Klhdc3 (kelch domain containing 3) - Rat Genome Database

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Gene: Klhdc3 (kelch domain containing 3) Rattus norvegicus
Analyze
Symbol: Klhdc3
Name: kelch domain containing 3
RGD ID: 1307105
Description: Predicted to enable chromatin binding activity and ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in ubiquitin-dependent protein catabolic process via the C-end degron rule pathway. Predicted to be located in chromatin and nucleoplasm. Predicted to be part of Cul2-RING ubiquitin ligase complex. Predicted to be active in cytoplasm. Orthologous to human KLHDC3 (kelch domain containing 3); INTERACTS WITH acrylamide; bis(2-ethylhexyl) phthalate; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: kelch domain-containing protein 3; LOC363192
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8921,799,870 - 21,806,337 (+)NCBIGRCr8
mRatBN7.2914,302,345 - 14,308,736 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,302,354 - 14,308,736 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx922,886,253 - 22,892,578 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0927,949,056 - 27,955,382 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0926,249,628 - 26,255,953 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0916,612,429 - 16,618,761 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,612,433 - 16,618,761 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0915,519,046 - 15,525,380 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4910,045,861 - 10,052,001 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1910,043,182 - 10,049,323 (-)NCBI
Celera912,050,694 - 12,057,023 (+)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (IEA,ISO)
Cul2-RING ubiquitin ligase complex  (IEA,ISO,ISS)
cytoplasm  (IBA,IEA,ISO)
nucleoplasm  (IEA,ISO)

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:12606021   PMID:15489334  


Genomics

Comparative Map Data
Klhdc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8921,799,870 - 21,806,337 (+)NCBIGRCr8
mRatBN7.2914,302,345 - 14,308,736 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,302,354 - 14,308,736 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx922,886,253 - 22,892,578 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0927,949,056 - 27,955,382 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0926,249,628 - 26,255,953 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0916,612,429 - 16,618,761 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,612,433 - 16,618,761 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0915,519,046 - 15,525,380 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4910,045,861 - 10,052,001 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1910,043,182 - 10,049,323 (-)NCBI
Celera912,050,694 - 12,057,023 (+)NCBICelera
Cytogenetic Map9q12NCBI
KLHDC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38643,014,249 - 43,021,294 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl643,014,103 - 43,021,298 (+)EnsemblGRCh38hg38GRCh38
GRCh37642,981,987 - 42,989,032 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36643,089,955 - 43,097,010 (+)NCBINCBI36Build 36hg18NCBI36
Build 34643,089,954 - 43,097,010NCBI
Celera644,534,218 - 44,541,273 (+)NCBICelera
Cytogenetic Map6p21.1NCBI
HuRef642,699,164 - 42,706,136 (+)NCBIHuRef
CHM1_1642,984,294 - 42,991,489 (+)NCBICHM1_1
T2T-CHM13v2.0642,843,347 - 42,850,393 (+)NCBIT2T-CHM13v2.0
Klhdc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391746,985,476 - 46,991,856 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1746,985,476 - 46,991,840 (-)EnsemblGRCm39 Ensembl
GRCm381746,674,550 - 46,680,930 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1746,674,550 - 46,680,914 (-)EnsemblGRCm38mm10GRCm38
MGSCv371746,811,499 - 46,817,879 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361746,137,745 - 46,144,095 (-)NCBIMGSCv36mm8
Celera1750,110,421 - 50,116,798 (-)NCBICelera
Cytogenetic Map17CNCBI
cM Map1722.9NCBI
Klhdc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554378,989,671 - 8,995,845 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554378,989,671 - 8,995,845 (+)NCBIChiLan1.0ChiLan1.0
KLHDC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2557,514,289 - 57,521,415 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1653,384,529 - 53,391,659 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0642,606,462 - 42,613,565 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1643,900,902 - 43,908,556 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl643,900,902 - 43,908,556 (+)Ensemblpanpan1.1panPan2
KLHDC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11211,542,449 - 11,549,012 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1211,542,538 - 11,548,622 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1211,569,361 - 11,576,029 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01212,023,718 - 12,030,385 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1212,023,726 - 12,036,330 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11211,552,345 - 11,559,010 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01211,636,413 - 11,643,076 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01211,730,475 - 11,737,140 (+)NCBIUU_Cfam_GSD_1.0
Klhdc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494647,040,076 - 47,046,708 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647616,913,493 - 16,918,524 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647616,913,494 - 16,920,108 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KLHDC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl738,080,366 - 38,087,166 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1738,080,377 - 38,087,170 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2743,529,107 - 43,535,538 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KLHDC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11729,138,568 - 29,145,794 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1729,138,459 - 29,145,787 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604443,077,010 - 43,084,281 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Klhdc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475416,479,389 - 16,483,824 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475416,479,389 - 16,485,573 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Klhdc3
22 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:319
Count of miRNA genes:191
Interacting mature miRNAs:220
Transcripts:ENSRNOT00000023979
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat

Markers in Region
RH141056  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2914,308,506 - 14,308,687 (+)MAPPERmRatBN7.2
Rnor_6.0916,618,536 - 16,618,716NCBIRnor6.0
Rnor_5.0915,525,151 - 15,525,331UniSTSRnor5.0
RGSC_v3.4910,045,906 - 10,046,086UniSTSRGSC3.4
Celera912,056,798 - 12,056,978UniSTS
Cytogenetic Map9q12UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000023979   ⟹   ENSRNOP00000023979
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl914,302,354 - 14,308,732 (+)Ensembl
Rnor_6.0 Ensembl916,612,433 - 16,618,761 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000102730   ⟹   ENSRNOP00000077460
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl914,302,369 - 14,308,736 (+)Ensembl
RefSeq Acc Id: NM_001012203   ⟹   NP_001012203
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8921,800,005 - 21,806,333 (+)NCBI
mRatBN7.2914,302,404 - 14,308,732 (+)NCBI
Rnor_6.0916,612,433 - 16,618,761 (+)NCBI
Rnor_5.0915,519,046 - 15,525,380 (+)NCBI
RGSC_v3.4910,045,861 - 10,052,001 (-)RGD
Celera912,050,694 - 12,057,023 (+)RGD
Sequence:
RefSeq Acc Id: XM_006244542   ⟹   XP_006244604
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8921,799,870 - 21,806,337 (+)NCBI
mRatBN7.2914,302,350 - 14,308,736 (+)NCBI
Rnor_6.0916,612,429 - 16,618,761 (+)NCBI
Rnor_5.0915,519,046 - 15,525,380 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039083822   ⟹   XP_038939750
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8921,799,932 - 21,806,337 (+)NCBI
mRatBN7.2914,302,350 - 14,308,736 (+)NCBI
RefSeq Acc Id: XM_063267358   ⟹   XP_063123428
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8921,801,581 - 21,806,337 (+)NCBI
RefSeq Acc Id: NP_001012203   ⟸   NM_001012203
- UniProtKB: Q6AYI2 (UniProtKB/Swiss-Prot),   A6JIP1 (UniProtKB/TrEMBL),   A0A8I5ZJH5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244604   ⟸   XM_006244542
- Peptide Label: isoform X2
- UniProtKB: Q6AYI2 (UniProtKB/Swiss-Prot),   A6JIP1 (UniProtKB/TrEMBL),   A0A8I5ZJH5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000023979   ⟸   ENSRNOT00000023979
RefSeq Acc Id: XP_038939750   ⟸   XM_039083822
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZJH5 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000077460   ⟸   ENSRNOT00000102730
RefSeq Acc Id: XP_063123428   ⟸   XM_063267358
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AYI2-F1-model_v2 AlphaFold Q6AYI2 1-382 view protein structure

Transcriptome

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

Promoters
RGD ID:13696510
Promoter ID:EPDNEW_R7034
Type:initiation region
Name:Klhdc3_1
Description:kelch domain containing 3
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_6.0916,612,414 - 16,612,474EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307105 AgrOrtholog
BioCyc Gene G2FUF-28238 BioCyc
Ensembl Genes ENSRNOG00000017495 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055008685 UniProtKB/Swiss-Prot
  ENSRNOG00060023951 UniProtKB/Swiss-Prot
  ENSRNOG00065027045 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000023979.7 UniProtKB/Swiss-Prot
  ENSRNOT00000102730.1 UniProtKB/TrEMBL
  ENSRNOT00055014683 UniProtKB/Swiss-Prot
  ENSRNOT00060041551 UniProtKB/Swiss-Prot
  ENSRNOT00065046664 UniProtKB/Swiss-Prot
Gene3D-CATH 2.120.10.80 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7114311 IMAGE-MGC_LOAD
InterPro CRL_complex_substrate-recog UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kelch-typ_b-propeller UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kelch_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:363192 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93964 IMAGE-MGC_LOAD
NCBI Gene 363192 ENTREZGENE
PANTHER KELCH DOMAIN-CONTAINING PROTEIN 3 UniProtKB/Swiss-Prot
  KELCH DOMAIN-CONTAINING PROTEIN 3 UniProtKB/Swiss-Prot
  KELCH DOMAIN-CONTAINING PROTEIN 3 UniProtKB/TrEMBL
  KELCH DOMAIN-CONTAINING PROTEIN 3 UniProtKB/TrEMBL
Pfam Kelch_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kelch_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kelch_4 UniProtKB/TrEMBL
  Kelch_6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Klhdc3 PhenoGen
RatGTEx ENSRNOG00000017495 RatGTEx
  ENSRNOG00055008685 RatGTEx
  ENSRNOG00060023951 RatGTEx
  ENSRNOG00065027045 RatGTEx
Superfamily-SCOP SSF117281 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZJH5 ENTREZGENE, UniProtKB/TrEMBL
  A6JIP1 ENTREZGENE, UniProtKB/TrEMBL
  A6JIP3_RAT UniProtKB/TrEMBL
  KLDC3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Klhdc3  kelch domain containing 3  Klhdc3_predicted  kelch domain containing 3 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Klhdc3_predicted  kelch domain containing 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED