Cnmd (chondromodulin) - Rat Genome Database

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Gene: Cnmd (chondromodulin) Rattus norvegicus
Analyze
Symbol: Cnmd
Name: chondromodulin
RGD ID: 620176
Description: Predicted to be involved in negative regulation of angiogenesis and negative regulation of endothelial cell proliferation. Predicted to act upstream of or within endothelial cell morphogenesis and negative regulation of vascular endothelial growth factor receptor signaling pathway. Predicted to be located in endomembrane system; extracellular region; and membrane. Orthologous to human CNMD (chondromodulin); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Chm-1; chM-I; chondromodulin-1; chondromodulin-I; Lect1; leukocyte cell derived chemotaxin 1; leukocyte cell-derived chemotaxin 1; MGC156632
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81561,450,617 - 61,475,382 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1561,450,450 - 61,475,350 (-)EnsemblGRCr8
mRatBN7.21555,041,548 - 55,066,297 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1555,041,561 - 55,066,297 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1559,174,540 - 59,199,179 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01560,292,937 - 60,317,571 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01557,117,794 - 57,142,428 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01561,923,291 - 61,947,840 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1561,923,299 - 61,947,764 (-)Ensemblrn6Rnor6.0
Rnor_5.01565,587,055 - 65,611,651 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41560,891,174 - 60,916,956 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1554,621,851 - 54,646,185 (-)NCBICelera
RGSC_v3.11560,906,953 - 60,932,733 (-)NCBI
Cytogenetic Map15q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Chondromodulin-I expression in the growth plate of young uremic rats. Amil B, etal., Kidney Int 2004 Jul;66(1):51-9.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Chondromodulin-I expression in rat articular cartilage. Kitahara H, etal., Arch Histol Cytol 2003 Aug;66(3):221-8.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11328727   PMID:12477932   PMID:12714610   PMID:16980969   PMID:18337200   PMID:24710035   PMID:28263889  


Genomics

Comparative Map Data
Cnmd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81561,450,617 - 61,475,382 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1561,450,450 - 61,475,350 (-)EnsemblGRCr8
mRatBN7.21555,041,548 - 55,066,297 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1555,041,561 - 55,066,297 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1559,174,540 - 59,199,179 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01560,292,937 - 60,317,571 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01557,117,794 - 57,142,428 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01561,923,291 - 61,947,840 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1561,923,299 - 61,947,764 (-)Ensemblrn6Rnor6.0
Rnor_5.01565,587,055 - 65,611,651 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41560,891,174 - 60,916,956 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1554,621,851 - 54,646,185 (-)NCBICelera
RGSC_v3.11560,906,953 - 60,932,733 (-)NCBI
Cytogenetic Map15q12NCBI
CNMD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381352,703,264 - 52,739,820 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1352,703,264 - 52,739,820 (-)Ensemblhg38GRCh38
GRCh371353,277,399 - 53,313,955 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361352,175,400 - 52,211,948 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341352,175,399 - 52,211,948NCBI
Celera1334,263,294 - 34,299,841 (-)NCBICelera
Cytogenetic Map13q14.3NCBI
HuRef1333,991,623 - 34,028,176 (-)NCBIHuRef
CHM1_11353,245,581 - 53,282,024 (-)NCBICHM1_1
T2T-CHM13v2.01351,918,713 - 51,955,280 (-)NCBIT2T-CHM13v2.0
Cnmd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391479,875,126 - 79,899,596 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1479,875,130 - 79,899,610 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381479,637,682 - 79,662,194 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1479,637,690 - 79,662,170 (-)Ensemblmm10GRCm38
MGSCv371480,037,497 - 80,061,977 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361478,371,848 - 78,396,325 (-)NCBIMGSCv36mm8
Celera1477,137,767 - 77,162,249 (-)NCBICelera
Cytogenetic Map14D3NCBI
cM Map1442.74NCBI
Cnmd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540450,863,651 - 50,889,249 (+)Ensembl
ChiLan1.0NW_00495540450,864,017 - 50,889,249 (+)NCBIChiLan1.0ChiLan1.0
CNMD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21454,040,301 - 54,079,870 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11352,684,492 - 52,724,027 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01333,737,029 - 33,776,588 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11352,547,938 - 52,584,729 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1352,547,943 - 52,584,720 (-)EnsemblpanPan2panpan1.1
CNMD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1229,745,959 - 9,792,663 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl229,753,441 - 9,759,713 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha229,742,283 - 9,767,844 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0229,970,194 - 9,995,769 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl229,970,198 - 9,995,869 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1229,667,210 - 9,692,729 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0229,717,099 - 9,742,785 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0229,731,938 - 9,757,504 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cnmd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945151,275,431 - 151,299,995 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936667599,711 - 624,999 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936667599,703 - 624,821 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CNMD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1125,961,926 - 25,994,651 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11125,959,192 - 25,994,773 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21126,648,222 - 26,666,245 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CNMD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1330,465,771 - 30,502,358 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl330,466,087 - 30,501,550 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605713,313,808 - 13,349,827 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cnmd
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474814,165,842 - 14,192,764 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474814,166,514 - 14,191,941 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Cnmd
137 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:48
Count of miRNA genes:41
Interacting mature miRNAs:48
Transcripts:ENSRNOT00000017400
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
724545Niddm54Non-insulin dependent diabetes mellitus QTL 540.02blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)155079449473699215Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2317050Aia24Adjuvant induced arthritis QTL 242.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)155284790873690657Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)155380615298806152Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)152788577486257085Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
14 10 43 129 33 33 13 15 13 6 173 81 9 117 58 53 20 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000017400   ⟹   ENSRNOP00000017400
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1561,450,450 - 61,475,350 (-)Ensembl
mRatBN7.2 Ensembl1555,041,561 - 55,066,297 (-)Ensembl
Rnor_6.0 Ensembl1561,923,299 - 61,947,764 (-)Ensembl
RefSeq Acc Id: NM_030854   ⟹   NP_110481
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81561,450,617 - 61,475,350 (-)NCBI
mRatBN7.21555,041,559 - 55,066,297 (-)NCBI
Rnor_6.01561,923,297 - 61,947,764 (-)NCBI
Rnor_5.01565,587,055 - 65,611,651 (-)NCBI
RGSC_v3.41560,891,174 - 60,916,956 (-)RGD
Celera1554,621,851 - 54,646,185 (-)RGD
Sequence:
RefSeq Acc Id: XM_006252346   ⟹   XP_006252408
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81561,450,617 - 61,475,382 (-)NCBI
mRatBN7.21555,041,548 - 55,066,297 (-)NCBI
Rnor_6.01561,923,291 - 61,947,840 (-)NCBI
Rnor_5.01565,587,055 - 65,611,651 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_110481 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252408 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC05574 (Get FASTA)   NCBI Sequence Viewer  
  AAI27494 (Get FASTA)   NCBI Sequence Viewer  
  EDM02371 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017400
GenBank Protein O70367 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_110481   ⟸   NM_030854
- UniProtKB: O70367 (UniProtKB/Swiss-Prot),   A0JPL7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252408   ⟸   XM_006252346
- Peptide Label: isoform X1
- UniProtKB: A0JPL7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000017400   ⟸   ENSRNOT00000017400
Protein Domains
BRICHOS

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O70367-F1-model_v2 AlphaFold O70367 1-334 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620176 AgrOrtholog
BioCyc Gene G2FUF-12986 BioCyc
Ensembl Genes ENSRNOG00000012821 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000017400 ENTREZGENE
Gene3D-CATH 3.30.390.150 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:8369609 IMAGE-MGC_LOAD
InterPro BRICHOS_dom UniProtKB/Swiss-Prot
  Chondromodulin/Tenomodulin UniProtKB/Swiss-Prot
KEGG Report rno:81512 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156632 IMAGE-MGC_LOAD
NCBI Gene 81512 ENTREZGENE
PANTHER LEUKOCYTE CELL-DERIVED CHEMOTAXIN 1 UniProtKB/Swiss-Prot
  PTHR14064 UniProtKB/Swiss-Prot
Pfam BRICHOS UniProtKB/Swiss-Prot
PhenoGen Cnmd PhenoGen
PROSITE BRICHOS UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000012821 RatGTEx
SMART BRICHOS UniProtKB/Swiss-Prot
UniProt A0JPL7 ENTREZGENE, UniProtKB/TrEMBL
  CNMD_RAT UniProtKB/Swiss-Prot
  F7EQ36_RAT UniProtKB/TrEMBL
  O70367 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-10-26 Cnmd  chondromodulin  Lect1  leukocyte cell derived chemotaxin 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Lect1  leukocyte cell derived chemotaxin 1      Symbol and Name status set to approved 1299863 APPROVED
2003-05-07 Lect1  leukocyte cell derived chemotaxin 1  Chm-1  chondromodulin-1  Symbol and Name updated to reflect Human and Mouse nomenclature 629477 PROVISIONAL
2002-08-07 Chm-1  chondromodulin-1      Symbol and Name status set to provisional 70820 PROVISIONAL