Kcnd1 (potassium voltage-gated channel subfamily D member 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Kcnd1 (potassium voltage-gated channel subfamily D member 1) Rattus norvegicus
Analyze
Symbol: Kcnd1
Name: potassium voltage-gated channel subfamily D member 1
RGD ID: 621364
Description: Predicted to have A-type (transient outward) potassium channel activity. Predicted to be involved in potassium ion transmembrane transport. Localizes to neuronal cell body. Orthologous to human KCND1 (potassium voltage-gated channel subfamily D member 1); PARTICIPATES IN excitatory synaptic transmission pathway; long term potentiation; INTERACTS WITH 1,3-dinitrobenzene; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Kv4.1; potassium channel, voltage gated Shal-related subfamily D, member 1; potassium voltage gated channel Shal-related family member 1; potassium voltage gated channel, Shal-related family, member 1; potassium voltage-gated channel, Shal-related family, member 1; potassium voltage-gated channel, Shal-related subfamily, member 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,661,688 - 14,678,745 (-)NCBI
Rnor_6.0 EnsemblX15,506,724 - 15,520,712 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,506,724 - 15,520,712 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X16,287,959 - 16,301,947 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,696,234 - 26,710,222 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,750,502 - 26,763,223 (-)NCBI
CeleraX14,746,408 - 14,760,394 (-)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References


Genomics

Comparative Map Data
Kcnd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,661,688 - 14,678,745 (-)NCBI
Rnor_6.0 EnsemblX15,506,724 - 15,520,712 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,506,724 - 15,520,712 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X16,287,959 - 16,301,947 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,696,234 - 26,710,222 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,750,502 - 26,763,223 (-)NCBI
CeleraX14,746,408 - 14,760,394 (-)NCBICelera
Cytogenetic MapXq12NCBI
KCND1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX48,961,378 - 48,971,844 (-)EnsemblGRCh38hg38GRCh38
GRCh38X48,960,983 - 48,972,103 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X48,818,641 - 48,828,251 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,703,583 - 48,713,195 (-)NCBINCBI36hg18NCBI36
Build 34X48,574,886 - 48,584,499NCBI
CeleraX52,835,266 - 52,844,878 (+)NCBI
Cytogenetic MapXp11.23NCBI
HuRefX46,474,963 - 46,485,532 (-)NCBIHuRef
CHM1_1X48,849,929 - 48,859,553 (-)NCBICHM1_1
Kcnd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X7,686,907 - 7,704,517 (+)NCBIGRCm39mm39
GRCm39 EnsemblX7,688,528 - 7,704,519 (+)Ensembl
GRCm38X7,823,759 - 7,838,278 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX7,822,289 - 7,838,280 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X7,400,969 - 7,413,629 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X6,980,802 - 6,993,462 (+)NCBImm8
CeleraX3,633,556 - 3,646,421 (-)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.53NCBI
Kcnd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955543487,312 - 498,626 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955543487,312 - 500,232 (-)NCBIChiLan1.0ChiLan1.0
KCND1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X49,115,933 - 49,127,030 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX49,115,933 - 49,127,030 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X41,258,803 - 41,270,036 (-)NCBIMhudiblu_PPA_v0panPan3
KCND1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X42,111,817 - 42,119,939 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX42,111,837 - 42,118,375 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,487,092 - 16,495,610 (-)NCBI
ROS_Cfam_1.0X42,247,518 - 42,256,331 (-)NCBI
UMICH_Zoey_3.1X42,234,071 - 42,242,589 (-)NCBI
UNSW_CanFamBas_1.0X42,221,985 - 42,230,798 (-)NCBI
UU_Cfam_GSD_1.0X42,316,221 - 42,325,034 (-)NCBI
Kcnd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,640,399 - 34,650,768 (-)NCBI
SpeTri2.0NW_004936721881,162 - 890,939 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KCND1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX43,032,357 - 43,041,760 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X43,032,355 - 43,043,310 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X47,770,985 - 47,780,563 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KCND1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X46,080,116 - 46,092,125 (-)NCBI
ChlSab1.1 EnsemblX46,081,711 - 46,089,762 (-)Ensembl
Kcnd1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624893739,980 - 752,924 (-)NCBI

Position Markers
PMC125678P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,668,339 - 14,668,589 (+)MAPPER
Rnor_6.0X15,513,376 - 15,513,625NCBIRnor6.0
Rnor_5.0X16,294,611 - 16,294,860UniSTSRnor5.0
RGSC_v3.4X26,702,886 - 26,703,135UniSTSRGSC3.4
CeleraX14,753,058 - 14,753,307UniSTS
Cytogenetic MapXq13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X166245321592783Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:285
Count of miRNA genes:184
Interacting mature miRNAs:220
Transcripts:ENSRNOT00000011994
Prediction methods:Miranda, Pita, 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.


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
Low 2 33 13 8 10 8 1 3 74 24 41 11 1
Below cutoff 1 10 37 26 9 26 7 8 11 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011994   ⟹   ENSRNOP00000011994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX15,506,724 - 15,520,712 (-)Ensembl
RefSeq Acc Id: NM_001105748   ⟹   NP_001099218
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,661,688 - 14,675,677 (-)NCBI
Rnor_6.0X15,506,724 - 15,520,712 (-)NCBI
Rnor_5.0X16,287,959 - 16,301,947 (-)NCBI
RGSC_v3.4X26,696,234 - 26,710,222 (-)RGD
CeleraX14,746,408 - 14,760,394 (-)RGD
Sequence:
RefSeq Acc Id: XM_039099409   ⟹   XP_038955337
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,662,286 - 14,678,745 (-)NCBI
RefSeq Acc Id: XM_039099410   ⟹   XP_038955338
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,662,286 - 14,678,745 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001099218 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955337 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955338 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL83824 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099218   ⟸   NM_001105748
- Peptide Label: precursor
- UniProtKB: D3ZYK3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011994   ⟸   ENSRNOT00000011994
RefSeq Acc Id: XP_038955338   ⟸   XM_039099410
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955337   ⟸   XM_039099409
- Peptide Label: isoform X1
Protein Domains
BTB

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621364 AgrOrtholog
Ensembl Genes ENSRNOG00000039544 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011994 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011994 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.120.350 UniProtKB/TrEMBL
InterPro BTB/POZ-like UniProtKB/TrEMBL
  BTB/POZ_fold UniProtKB/TrEMBL
  Ion_trans UniProtKB/TrEMBL
  K_chnl_volt-dep_Kv UniProtKB/TrEMBL
  K_chnl_volt-dep_Kv4 UniProtKB/TrEMBL
  K_chnl_volt-dep_Kv4.1 UniProtKB/TrEMBL
  K_chnl_volt-dep_Kv4_C UniProtKB/TrEMBL
  K_chnl_volt-dep_Kv_tetra UniProtKB/TrEMBL
  Shal-type UniProtKB/TrEMBL
  VG_K_chnl UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/TrEMBL
KEGG Report rno:116695 UniProtKB/TrEMBL
NCBI Gene 116695 ENTREZGENE
PANTHER PTHR11537 UniProtKB/TrEMBL
Pfam DUF3399 UniProtKB/TrEMBL
  Ion_trans UniProtKB/TrEMBL
  K_tetra UniProtKB/TrEMBL
  Shal-type UniProtKB/TrEMBL
PhenoGen Kcnd1 PhenoGen
PRINTS KV41CHANNEL UniProtKB/TrEMBL
  KVCHANNEL UniProtKB/TrEMBL
  SHALCHANNEL UniProtKB/TrEMBL
SMART BTB UniProtKB/TrEMBL
Superfamily-SCOP BTB/POZ_fold UniProtKB/TrEMBL
UniProt D3ZYK3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Kcnd1  potassium voltage-gated channel subfamily D member 1  Kcnd1  potassium channel, voltage gated Shal-related subfamily D, member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-01-26 Kcnd1  potassium channel, voltage gated Shal-related subfamily D, member 1  Kcnd1  potassium voltage-gated channel, Shal-related subfamily, member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-20 Kcnd1  potassium voltage-gated channel, Shal-related subfamily, member 1  Kcnd1  potassium voltage-gated channel, Shal-related family, member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Kcnd1  potassium voltage-gated channel, Shal-related family, member 1    potassium voltage gated channel, Shal-related family, member 1  Name updated 1299863 APPROVED
2002-08-07 Kcnd1  potassium voltage gated channel, Shal-related family, member 1      Symbol and Name status set to provisional 70820 PROVISIONAL