Hcn1 (hyperpolarization-activated cyclic nucleotide-gated potassium channel 1) - Rat Genome Database

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Gene: Hcn1 (hyperpolarization-activated cyclic nucleotide-gated potassium channel 1) Rattus norvegicus
Symbol: Hcn1
Name: hyperpolarization-activated cyclic nucleotide-gated potassium channel 1
RGD ID: 620688
Description: Enables identical protein binding activity; phosphatidylinositol-3,4,5-trisphosphate binding activity; and phosphatidylinositol-4,5-bisphosphate binding activity. Involved in several processes, including cellular response to interferon-beta; maternal behavior; and positive regulation of membrane hyperpolarization. Located in several cellular components, including basolateral plasma membrane; dendrite; and neuronal cell body. Used to study anxiety disorder; essential tremor; and mood disorder. Biomarker of complex cortical dysplasia with other brain malformations; epilepsy (multiple); and meningitis. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 24 and generalized epilepsy with febrile seizures plus 10. Orthologous to human HCN1 (hyperpolarization activated cyclic nucleotide gated potassium channel 1); INTERACTS WITH (+)-pilocarpine; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hyperpolarization-activated, cyclic nucleotide-gated potassium channel 1 (HCN1); potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: Hcn1A354V   Hcn1em1Kyo  
Genetic Models: F344 -Aspaem34Kyo Hcn1em1Kyo F344-Hcn1em1Kyo
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
GRCr8251,228,710 - 51,632,806 (+)NCBIGRCr8
mRatBN7.2249,495,771 - 49,899,983 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl249,495,771 - 49,899,774 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx256,591,338 - 56,990,181 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0254,650,014 - 55,048,852 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0249,560,176 - 49,958,195 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0250,099,576 - 50,499,799 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl250,099,576 - 50,499,799 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0268,473,431 - 68,874,494 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4249,525,949 - 49,939,066 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1249,454,181 - 49,867,299 (+)NCBI
Celera245,196,523 - 45,593,603 (+)NCBICelera
Cytogenetic Map2q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype

References - curated
# Reference Title Reference Citation
1. Postnatal development of dendritic synaptic integration in rat neocortical pyramidal neurons. Atkinson SE and Williams SR, J Neurophysiol. 2009 Aug;102(2):735-51. doi: 10.1152/jn.00083.2009. Epub 2009 May 20.
2. I(h) "run-up" in rat neocortical neurons and transiently rat or human HCN1-expressing HEK293 cells. Battefeld A, etal., J Neurosci Res. 2010 Nov 1;88(14):3067-78. doi: 10.1002/jnr.22475.
3. Enhanced expression of a specific hyperpolarization-activated cyclic nucleotide-gated cation channel (HCN) in surviving dentate gyrus granule cells of human and experimental epileptic hippocampus. Bender RA, etal., J Neurosci. 2003 Jul 30;23(17):6826-36.
4. Localization of HCN1 channels to presynaptic compartments: novel plasticity that may contribute to hippocampal maturation. Bender RA, etal., J Neurosci. 2007 Apr 25;27(17):4697-706.
5. Functional presynaptic HCN channels in the rat globus pallidus. Boyes J, etal., Eur J Neurosci. 2007 Apr;25(7):2081-92.
6. Molecular and functional analysis of hyperpolarization-activated pacemaker channels in the hippocampus after entorhinal cortex lesion. Brauer AU, etal., FASEB J. 2001 Dec;15(14):2689-701.
7. Formation of heteromeric hyperpolarization-activated cyclic nucleotide-gated (HCN) channels in the hippocampus is regulated by developmental seizures. Brewster AL, etal., Neurobiol Dis. 2005 Jun-Jul;19(1-2):200-7.
8. Inflammation-induced increase in hyperpolarization-activated, cyclic nucleotide-gated channel protein in trigeminal ganglion neurons and the effect of buprenorphine. Cho HJ, etal., Neuroscience. 2009 Aug 18;162(2):453-61. Epub 2009 May 3.
9. Differential expression of HCN subunits alters voltage-dependent gating of h-channels in CA1 pyramidal neurons from dorsal and ventral hippocampus. Dougherty KA, etal., J Neurophysiol. 2013 Apr;109(7):1940-53. doi: 10.1152/jn.00010.2013. Epub 2013 Jan 16.
10. 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.
11. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
12. Abnormal pyramidal cell morphology and HCN channel expression in cortical dysplasia. Hablitz JJ and Yang J, Epilepsia. 2010 Jul;51 Suppl 3:52-5. doi: 10.1111/j.1528-1167.2010.02610.x.
13. Rapid loss of dendritic HCN channel expression in hippocampal pyramidal neurons following status epilepticus. Jung S, etal., J Neurosci. 2011 Oct 5;31(40):14291-5. doi: 10.1523/JNEUROSCI.1148-11.2011.
14. Enhancement of dorsal hippocampal activity by knockdown of HCN1 channels leads to anxiolytic- and antidepressant-like behaviors. Kim CS, etal., Neuron. 2012 Aug 9;75(3):503-16. doi: 10.1016/j.neuron.2012.05.027.
15. Role of HCN channels in neuronal hyperexcitability after subarachnoid hemorrhage in rats. Li B, etal., J Neurosci. 2012 Feb 29;32(9):3164-75. doi: 10.1523/JNEUROSCI.5143-11.2012.
16. Activation of GABAB receptors ameliorates cognitive impairment via restoring the balance of HCN1/HCN2 surface expression in the hippocampal CA1 area in rats with chronic cerebral hypoperfusion. Li CJ, etal., Mol Neurobiol. 2014 Oct;50(2):704-20. doi: 10.1007/s12035-014-8736-3. Epub 2014 May 18.
17. Behavioral alterations associated with a down regulation of HCN1 mRNA in hippocampal cornus ammon 1 region and neocortex after chronic incomplete global cerebral ischemia in rats. Li S, etal., Neuroscience. 2010 Feb 3;165(3):654-61. doi: 10.1016/j.neuroscience.2009.10.053. Epub 2009 Nov 3.
18. Polarized and compartment-dependent distribution of HCN1 in pyramidal cell dendrites. Lorincz A, etal., Nat Neurosci 2002 Nov;5(11):1185-93.
19. Neuron-restrictive silencer factor-mediated hyperpolarization-activated cyclic nucleotide gated channelopathy in experimental temporal lobe epilepsy. McClelland S, etal., Ann Neurol. 2011 Sep;70(3):454-64. doi: 10.1002/ana.22479.
20. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
21. Cloning and localization of the hyperpolarization-activated cyclic nucleotide-gated channel family in rat brain. Monteggia LM, etal., Brain Res Mol Brain Res 2000 Sep 30;81(1-2):129-39.
22. HCN channels are expressed differentially in retinal bipolar cells and concentrated at synaptic terminals. Muller F, etal., Eur J Neurosci 2003 May;17(10):2084-96.
23. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
24. Loss of HCN1 subunits causes absence epilepsy in rats. Nishitani A, etal., Brain Res. 2019 Mar 1;1706:209-217. doi: 10.1016/j.brainres.2018.11.004. Epub 2018 Nov 5.
25. Trafficking and surface expression of hyperpolarization-activated cyclic nucleotide-gated channels in hippocampal neurons. Noam Y, etal., J Biol Chem. 2010 May 7;285(19):14724-36. doi: 10.1074/jbc.M109.070391. Epub 2010 Mar 9.
26. In the ventral cochlear nucleus Kv1.1 and subunits of HCN1 are colocalized at surfaces of neurons that have low-voltage-activated and hyperpolarization-activated conductances. Oertel D, etal., Neuroscience. 2008 Jun 12;154(1):77-86. doi: 10.1016/j.neuroscience.2008.01.085. Epub 2008 Feb 29.
27. Hcn1 is a tremorgenic genetic component in a rat model of essential tremor. Ohno Y, etal., PLoS One. 2015 May 13;10(5):e0123529. doi: 10.1371/journal.pone.0123529. eCollection 2015.
28. Calcium-dependent binding of HCN1 channel protein to hair cell stereociliary tip link protein protocadherin 15 CD3. Ramakrishnan NA, etal., J Biol Chem. 2009 Jan 30;284(5):3227-38. doi: 10.1074/jbc.M806177200. Epub 2008 Nov 13.
29. HCN1 and HCN2 proteins are expressed in cochlear hair cells: HCN1 can form a ternary complex with protocadherin 15 CD3 and F-actin-binding filamin A or can interact with HCN2. Ramakrishnan NA, etal., J Biol Chem. 2012 Nov 2;287(45):37628-46. doi: 10.1074/jbc.M112.375832. Epub 2012 Sep 4.
30. GOA pipeline RGD automated data pipeline
31. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
33. Environmental manipulations early in development alter seizure activity, Ih and HCN1 protein expression later in life. Schridde U, etal., Eur J Neurosci. 2006 Jun;23(12):3346-58.
34. Distribution and prevalence of hyperpolarization-activated cation channel (HCN) mRNA expression in cardiac tissues. Shi W, etal., Circ Res 1999 Jul 9;85(1):e1-6.
35. Elevation in type I interferons inhibits HCN1 and slows cortical neuronal oscillations. Stadler K, etal., Cereb Cortex. 2014 Jan;24(1):199-210. doi: 10.1093/cercor/bhs305. Epub 2012 Oct 4.
36. Hyperpolarization-activated channels HCN1 and HCN4 mediate responses to sour stimuli. Stevens DR, etal., Nature. 2001 Oct 11;413(6856):631-5.
37. Colocalization of hyperpolarization-activated, cyclic nucleotide-gated channel subunits in rat retinal ganglion cells. Stradleigh TW, etal., J Comp Neurol. 2011 Sep 1;519(13):2546-73. doi: 10.1002/cne.22638.
38. An impaired neocortical Ih is associated with enhanced excitability and absence epilepsy. Strauss U, etal., Eur J Neurosci. 2004 Jun;19(11):3048-58.
39. Diabetes alters protein expression of hyperpolarization-activated cyclic nucleotide-gated channel subunits in rat nodose ganglion cells. Tu H, etal., Neuroscience. 2010 Jan 13;165(1):39-52. doi: 10.1016/j.neuroscience.2009.10.002. Epub 2009 Oct 6.
40. Hyperpolarization-activated channels in trigeminal ganglia innervating healthy and pulp-exposed teeth. Wells JE, etal., Int Endod J. 2007 Sep;40(9):715-21. Epub 2007 Jul 23.
41. Nedd4-2 regulates surface expression and may affect N-glycosylation of hyperpolarization-activated cyclic nucleotide-gated (HCN)-1 channels. Wilkars W, etal., FASEB J. 2014 May;28(5):2177-90. doi: 10.1096/fj.13-242032. Epub 2014 Jan 22.
42. Declines in levels of hyperpolarization-activated cation (HCN) channels in the rat ovary after cisplatin exposure. Yeh J, etal., Reprod Sci. 2009 Oct;16(10):986-94. Epub 2009 Jul 7.
43. Activity-dependent heteromerization of the hyperpolarization-activated, cyclic-nucleotide gated (HCN) channels: role of N-linked glycosylation. Zha Q, etal., J Neurochem. 2008 Apr;105(1):68-77. Epub 2007 Nov 5.
Additional References at PubMed
PMID:14991560   PMID:15056713   PMID:15245481   PMID:15479642   PMID:15525777   PMID:15564593   PMID:15869503   PMID:15958747   PMID:16503331   PMID:16648453   PMID:16870744   PMID:17095562  
PMID:17196750   PMID:17311321   PMID:17687042   PMID:17848552   PMID:18397293   PMID:18450385   PMID:18524809   PMID:18657617   PMID:20220080   PMID:21052544   PMID:21185265   PMID:21326231  
PMID:21504900   PMID:21753027   PMID:21795621   PMID:21798320   PMID:22006928   PMID:22363812   PMID:22722099   PMID:22748890   PMID:22871113   PMID:23187002   PMID:23821600   PMID:24403084  
PMID:25659346   PMID:26021557   PMID:26341471   PMID:27184742   PMID:27496876   PMID:27542339   PMID:27568501   PMID:27569278   PMID:27685769   PMID:27965425   PMID:28086084   PMID:30053369  
PMID:30351409   PMID:31292305   PMID:31923455   PMID:32198387   PMID:32248813   PMID:34845181   PMID:34875252   PMID:36336089   PMID:38555654  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
GRCr8251,228,710 - 51,632,806 (+)NCBIGRCr8
mRatBN7.2249,495,771 - 49,899,983 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl249,495,771 - 49,899,774 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx256,591,338 - 56,990,181 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0254,650,014 - 55,048,852 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0249,560,176 - 49,958,195 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0250,099,576 - 50,499,799 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl250,099,576 - 50,499,799 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0268,473,431 - 68,874,494 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4249,525,949 - 49,939,066 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1249,454,181 - 49,867,299 (+)NCBI
Celera245,196,523 - 45,593,603 (+)NCBICelera
Cytogenetic Map2q14NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh38545,254,948 - 45,696,380 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl545,254,948 - 45,696,498 (-)EnsemblGRCh38hg38GRCh38
GRCh37545,255,050 - 45,696,482 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36545,295,109 - 45,731,977 (-)NCBINCBI36Build 36hg18NCBI36
Build 34545,297,729 - 45,731,977NCBI
Celera545,153,108 - 45,590,074 (-)NCBICelera
Cytogenetic Map5p12NCBI
HuRef545,207,222 - 45,649,517 (-)NCBIHuRef
CHM1_1545,254,898 - 45,696,071 (-)NCBICHM1_1
T2T-CHM13v2.0545,508,691 - 45,949,554 (-)NCBIT2T-CHM13v2.0
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm3913117,738,856 - 118,117,564 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl13117,738,856 - 118,123,954 (+)EnsemblGRCm39 Ensembl
GRCm3813117,602,320 - 117,981,028 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl13117,602,320 - 117,987,418 (+)EnsemblGRCm38mm10GRCm38
MGSCv3713118,391,127 - 118,769,835 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3613118,721,981 - 119,096,083 (+)NCBIMGSCv36mm8
Celera13122,021,998 - 122,417,756 (+)NCBICelera
Cytogenetic Map13D2.3NCBI
cM Map1366.34NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_00495544617,151,311 - 17,457,888 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544617,146,915 - 17,457,843 (+)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
NHGRI_mPanPan1-v2464,622,101 - 65,065,737 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1562,775,463 - 63,219,363 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0564,673,392 - 65,116,259 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1569,724,749 - 70,161,427 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl569,724,767 - 70,158,761 (+)Ensemblpanpan1.1panPan2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
CanFam3.1464,777,069 - 65,162,603 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl464,775,577 - 65,160,444 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha464,536,272 - 64,921,927 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0465,274,982 - 65,661,386 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl465,273,568 - 65,658,697 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1465,037,683 - 65,423,922 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0465,160,205 - 65,546,474 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0465,696,155 - 66,082,848 (+)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_024407213208,115,409 - 208,479,849 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648017,051,898 - 17,413,657 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648017,051,902 - 17,416,335 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl1629,439,264 - 29,808,993 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11629,439,294 - 29,808,855 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21630,946,691 - 31,323,942 (-)NCBISscrofa10.2Sscrofa10.2susScr3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.1444,029,173 - 44,443,669 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607134,696,131 - 35,142,081 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_0046247599,636,457 - 10,049,403 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247599,636,380 - 10,044,832 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Hcn1
4098 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:15
Count of miRNA genes:15
Interacting mature miRNAs:15
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
10755436Coatc8Coat color QTL 80.02431coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23502311780023117Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
10755434Coatc7Coat color QTL 70.04794coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23064806575648065Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243162366111362592Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)243162366111362592Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1300160Hrtrt3Heart rate QTL 33.62heart pumping trait (VT:2000009)absolute change in heart rate (CMO:0000534)22997159351729300Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)240067944102785628Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
631208Bw1Body weight QTL15.09mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)24317101783575226Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1300155Bp174Blood pressure QTL 1744.09arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)24280460760653831Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
12879863Bp402Blood pressure QTL 4020.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24112578956532139Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23513484188029593Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2249,657,069 - 49,657,252 (+)MAPPERmRatBN7.2
Rnor_6.0250,260,210 - 50,260,392NCBIRnor6.0
Rnor_5.0268,633,684 - 68,633,866UniSTSRnor5.0
RGSC_v3.4249,691,463 - 49,691,646RGDRGSC3.4
RGSC_v3.4249,691,464 - 49,691,646UniSTSRGSC3.4
RGSC_v3.1249,619,697 - 49,619,879RGD
Celera245,357,036 - 45,357,216UniSTS
RH 3.4 Map2335.0RGD
RH 3.4 Map2335.0UniSTS
RH 2.0 Map2303.0RGD
SHRSP x BN Map219.5698RGD
Cytogenetic Map2q15UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2249,899,619 - 49,899,836 (+)MAPPERmRatBN7.2
Rnor_6.0250,499,717 - 50,499,933NCBIRnor6.0
Rnor_5.0268,874,412 - 68,874,628UniSTSRnor5.0
RGSC_v3.4249,938,984 - 49,939,200UniSTSRGSC3.4
Celera245,593,521 - 45,593,737UniSTS
RH 3.4 Map1883.8UniSTS
Cytogenetic Map2q15UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2249,801,276 - 49,801,495 (+)MAPPERmRatBN7.2
Rnor_6.0250,402,380 - 50,402,598NCBIRnor6.0
Rnor_5.0268,776,557 - 68,776,775UniSTSRnor5.0
RGSC_v3.4249,840,417 - 49,840,635UniSTSRGSC3.4
Celera245,496,583 - 45,496,801UniSTS
RH 3.4 Map2333.4UniSTS
Cytogenetic Map2q15UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2249,898,874 - 49,899,735 (+)MAPPERmRatBN7.2
Rnor_6.0250,498,972 - 50,499,832NCBIRnor6.0
Rnor_5.0268,873,667 - 68,874,527UniSTSRnor5.0
RGSC_v3.4249,938,239 - 49,939,099UniSTSRGSC3.4
Celera245,592,776 - 45,593,636UniSTS
Cytogenetic Map2q15UniSTS

Genetic Models
This gene Hcn1 is modified in the following models/strains:


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
Medium 31
Low 8 6 33 19
Below cutoff 2 29 20 12 7 12 7 7 10 21 22 9 7


RefSeq Acc Id: ENSRNOT00000089218   ⟹   ENSRNOP00000073952
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl249,495,771 - 49,899,774 (+)Ensembl
Rnor_6.0 Ensembl250,099,576 - 50,499,799 (+)Ensembl
RefSeq Acc Id: NM_053375   ⟹   NP_445827
RefSeq Status: VALIDATED
Rat AssemblyChrPosition (strand)Source
GRCr8251,228,710 - 51,632,806 (+)NCBI
mRatBN7.2249,495,771 - 49,899,983 (+)NCBI
Rnor_6.0250,099,576 - 50,499,799 (+)NCBI
Rnor_5.0268,473,431 - 68,874,494 (+)NCBI
RGSC_v3.4249,525,949 - 49,939,066 (+)RGD
Celera245,196,523 - 45,593,603 (+)RGD
Protein Sequences
Protein RefSeqs NP_445827 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF01490 (Get FASTA)   NCBI Sequence Viewer  
  AAF62173 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000073952.1
GenBank Protein Q9JKB0 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_445827   ⟸   NM_053375
- UniProtKB: Q9JKB0 (UniProtKB/Swiss-Prot),   F1LSH6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073952   ⟸   ENSRNOT00000089218

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JKB0-F1-model_v2 AlphaFold Q9JKB0 1-910 view protein structure


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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620688 AgrOrtholog
BioCyc Gene G2FUF-54304 BioCyc
Ensembl Genes ENSRNOG00000055382 Ensembl, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000089218.2 UniProtKB/Swiss-Prot
Gene3D-CATH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL UniProtKB/Swiss-Prot
  Helix hairpin bin UniProtKB/Swiss-Prot
InterPro cNMP-bd-like UniProtKB/Swiss-Prot
  cNMP-bd_CS UniProtKB/Swiss-Prot
  cNMP-bd_dom UniProtKB/Swiss-Prot
  Ion_trans_dom UniProtKB/Swiss-Prot
  Ion_trans_N UniProtKB/Swiss-Prot
  K_chnl_volt-dep_EAG/ELK/ERG UniProtKB/Swiss-Prot
  RmlC-like_jellyroll UniProtKB/Swiss-Prot
KEGG Report rno:84390 UniProtKB/Swiss-Prot
  PTHR45689:SF3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam cNMP_binding UniProtKB/Swiss-Prot
  Ion_trans UniProtKB/Swiss-Prot
  Ion_trans_N UniProtKB/Swiss-Prot
PhenoGen Hcn1 PhenoGen
  CNMP_BINDING_3 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000055382 RatGTEx
SMART cNMP UniProtKB/Swiss-Prot
Superfamily-SCOP SSF51206 UniProtKB/Swiss-Prot
  Voltage-gated potassium channels UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt Secondary F1LSH6 UniProtKB/Swiss-Prot

Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Hcn1  hyperpolarization-activated, cyclic nucleotide-gated potassium channel 1    hyperpolarization-activated, cyclic nucleotide-gated potassium channel 1 (HCN1)  Name updated 1299863 APPROVED
2002-08-07 Hcn1  hyperpolarization-activated, cyclic nucleotide-gated potassium channel 1 (HCN1)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression localized to cerebral cortex, hippocampus, cerebellum, and facial motor neurons  
gene_product member of a family of pacemaker channels activated by hyperpolarization and regulated by cyclic nucleotides 70760