Chodl (chondrolectin) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Chodl (chondrolectin) Rattus norvegicus
Analyze
Symbol: Chodl
Name: chondrolectin
RGD ID: 1309885
Description: Predicted to enable carbohydrate binding activity. Predicted to be involved in positive regulation of axonogenesis. Predicted to act upstream of or within regulation of neuron projection development. Predicted to be located in perinuclear region of cytoplasm. Predicted to be active in cytoplasm. Orthologous to human CHODL (chondrolectin); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC288289
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81131,141,030 - 31,163,342 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1131,141,021 - 31,163,334 (+)EnsemblGRCr8
mRatBN7.21117,654,137 - 17,676,450 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1117,654,206 - 17,676,441 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1126,286,043 - 26,308,301 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01119,018,715 - 19,040,669 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01118,188,315 - 18,210,575 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01117,537,980 - 17,560,305 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1117,538,063 - 17,560,296 (+)Ensemblrn6Rnor6.0
Rnor_5.01121,183,908 - 21,206,150 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41117,993,680 - 18,015,913 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1117,622,644 - 17,644,864 (+)NCBICelera
RGSC_v3.11117,994,114 - 18,014,631 (+)NCBI
Cytogenetic Map11q11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12079284   PMID:22042635   PMID:24067532  


Genomics

Comparative Map Data
Chodl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81131,141,030 - 31,163,342 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1131,141,021 - 31,163,334 (+)EnsemblGRCr8
mRatBN7.21117,654,137 - 17,676,450 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1117,654,206 - 17,676,441 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1126,286,043 - 26,308,301 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01119,018,715 - 19,040,669 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01118,188,315 - 18,210,575 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01117,537,980 - 17,560,305 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1117,538,063 - 17,560,296 (+)Ensemblrn6Rnor6.0
Rnor_5.01121,183,908 - 21,206,150 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41117,993,680 - 18,015,913 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1117,622,644 - 17,644,864 (+)NCBICelera
RGSC_v3.11117,994,114 - 18,014,631 (+)NCBI
Cytogenetic Map11q11NCBI
CHODL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382117,917,340 - 18,267,370 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2117,901,263 - 18,267,373 (+)Ensemblhg38GRCh38
GRCh372119,289,657 - 19,639,687 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362118,539,021 - 18,561,558 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342118,539,020 - 18,561,556NCBI
Celera214,792,870 - 4,815,407 (+)NCBICelera
Cytogenetic Map21q21.1NCBI
HuRef214,786,788 - 5,027,789 (+)NCBIHuRef
CHM1_12118,961,661 - 19,201,030 (+)NCBICHM1_1
T2T-CHM13v2.02116,276,723 - 16,627,191 (+)NCBIT2T-CHM13v2.0
Chodl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391678,727,729 - 78,748,624 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1678,727,836 - 78,748,621 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381678,930,841 - 78,951,736 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1678,930,948 - 78,951,733 (+)Ensemblmm10GRCm38
MGSCv371678,931,193 - 78,951,973 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361678,813,717 - 78,834,322 (+)NCBIMGSCv36mm8
Celera1679,159,446 - 79,180,171 (+)NCBICelera
Cytogenetic Map16C3.1NCBI
cM Map1645.39NCBI
Chodl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540719,483,561 - 19,508,328 (+)Ensembl
ChiLan1.0NW_00495540719,483,569 - 19,507,270 (+)NCBIChiLan1.0ChiLan1.0
CHODL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22214,736,373 - 14,759,574 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1219,565,987 - 9,588,333 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0214,554,608 - 5,001,725 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12117,919,676 - 18,365,241 (+)NCBIPanPan1.1PanPan1.1panPan2
CHODL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13114,583,236 - 14,604,583 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3114,495,684 - 14,604,562 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3114,602,689 - 14,624,008 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03114,611,439 - 14,632,757 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3114,611,002 - 14,633,953 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13114,614,329 - 14,635,629 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03114,613,762 - 14,635,078 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03115,024,650 - 15,045,967 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Chodl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497115,503,468 - 15,684,092 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650510,581,393 - 10,603,861 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493650510,581,676 - 10,603,863 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHODL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13182,461,757 - 182,826,753 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.113182,409,113 - 182,829,797 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213192,820,209 - 192,994,069 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHODL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1274,328,127 - 74,349,919 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl274,328,133 - 74,338,821 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605079,430,349 - 79,674,718 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chodl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247456,728,750 - 6,756,958 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247456,728,634 - 6,756,867 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Chodl
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1462,971,099 - 62,992,935 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Chodl
194 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:480
Count of miRNA genes:236
Interacting mature miRNAs:283
Transcripts:ENSRNOT00000031889
Prediction methods:Microtar, Miranda, 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
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)112252474682951192Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)112631803155806125Rat
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11381815448818154Rat
1600394Edcs1Endometrial carcinoma susceptibility QTL12.90.04uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)111282315257823152Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112019354996351019Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)111080612555806125Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)112995899657754989Rat
631510Spl2Serum phospholipid level QTL 24.1blood phospholipid amount (VT:0006084)serum phospholipid level (CMO:0001171)112755668572556685Rat

Markers in Region
RH130465  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21117,676,086 - 17,676,267 (+)MAPPERmRatBN7.2
Rnor_6.01117,559,942 - 17,560,122NCBIRnor6.0
Rnor_5.01121,205,787 - 21,205,967UniSTSRnor5.0
RGSC_v3.41118,015,559 - 18,015,739UniSTSRGSC3.4
Celera1117,644,510 - 17,644,690UniSTS
RH 3.4 Map1165.8UniSTS
Cytogenetic Map11q11UniSTS
Chodl  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21117,665,230 - 17,665,591 (+)MAPPERmRatBN7.2
Rnor_6.01117,549,088 - 17,549,448NCBIRnor6.0
Rnor_5.01121,194,933 - 21,195,293UniSTSRnor5.0
RGSC_v3.41118,004,705 - 18,005,065UniSTSRGSC3.4
Celera1117,633,667 - 17,634,027UniSTS
Cytogenetic Map11q11UniSTS


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
13 12 36 134 84 83 53 26 53 6 216 95 11 113 47 88 30 11 11

Sequence


Ensembl Acc Id: ENSRNOT00000031889   ⟹   ENSRNOP00000032956
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1131,141,100 - 31,163,334 (+)Ensembl
mRatBN7.2 Ensembl1117,654,206 - 17,676,441 (+)Ensembl
Rnor_6.0 Ensembl1117,538,063 - 17,560,296 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000090878   ⟹   ENSRNOP00000072243
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1131,141,021 - 31,162,664 (+)Ensembl
mRatBN7.2 Ensembl1117,654,206 - 17,675,760 (+)Ensembl
Rnor_6.0 Ensembl1117,538,115 - 17,560,288 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000124696   ⟹   ENSRNOP00000101267
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1131,141,021 - 31,163,334 (+)Ensembl
RefSeq Acc Id: NM_001415061   ⟹   NP_001401990
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81131,141,115 - 31,163,342 (+)NCBI
mRatBN7.21117,654,221 - 17,676,450 (+)NCBI
RefSeq Acc Id: XM_006248004   ⟹   XP_006248066
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81131,141,030 - 31,163,342 (+)NCBI
mRatBN7.21117,654,137 - 17,676,450 (+)NCBI
Rnor_6.01117,537,980 - 17,560,305 (+)NCBI
Rnor_5.01121,183,908 - 21,206,150 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001401990 (Get FASTA)   NCBI Sequence Viewer  
  XP_006248066 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM10611 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000032956
  ENSRNOP00000032956.5
  ENSRNOP00000072243.2
  ENSRNOP00000101267
  ENSRNOP00000101267.1
RefSeq Acc Id: XP_006248066   ⟸   XM_006248004
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K2H3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000032956   ⟸   ENSRNOT00000031889
Ensembl Acc Id: ENSRNOP00000072243   ⟸   ENSRNOT00000090878
RefSeq Acc Id: NP_001401990   ⟸   NM_001415061
- Peptide Label: precursor
- UniProtKB: A6JL46 (UniProtKB/TrEMBL),   D3ZI86 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000101267   ⟸   ENSRNOT00000124696
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZI86-F1-model_v2 AlphaFold D3ZI86 1-318 view protein structure

Transcriptome

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

Promoters
RGD ID:13698011
Promoter ID:EPDNEW_R8536
Type:multiple initiation site
Name:Chodl_1
Description:chondrolectin
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01117,538,040 - 17,538,100EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309885 AgrOrtholog
BioCyc Gene G2FUF-22124 BioCyc
Ensembl Genes ENSRNOG00000001915 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031889 ENTREZGENE
  ENSRNOT00000031889.7 UniProtKB/TrEMBL
  ENSRNOT00000090878.3 UniProtKB/TrEMBL
  ENSRNOT00000124696 ENTREZGENE
  ENSRNOT00000124696.1 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/TrEMBL
InterPro C-type_lectin UniProtKB/TrEMBL
  C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin_domain UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
NCBI Gene 288289 ENTREZGENE
PANTHER CHONDROLECTIN VARIANT CHODLFDELTAE UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
PhenoGen Chodl PhenoGen
PROSITE C_TYPE_LECTIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000001915 RatGTEx
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt A0A0G2K2H3 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0L9J7_RAT UniProtKB/TrEMBL
  A6JL46 ENTREZGENE, UniProtKB/TrEMBL
  D3ZI86 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Chodl  chondrolectin   Chodl_predicted  chondrolectin (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Chodl_predicted  chondrolectin (predicted)      Symbol and Name status set to approved 70820 APPROVED