQ217) mRNA, complete cds.
BC112345 - Homo sapiens chordin, transcript variant 1, mRNA (cDNA clone MGC:133038 IMAGE:40008417), complete cds.
LF210557 - JP 2014500723-A/18060: Polycomb-Associated Non-Coding RNAs.
MA446134 - JP 2018138019-A/18060: Polycomb-Associated Non-Coding RNAs.
AB208947 - Homo sapiens mRNA for chordin isoform a variant protein.
AK074147 - Homo sapiens mRNA for FLJ00220 protein.
AK293456 - Homo sapiens cDNA FLJ50077 complete cds, highly similar to Chordin precursor.
AK295632 - Homo sapiens cDNA FLJ60564 complete cds, highly similar to Chordin precursor.
AK296316 - Homo sapiens cDNA FLJ53797 complete cds, highly similar to Chordin precursor.
LF213384 - JP 2014500723-A/20887: Polycomb-Associated Non-Coding RNAs.
MA448961 - JP 2018138019-A/20887: Polycomb-Associated Non-Coding RNAs.
JD514593 - Sequence 495617 from Patent EP1572962.
LF338789 - JP 2014500723-A/146292: Polycomb-Associated Non-Coding RNAs.
MA574366 - JP 2018138019-A/146292: Polycomb-Associated Non-Coding RNAs.
JD069287 - Sequence 50311 from Patent EP1572962.
AF076612 - Homo sapiens chordin (CHRD) mRNA, partial cds.
JD164436 - Sequence 145460 from Patent EP1572962.
JD258730 - Sequence 239754 from Patent EP1572962.
JD086253 - Sequence 67277 from Patent EP1572962.
JD414083 - Sequence 395107 from Patent EP1572962.
JD531952 - Sequence 512976 from Patent EP1572962.
AK300213 - Homo sapiens cDNA FLJ54880 complete cds, moderately similar to Chordin precursor.
JD462749 - Sequence 443773 from Patent EP1572962.
JD475848 - Sequence 456872 from Patent EP1572962.
JD077241 - Sequence 58265 from Patent EP1572962.
JD288033 - Sequence 269057 from Patent EP1572962.
JD547891 - Sequence 528915 from Patent EP1572962.
JD104346 - Sequence 85370 from Patent EP1572962.
JD372443 - Sequence 353467 from Patent EP1572962.
JD118222 - Sequence 99246 from Patent EP1572962.
JD174653 - Sequence 155677 from Patent EP1572962.
JD060587 - Sequence 41611 from Patent EP1572962.
JD158274 - Sequence 139298 from Patent EP1572962.
JD541396 - Sequence 522420 from Patent EP1572962.
JD498447 - Sequence 479471 from Patent EP1572962.
JD515899 - Sequence 496923 from Patent EP1572962.
JD221740 - Sequence 202764 from Patent EP1572962.
JD534051 - Sequence 515075 from Patent EP1572962.
AK300476 - Homo sapiens cDNA FLJ54312 complete cds, highly similar to Chordin precursor.
JD231662 - Sequence 212686 from Patent EP1572962.
JD446818 - Sequence 427842 from Patent EP1572962.
JD229940 - Sequence 210964 from Patent EP1572962.
JD115290 - Sequence 96314 from Patent EP1572962.
JD363829 - Sequence 344853 from Patent EP1572962.
JD052870 - Sequence 33894 from Patent EP1572962.
JD111817 - Sequence 92841 from Patent EP1572962.
JD157590 - Sequence 138614 from Patent EP1572962.
JD186080 - Sequence 167104 from Patent EP1572962.
BC029879 - Homo sapiens, clone IMAGE:5175884, mRNA, partial cds.
AF038198 - Homo sapiens clone 23928 mRNA sequence.
JD370668 - Sequence 351692 from Patent EP1572962.
JD100535 - Sequence 81559 from Patent EP1572962.
JD273968 - Sequence 254992 from Patent EP1572962.
JD044710 - Sequence 25734 from Patent EP1572962.
JD074617 - Sequence 55641 from Patent EP1572962.
JD474181 - Sequence 455205 from Patent EP1572962.
JD185708 - Sequence 166732 from Patent EP1572962.
JD384212 - Sequence 365236 from Patent EP1572962.
JD338071 - Sequence 319095 from Patent EP1572962.
JD416216 - Sequence 397240 from Patent EP1572962.
LF338790 - JP 2014500723-A/146293: Polycomb-Associated Non-Coding RNAs.
MA574367 - JP 2018138019-A/146293: Polycomb-Associated Non-Coding RNAs.
JD269308 - Sequence 250332 from Patent EP1572962.
JD339831 - Sequence 320855 from Patent EP1572962.
JD136748 - Sequence 117772 from Patent EP1572962.
JD390137 - Sequence 371161 from Patent EP1572962.
JD501565 - Sequence 482589 from Patent EP1572962.
JD248267 - Sequence 229291 from Patent EP1572962.
JD560125 - Sequence 541149 from Patent EP1572962.
JD190667 - Sequence 171691 from Patent EP1572962.
JD098242 - Sequence 79266 from Patent EP1572962.
JD324716 - Sequence 305740 from Patent EP1572962.
JD248523 - Sequence 229547 from Patent EP1572962.
JD067618 - Sequence 48642 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04350 - TGF-beta signaling pathway

BioCarta from NCI Cancer Genome Anatomy Project
h_alkPathway - ALK in cardiac myocytes

-  Other Names for This Gene
  Alternate Gene Symbols: AF209930, CHRD_HUMAN, ENST00000448472.1, ENST00000448472.2, ENST00000448472.3, ENST00000448472.4, O95254, Q2M1I8, Q6UW83, Q9H2D3, Q9H2W8, Q9H2W9, Q9H2X0, Q9P0Z2, Q9P0Z3, Q9P0Z4, Q9P0Z5, uc003fow.1, uc003fow.2, uc003fow.3, uc003fow.4, UNQ217/PRO243
UCSC ID: ENST00000448472.5
RefSeq Accession: NM_003741
Protein: Q9H2X0 (aka CHRD_HUMAN)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.