Hcn3 hyperpolarization-activated cyclic nucleotide-gated potassium channel 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hcn3provided by RGD
Official Full Name: hyperpolarization-activated cyclic nucleotide-gated potassium channel 3provided by RGD
Primary source: RGD:620691
See related: EnsemblRapid:ENSRNOG00000020444 AllianceGenome:RGD:620691
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable voltage-gated potassium channel activity and voltage-gated sodium channel activity. Involved in cellular response to dopamine. Located in cone cell pedicle; dendrite; and neuronal cell body. Biomarker of Parkinson's disease. Orthologous to human HCN3 (hyperpolarization activated cyclic nucleotide gated potassium channel 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 22.0), Liver (RPKM 14.6) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q34

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (176849635..176867726, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (174551861..174567459, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (188458851..188471916, complement)

Chromosome 2 - NC_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Involvement of Hyperpolarization-Activated Cyclic Nucleotide-Gated Channel 3 in Oxytocin Neuronal Activity in Lactating Rats With Pup Deprivation.
Title: Involvement of Hyperpolarization-Activated Cyclic Nucleotide-Gated Channel 3 in Oxytocin Neuronal Activity in Lactating Rats With Pup Deprivation.
Data suggest that HCN channels might play an important role in affecting contraction frequency of lymphatic muscle cells.
Title: Hyperpolarization-activated cyclic nucleotide-gated channels in peripheral diaphragmatic lymphatics.
the expression and relative abundances of HCN channels in cerebellum and primary cultures of cerebellar granule neurons, is described.
Title: Expression and cellular localization of HCN channels in rat cerebellar granule neurons.
During the senescent process, the HCN2 and HCN4 protein levels declined.
Title: Age-associated expression of HCN channel isoforms in rat sinoatrial node.
The data of this study indicated a HCN subunit shift initiated in the first 24 hours after birth and implicate a prominent perinatal role of the phylogenetically older HCN3 and/or HCN4 subunits in the developing neocortex.
Title: Distinct perinatal features of the hyperpolarization-activated non-selective cation current I(h) in the rat cortical plate.
The low-intensity HCN3 band density in trigeminal ganglion neurons increased with postnatal age P1-P35.
Title: Postnatal maturation of the hyperpolarization-activated cation current, I(h), in trigeminal sensory neurons.
This study demonistrated that the majority of LHb neurons projecting to the monoaminergic brainstem nuclei express a similar pattern of HCN transcripts, with high levels of HCN2 to HCN4 mRNAs and low levels of HCN1 mRNA.
Title: Lateral habenular neurons projecting to reward-processing monoaminergic nuclei express hyperpolarization-activated cyclic nucleotid-gated cation channels.
These data establish HCN3 up-regulation as a novel candidate mechanism that might contribute to the in vivo changes of electrical activity in basal ganglia output neurons of the parkinsonian brain.
Title: Dopamine depletion induced up-regulation of HCN3 enhances rebound excitability of basal ganglia output neurons.
HCN3 mRNA was preferentially expressed in small diameter (20-30 microm) neurons and HCN3 are present in large diameter neurons and small diameter neurons.
Title: Hyperpolarization-activated cyclic nucleotide-gated channel mRNA and protein expression in large versus small diameter dorsal root ganglion neurons: correlation with hyperpolarization-activated current gating.
Immunoreactivity for HCN3 in rat brain shows subcortical distribution mainly concentrated in the hypothalamus.
Title: Immunohistochemical localization of Ih channel subunits, HCN1-4, in the rat brain.

Submit: New GeneRIF Correction See all GeneRIFs (12)

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables cAMP binding	IEA Inferred from Electronic Annotation more info
NOT enables intracellularly cAMP-activated cation channel activity	ISO Inferred from Sequence Orthology more info
enables voltage-gated potassium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables voltage-gated potassium channel activity	ISO Inferred from Sequence Orthology more info
enables voltage-gated sodium channel activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
NOT involved_in cellular response to cAMP	ISO Inferred from Sequence Orthology more info
involved_in cellular response to dopamine	IEP Inferred from Expression Pattern more info	PubMed
involved_in potassium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in potassium ion transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in regulation of membrane depolarization	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of membrane potential	ISO Inferred from Sequence Orthology more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in sodium ion transmembrane transport	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of HCN channel complex	IBA Inferred from Biological aspect of Ancestor more info
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in cone cell pedicle	IDA Inferred from Direct Assay more info	PubMed
is_active_in dendrite	IBA Inferred from Biological aspect of Ancestor more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_053685.2 → NP_446137.1 potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3

See identical proteins and their annotated locations for NP_446137.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/Swiss-Prot

Q9JKA8

Related

ENSRNOP00000027785.2, ENSRNOT00000027785.5

Conserved Domains (4) summary

COG0664
Location:421 → 557

Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]

cd00038
Location:427 → 535

CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

pfam00520
Location:110 → 357

Ion_trans; Ion transport protein

pfam08412
Location:48 → 90

Ion_trans_N; Ion transport protein N-terminal

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086020.1 Reference GRCr8

Range

176849635..176867726 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063281145.1 → XP_063137215.1 potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 isoform X1

UniProtKB/TrEMBL

A6J6C2

Related

ENSRNOP00000101628.1, ENSRNOT00000134927.1
XM_063281147.1 → XP_063137217.1 potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 isoform X2
XM_063281144.1 → XP_063137214.1 potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 isoform X1

UniProtKB/TrEMBL

A6J6C2

Related

ENSRNOP00000110689.1, ENSRNOT00000153967.1
XM_039101557.2 → XP_038957485.1 potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 isoform X2

Conserved Domains (3) summary

PLN03192
Location:37 → 305

PLN03192; Voltage-dependent potassium channel; Provisional

PHA03247
Location:388 → 564

PHA03247; large tegument protein UL36; Provisional

cd00038
Location:216 → 324

CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
XM_039101558.2 → XP_038957486.1 potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 isoform X2

Conserved Domains (3) summary

PLN03192
Location:37 → 305

PLN03192; Voltage-dependent potassium channel; Provisional

PHA03247
Location:388 → 564

PHA03247; large tegument protein UL36; Provisional

cd00038
Location:216 → 324

CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
XM_039101556.2 → XP_038957484.1 potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 isoform X1

UniProtKB/TrEMBL

A6J6C2

Conserved Domains (3) summary

PHA03307
Location:491 → 674

PHA03307; transcriptional regulator ICP4; Provisional

cd00038
Location:329 → 437

CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

pfam00520
Location:1 → 259

Ion_trans; Ion transport protein
XM_039101559.2 → XP_038957487.1 potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 isoform X3

Conserved Domains (3) summary

PLN03192
Location:10 → 278

PLN03192; Voltage-dependent potassium channel; Provisional

PHA03247
Location:361 → 537

PHA03247; large tegument protein UL36; Provisional

cd00038
Location:189 → 297

CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...