Kctd3 (potassium channel tetramerization domain containing 3) - Rat Genome Database

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Gene: Kctd3 (potassium channel tetramerization domain containing 3) Rattus norvegicus
Analyze
Symbol: Kctd3
Name: potassium channel tetramerization domain containing 3
RGD ID: 1310658
Description: Predicted to be involved in protein homooligomerization. Predicted to be located in plasma membrane. Orthologous to human KCTD3 (potassium channel tetramerization domain containing 3); INTERACTS WITH 17beta-estradiol; 2,6-dinitrotoluene; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: BTB/POZ domain-containing protein KCTD3; LOC305055; potassium channel tetramerisation domain containing 3; Ren-45
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
GRCr813103,041,488 - 103,080,069 (-)NCBIGRCr8
mRatBN7.213100,510,193 - 100,548,765 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13100,510,195 - 100,548,718 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13103,025,630 - 103,064,151 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013104,414,429 - 104,452,952 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013101,616,996 - 101,655,605 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.013107,433,588 - 107,471,843 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13107,433,588 - 107,471,843 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013112,063,807 - 112,101,984 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413105,117,483 - 105,155,705 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.113105,307,551 - 105,373,106 (-)NCBI
Celera13100,000,837 - 100,039,378 (-)NCBICelera
Cytogenetic Map13q26NCBI
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

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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:23382386  


Genomics

Comparative Map Data
Kctd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813103,041,488 - 103,080,069 (-)NCBIGRCr8
mRatBN7.213100,510,193 - 100,548,765 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13100,510,195 - 100,548,718 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13103,025,630 - 103,064,151 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013104,414,429 - 104,452,952 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013101,616,996 - 101,655,605 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.013107,433,588 - 107,471,843 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13107,433,588 - 107,471,843 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013112,063,807 - 112,101,984 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413105,117,483 - 105,155,705 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.113105,307,551 - 105,373,106 (-)NCBI
Celera13100,000,837 - 100,039,378 (-)NCBICelera
Cytogenetic Map13q26NCBI
KCTD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381215,567,304 - 215,621,807 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1215,567,304 - 215,621,807 (+)EnsemblGRCh38hg38GRCh38
GRCh371215,740,647 - 215,795,149 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361213,807,358 - 213,861,772 (+)NCBINCBI36Build 36hg18NCBI36
Build 341212,129,129 - 212,183,542NCBI
Celera1188,964,556 - 189,018,971 (+)NCBICelera
Cytogenetic Map1q41NCBI
HuRef1186,414,971 - 186,469,413 (+)NCBIHuRef
CHM1_11217,013,056 - 217,067,482 (+)NCBICHM1_1
T2T-CHM13v2.01214,807,705 - 214,862,209 (+)NCBIT2T-CHM13v2.0
Kctd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391188,703,292 - 188,740,095 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1188,703,292 - 188,740,038 (-)EnsemblGRCm39 Ensembl
GRCm381188,971,095 - 189,007,898 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1188,971,095 - 189,007,841 (-)EnsemblGRCm38mm10GRCm38
MGSCv371190,794,977 - 190,831,719 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361190,671,886 - 190,708,628 (-)NCBIMGSCv36mm8
Celera1195,882,760 - 195,919,558 (-)NCBICelera
Cytogenetic Map1H6NCBI
cM Map193.51NCBI
Kctd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554062,501,083 - 2,540,125 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554062,500,619 - 2,539,123 (-)NCBIChiLan1.0ChiLan1.0
KCTD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2133,782,743 - 33,837,316 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1133,740,794 - 33,795,442 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01191,138,755 - 191,193,352 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11195,992,828 - 196,047,013 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1195,992,842 - 196,051,606 (+)Ensemblpanpan1.1panPan2
KCTD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13811,016,344 - 11,059,843 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3811,008,857 - 11,084,871 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3811,042,385 - 11,097,556 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03811,030,105 - 11,085,477 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3811,030,097 - 11,085,471 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13811,042,689 - 11,098,109 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03811,395,043 - 11,450,335 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03811,680,643 - 11,736,064 (+)NCBIUU_Cfam_GSD_1.0
Kctd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934460,852,512 - 60,902,757 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366282,862,617 - 2,912,790 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366282,862,536 - 2,912,784 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KCTD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl105,754,156 - 5,815,086 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1105,754,180 - 5,815,126 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2107,733,711 - 7,777,690 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KCTD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12513,951,569 - 14,008,370 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2513,950,775 - 14,008,338 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605514,398,224 - 14,454,888 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kctd3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462483511,110 - 46,480 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Kctd3
140 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:621
Count of miRNA genes:286
Interacting mature miRNAs:366
Transcripts:ENSRNOT00000003556
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
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat

Markers in Region
RH131269  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.213100,510,322 - 100,510,522 (+)MAPPERmRatBN7.2
Rnor_6.013107,433,716 - 107,433,915NCBIRnor6.0
Rnor_5.013112,063,935 - 112,064,134UniSTSRnor5.0
RGSC_v3.413105,117,611 - 105,117,810UniSTSRGSC3.4
Celera13100,000,965 - 100,001,164UniSTS
RH 3.4 Map13685.1UniSTS
Cytogenetic Map13q26UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 34 45 29 19 29 2 2 74 35 40 11 2
Low 9 12 12 12 6 9 1 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003556   ⟹   ENSRNOP00000003556
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl13100,510,195 - 100,548,718 (-)Ensembl
Rnor_6.0 Ensembl13107,433,588 - 107,471,843 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102777   ⟹   ENSRNOP00000090327
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl13100,510,195 - 100,544,407 (-)Ensembl
RefSeq Acc Id: NM_001107199   ⟹   NP_001100669
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813103,041,490 - 103,080,009 (-)NCBI
mRatBN7.213100,510,195 - 100,548,718 (-)NCBI
Rnor_6.013107,433,588 - 107,471,843 (-)NCBI
Rnor_5.013112,063,807 - 112,101,984 (-)NCBI
RGSC_v3.413105,117,483 - 105,155,705 (-)RGD
Celera13100,000,837 - 100,039,378 (-)RGD
Sequence:
RefSeq Acc Id: XM_039090826   ⟹   XP_038946754
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813103,041,488 - 103,080,069 (-)NCBI
mRatBN7.213100,510,193 - 100,548,765 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100669 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946754 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL94957 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003556
  ENSRNOP00000003556.7
  ENSRNOP00000090327.1
Reference Protein Sequences
RefSeq Acc Id: NP_001100669   ⟸   NM_001107199
- UniProtKB: A6JGV1 (UniProtKB/TrEMBL),   A0A8I6A9V0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003556   ⟸   ENSRNOT00000003556
RefSeq Acc Id: XP_038946754   ⟸   XM_039090826
- Peptide Label: isoform X1
- UniProtKB: D3ZNX0 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000090327   ⟸   ENSRNOT00000102777
Protein Domains
BTB

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZNX0-F1-model_v2 AlphaFold D3ZNX0 1-816 view protein structure

Transcriptome

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

Promoters
RGD ID:13699103
Promoter ID:EPDNEW_R9627
Type:multiple initiation site
Name:Kctd3_1
Description:potassium channel tetramerization 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_6.013107,471,842 - 107,471,902EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310658 AgrOrtholog
BioCyc Gene G2FUF-16914 BioCyc
Ensembl Genes ENSRNOG00000002627 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003556 ENTREZGENE
  ENSRNOT00000003556.7 UniProtKB/TrEMBL
  ENSRNOT00000102777.1 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
InterPro BTB/POZ-like UniProtKB/TrEMBL
  BTB/POZ_fold UniProtKB/TrEMBL
  K_chnl_volt-dep_Kv_tetra UniProtKB/TrEMBL
  SHKBP1/KCTD3 UniProtKB/TrEMBL
  SHKBP1_KCTD3_BTB_POZ UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
KEGG Report rno:305055 UniProtKB/TrEMBL
NCBI Gene 305055 ENTREZGENE
PANTHER BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD3 UniProtKB/TrEMBL
  SETA BINDING PROTEIN 1 UniProtKB/TrEMBL
Pfam K_tetra UniProtKB/TrEMBL
PhenoGen Kctd3 PhenoGen
PROSITE BTB UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002627 RatGTEx
SMART BTB UniProtKB/TrEMBL
  WD40 UniProtKB/TrEMBL
Superfamily-SCOP BTB/POZ_fold UniProtKB/TrEMBL
  WD40_like UniProtKB/TrEMBL
UniProt A0A8I6A9V0 ENTREZGENE, UniProtKB/TrEMBL
  A6JGV1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZNX0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-07-09 Kctd3  potassium channel tetramerization domain containing 3  Kctd3  potassium channel tetramerisation domain containing 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Kctd3  potassium channel tetramerisation domain containing 3  Kctd3_predicted  potassium channel tetramerisation domain containing 3 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Kctd3_predicted  potassium channel tetramerisation domain containing 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED