Hcn2 (hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2) - Rat Genome Database

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Gene: Hcn2 (hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2) Rattus norvegicus
Analyze
Symbol: Hcn2
Name: hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2
RGD ID: 620689
Description: Exhibits PDZ domain binding activity and molecular adaptor activity. Involved in several processes, including cellular response to aldosterone; response to cisplatin; and response to drug. Localizes to several cellular components, including axon; dendrite; and neuronal cell body. Biomarker of dermatitis; meningitis; and visual epilepsy. Orthologous to human HCN2 (hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,6-dinitrotoluene; 4-amino-2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: hyperpolarization activated cyclic nucleotide-gated potassium channel 2; potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
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
mRatBN7.279,969,801 - 9,988,839 (-)NCBI
Rnor_6.0 Ensembl712,851,739 - 12,874,215 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0712,851,730 - 12,870,087 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0713,021,934 - 13,051,802 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,485,257 - 11,503,614 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1711,485,256 - 11,503,614 (-)NCBI
Celera78,143,888 - 8,161,946 (-)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
1. Acosta C, etal., PLoS One. 2012;7(12):e50442. doi: 10.1371/journal.pone.0050442. Epub 2012 Dec 7.
2. Boyes J, etal., Eur J Neurosci. 2007 Apr;25(7):2081-92.
3. Brewster AL, etal., Neurobiol Dis. 2005 Jun-Jul;19(1-2):200-7.
4. Budde T, etal., Pflugers Arch. 2008 Sep;456(6):1061-73. Epub 2008 May 14.
5. Buniel M, etal., J Comp Neurol. 2008 Oct 1;510(4):367-77.
6. Cho HJ, etal., Neuroscience. 2009 Aug 18;162(2):453-61. Epub 2009 May 3.
7. Dougherty KA, etal., J Neurophysiol. 2013 Apr;109(7):1940-53. doi: 10.1152/jn.00010.2013. Epub 2013 Jan 16.
8. GOA data from the GO Consortium
9. Huang X, etal., Basic Res Cardiol. 2007 Sep;102(5):429-35. Epub 2007 Jun 18.
10. Kanyshkova T, etal., J Neurosci. 2009 Jul 8;29(27):8847-57.
11. Kimura K, etal., Genes Cells. 2004 Jul;9(7):631-40.
12. Li CJ, etal., Mol Neurobiol. 2014 Oct;50(2):704-20. doi: 10.1007/s12035-014-8736-3. Epub 2014 May 18.
13. Lin H, etal., Cell Physiol Biochem. 2009;23(4-6):317-26. doi: 10.1159/000218178. Epub 2009 May 6.
14. MGD data from the GO Consortium
15. Monteggia LM, etal., Brain Res Mol Brain Res 2000 Sep 30;81(1-2):129-39.
16. Muller F, etal., Eur J Neurosci 2003 May;17(10):2084-96.
17. Muto T, etal., Am J Physiol Heart Circ Physiol. 2007 Nov;293(5):H2710-8. Epub 2007 Jul 20.
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Pachucki J, etal., Circ Res. 1999 Sep 17;85(6):498-503.
20. Ramakrishnan NA, etal., J Biol Chem. 2012 Nov 2;287(45):37628-46. doi: 10.1074/jbc.M112.375832. Epub 2012 Sep 4.
21. RGD automated data pipeline
22. RGD automated import pipeline for gene-chemical interactions
23. Shi W, etal., Circ Res 1999 Jul 9;85(1):e1-6.
24. Tu H, etal., Neuroscience. 2010 Jan 13;165(1):39-52. doi: 10.1016/j.neuroscience.2009.10.002. Epub 2009 Oct 6.
25. Wells JE, etal., Int Endod J. 2007 Sep;40(9):715-21. Epub 2007 Jul 23.
26. Whitaker GM, etal., J Biol Chem. 2007 Aug 3;282(31):22900-9. Epub 2007 Jun 6.
27. Xiao J, etal., J Cell Physiol. 2007 Aug;212(2):285-92.
28. Yeh J, etal., Reprod Sci. 2009 Oct;16(10):986-94. Epub 2009 Jul 7.
29. Zha Q, etal., J Neurochem. 2008 Apr;105(1):68-77. Epub 2007 Nov 5.
Additional References at PubMed
PMID:10228147   PMID:14991560   PMID:15016091   PMID:15056713   PMID:15245481   PMID:15292247   PMID:15525777   PMID:15564593   PMID:15958747   PMID:16175581   PMID:16395601   PMID:16648453  
PMID:16760342   PMID:16979600   PMID:17065201   PMID:17311321   PMID:18255311   PMID:18326556   PMID:18397293   PMID:18450385   PMID:18524809   PMID:18614814   PMID:18768480   PMID:19236845  
PMID:19500574   PMID:20220080   PMID:20726890   PMID:21753027   PMID:21796099   PMID:21798320   PMID:22006928   PMID:22377439   PMID:22748890   PMID:22871113   PMID:23620341   PMID:24460767  
PMID:24592881   PMID:25290015   PMID:25659346   PMID:25813712   PMID:25998542   PMID:26021557   PMID:26065643   PMID:26341471   PMID:27496876   PMID:27542339   PMID:27569278   PMID:29806529  
PMID:31432175  


Genomics

Comparative Map Data
Hcn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.279,969,801 - 9,988,839 (-)NCBI
Rnor_6.0 Ensembl712,851,739 - 12,874,215 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0712,851,730 - 12,870,087 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0713,021,934 - 13,051,802 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,485,257 - 11,503,614 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1711,485,256 - 11,503,614 (-)NCBI
Celera78,143,888 - 8,161,946 (-)NCBICelera
Cytogenetic Map7q11NCBI
HCN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl19589,881 - 617,159 (+)EnsemblGRCh38hg38GRCh38
GRCh3819589,881 - 617,159 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3719589,881 - 617,159 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3619540,893 - 568,159 (+)NCBINCBI36hg18NCBI36
Build 3419540,892 - 568,157NCBI
Celera19200,463 - 228,092 (-)NCBI
Cytogenetic Map19p13.3NCBI
HuRef19373,968 - 384,301 (+)NCBIHuRef
CHM1_119589,749 - 616,575 (+)NCBICHM1_1
Hcn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391079,552,468 - 79,571,942 (+)NCBIGRCm39mm39
GRCm39 Ensembl1079,552,468 - 79,571,942 (+)Ensembl
GRCm381079,716,634 - 79,736,108 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1079,716,634 - 79,736,108 (+)EnsemblGRCm38mm10GRCm38
MGSCv371079,179,379 - 79,198,853 (+)NCBIGRCm37mm9NCBIm37
MGSCv361079,119,763 - 79,139,237 (+)NCBImm8
Celera1080,731,157 - 80,750,702 (+)NCBICelera
Cytogenetic Map10C1NCBI
Hcn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554957,124,640 - 7,194,223 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554957,124,060 - 7,143,730 (-)NCBIChiLan1.0ChiLan1.0
HCN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.119559,108 - 584,128 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v019521,348 - 528,203 (-)NCBIMhudiblu_PPA_v0panPan3
HCN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12057,920,089 - 57,941,057 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2057,920,740 - 57,938,374 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2057,722,746 - 57,741,278 (-)NCBI
ROS_Cfam_1.02058,663,358 - 58,681,919 (-)NCBI
UMICH_Zoey_3.12057,717,402 - 57,735,597 (-)NCBI
UNSW_CanFamBas_1.02058,196,864 - 58,215,545 (-)NCBI
UU_Cfam_GSD_1.02058,400,096 - 58,421,283 (-)NCBI
Hcn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118217,625,528 - 217,639,390 (-)NCBI
SpeTri2.0NW_004936588202,101 - 209,255 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HCN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl277,708,161 - 77,730,881 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1277,708,159 - 77,730,881 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
HCN2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.16326,437 - 358,119 (+)NCBI
ChlSab1.1 Ensembl6324,517 - 358,119 (+)Ensembl
Hcn2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248287,889,616 - 7,908,855 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7134147172Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)71164710256647102Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71232846767193263Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71268785067801690Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir1rno-miR-1-3pMirtarbaseexternal_infoWestern blot;qRT-PCRFunctional MTI18458081
Mir133a1rno-miR-133a-3pMirtarbaseexternal_infoReporter assay//real-timeRT-PCR//Western blotFunctional MTI17516552

Predicted Target Of
Summary Value
Count of predictions:78
Count of miRNA genes:69
Interacting mature miRNAs:76
Transcripts:ENSRNOT00000011837
Prediction methods: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.


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 18 2 48 3
Low 3 25 26 14 12 14 8 9 26 32 37 11 8
Below cutoff 30 26 7 26 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011837   ⟹   ENSRNOP00000011837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl712,851,739 - 12,874,215 (-)Ensembl
RefSeq Acc Id: NM_053684   ⟹   NP_446136
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,970,368 - 9,988,839 (-)NCBI
Rnor_6.0712,851,730 - 12,870,087 (-)NCBI
Rnor_5.0713,021,934 - 13,051,802 (-)NCBI
RGSC_v3.4711,485,257 - 11,503,614 (-)RGD
Celera78,143,888 - 8,161,946 (-)RGD
Sequence:
RefSeq Acc Id: XM_039078239   ⟹   XP_038934167
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,969,801 - 9,978,022 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_446136   ⟸   NM_053684
- UniProtKB: Q9JKA9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011837   ⟸   ENSRNOT00000011837
RefSeq Acc Id: XP_038934167   ⟸   XM_039078239
- Peptide Label: isoform X1
Protein Domains
Cyclic nucleotide-binding

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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:620689 AgrOrtholog
Ensembl Genes ENSRNOG00000008831 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011837 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011837 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro cNMP-bd-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  cNMP-bd_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  cNMP-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  K_chnl_volt-dep_EAG/ELK/ERG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RmlC-like_jellyroll UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114244 UniProtKB/Swiss-Prot
NCBI Gene 114244 ENTREZGENE
Pfam cNMP_binding UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB HCN2 RGD
PhenoGen Hcn2 PhenoGen
PRINTS EAGCHANLFMLY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CNMP_BINDING_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CNMP_BINDING_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART cNMP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF51206 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1LRY7_RAT UniProtKB/TrEMBL
  HCN2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6BCT5 UniProtKB/Swiss-Prot
  Q9QZW6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-06-12 Hcn2  hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2  Hcn2  hyperpolarization activated cyclic nucleotide-gated potassium channel 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Hcn2  hyperpolarization activated cyclic nucleotide-gated potassium channel 2      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Hcn2  hyperpolarization activated cyclic nucleotide-gated potassium channel 2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in neonatal and adult cardiac ventricle  
gene_product member of a family of pacemaker channels activated by hyperpolarization and regulated by cyclic nucleotides 70760