Kera (keratocan) - Rat Genome Database

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Gene: Kera (keratocan) Rattus norvegicus
Analyze
Symbol: Kera
Name: keratocan
RGD ID: 1305816
Description: Predicted to act upstream of or within cornea development in camera-type eye. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Human ortholog(s) of this gene implicated in arcus senilis; cornea plana; and corneal dystrophy. Orthologous to human KERA (keratocan); INTERACTS WITH 1,2-dimethylhydrazine; acrylamide; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC314771
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
GRCr8734,284,100 - 34,291,555 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl734,284,100 - 34,291,555 (+)EnsemblGRCr8
mRatBN7.2732,397,382 - 32,404,837 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl732,397,382 - 32,404,837 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx734,364,558 - 34,372,019 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0736,552,782 - 36,560,241 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0736,287,110 - 36,294,571 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0738,858,062 - 38,865,515 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl738,858,062 - 38,865,515 (+)Ensemblrn6Rnor6.0
Rnor_5.0738,899,411 - 38,906,864 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4735,121,875 - 35,129,326 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera729,434,981 - 29,442,436 (+)NCBICelera
RGSC_v3.1735,142,278 - 35,148,859 (+)NCBI
Cytogenetic Map7q13NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. Mutations in KERA, encoding keratocan, cause cornea plana. Pellegata NS, etal., Nat Genet. 2000 May;25(1):91-5.
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. Keratocan expression is increased in the stroma of keratoconus corneas. Wentz-Hunter K, etal., Mol Med. 2001 Jul;7(7):470-7.
Additional References at PubMed
PMID:32235499  


Genomics

Comparative Map Data
Kera
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8734,284,100 - 34,291,555 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl734,284,100 - 34,291,555 (+)EnsemblGRCr8
mRatBN7.2732,397,382 - 32,404,837 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl732,397,382 - 32,404,837 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx734,364,558 - 34,372,019 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0736,552,782 - 36,560,241 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0736,287,110 - 36,294,571 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0738,858,062 - 38,865,515 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl738,858,062 - 38,865,515 (+)Ensemblrn6Rnor6.0
Rnor_5.0738,899,411 - 38,906,864 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4735,121,875 - 35,129,326 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera729,434,981 - 29,442,436 (+)NCBICelera
RGSC_v3.1735,142,278 - 35,148,859 (+)NCBI
Cytogenetic Map7q13NCBI
KERA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381291,050,491 - 91,058,024 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1291,050,491 - 91,058,024 (-)Ensemblhg38GRCh38
GRCh371291,444,268 - 91,451,801 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361289,968,399 - 89,976,262 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341289,946,738 - 89,954,599NCBI
Celera1291,115,429 - 91,123,289 (-)NCBICelera
Cytogenetic Map12q21.33NCBI
HuRef1288,512,052 - 88,519,912 (-)NCBIHuRef
CHM1_11291,409,247 - 91,417,110 (-)NCBICHM1_1
T2T-CHM13v2.01291,028,004 - 91,035,533 (-)NCBIT2T-CHM13v2.0
Kera
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391097,442,873 - 97,449,555 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1097,442,741 - 97,449,554 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381097,606,962 - 97,613,688 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1097,606,879 - 97,613,692 (+)Ensemblmm10GRCm38
MGSCv371097,069,839 - 97,076,322 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361097,036,893 - 97,043,376 (+)NCBIMGSCv36mm8
Celera1099,578,265 - 99,584,748 (+)NCBICelera
Cytogenetic Map10C3NCBI
cM Map1050.34NCBI
Kera
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540528,256,001 - 28,263,600 (-)Ensembl
ChiLan1.0NW_00495540528,256,054 - 28,263,559 (-)NCBIChiLan1.0ChiLan1.0
KERA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21099,083,778 - 99,091,277 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11299,080,172 - 99,087,671 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01288,583,919 - 88,591,418 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11291,899,373 - 91,907,201 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1291,899,381 - 91,911,615 (-)EnsemblpanPan2panpan1.1
KERA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11531,750,768 - 31,758,588 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1531,670,924 - 31,758,871 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1532,205,471 - 32,213,266 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01532,406,626 - 32,414,412 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1532,406,917 - 32,414,688 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11531,699,512 - 31,707,323 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01531,763,195 - 31,770,989 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01532,056,262 - 32,064,052 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Kera
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494528,424,223 - 28,433,345 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365077,801,577 - 7,811,196 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365077,802,091 - 7,811,123 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KERA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl591,796,324 - 91,802,468 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1591,794,317 - 91,802,362 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2596,273,468 - 96,281,118 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KERA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11186,467,315 - 86,475,217 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1186,468,181 - 86,473,097 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666037158,710,719 - 158,718,002 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kera
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475015,600,703 - 15,608,320 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475015,600,857 - 15,608,259 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Kera
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11176,795,652 - 176,806,583 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Kera
46 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:66
Interacting mature miRNAs:68
Transcripts:ENSRNOT00000006234
Prediction methods:Miranda, Rnahybrid
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
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)72154197751639954Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72380760668807606Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7721609752216097Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71051708662346019Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7170952746709527Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72663805771638057Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72417947886817926Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)731770293110435881Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71011291660150541Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7946087754460877Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)72154197751639954Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73299870277998702Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134650782Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)72154197735707405Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7166965846669658Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)71011291699900612Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72862457565788017Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72154197786817926Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)71049882055498820Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72092049437412865Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71746044762460447Rat
70207Niddm31Non-insulin dependent diabetes mellitus QTL 313.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)72005723265057232Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)72718291472182914Rat


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
5 11 9 40 20 26 11 2 11 5 77 28 9 31 25 43 15

Sequence


Ensembl Acc Id: ENSRNOT00000006234   ⟹   ENSRNOP00000006234
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl734,284,100 - 34,291,555 (+)Ensembl
mRatBN7.2 Ensembl732,397,382 - 32,404,837 (+)Ensembl
Rnor_6.0 Ensembl738,858,062 - 38,865,515 (+)Ensembl
RefSeq Acc Id: NM_001108087   ⟹   NP_001101557
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8734,284,100 - 34,291,555 (+)NCBI
mRatBN7.2732,397,382 - 32,404,837 (+)NCBI
Rnor_6.0738,858,062 - 38,865,515 (+)NCBI
Rnor_5.0738,899,411 - 38,906,864 (+)NCBI
RGSC_v3.4735,121,875 - 35,129,326 (+)RGD
Celera729,434,981 - 29,442,436 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101557 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM16830 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006234
  ENSRNOP00000006234.4
RefSeq Acc Id: NP_001101557   ⟸   NM_001108087
- Peptide Label: precursor
- UniProtKB: D3ZVD7 (UniProtKB/TrEMBL),   A6IG68 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000006234   ⟸   ENSRNOT00000006234
Protein Domains
LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZVD7-F1-model_v2 AlphaFold D3ZVD7 1-351 view protein structure

Transcriptome

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

Promoters
RGD ID:13695165
Promoter ID:EPDNEW_R5689
Type:single initiation site
Name:Kera_1
Description:keratocan
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_6.0738,858,064 - 38,858,124EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305816 AgrOrtholog
BioCyc Gene G2FUF-34283 BioCyc
Ensembl Genes ENSRNOG00000004635 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006234 ENTREZGENE
  ENSRNOT00000006234.7 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LRR-contain_N UniProtKB/TrEMBL
  SLRP UniProtKB/TrEMBL
KEGG Report rno:314771 UniProtKB/TrEMBL
NCBI Gene 314771 ENTREZGENE
PANTHER AGAP008170-PA UniProtKB/TrEMBL
  KERATOCAN UniProtKB/TrEMBL
Pfam LRR_6 UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
PhenoGen Kera PhenoGen
PROSITE LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004635 RatGTEx
SMART LRR_BAC UniProtKB/TrEMBL
  LRR_TYP UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt A6IG68 ENTREZGENE, UniProtKB/TrEMBL
  D3ZVD7 ENTREZGENE, UniProtKB/TrEMBL


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