Chrnd (cholinergic receptor nicotinic delta subunit) - Rat Genome Database

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Gene: Chrnd (cholinergic receptor nicotinic delta subunit) Rattus norvegicus
Analyze
Symbol: Chrnd
Name: cholinergic receptor nicotinic delta subunit
RGD ID: 2352
Description: Enables acetylcholine-gated cation-selective channel activity. Involved in cation transport and skeletal muscle contraction. Part of acetylcholine-gated channel complex. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome 3A; congenital myasthenic syndrome 3B; and congenital myasthenic syndrome 3C. Orthologous to human CHRND (cholinergic receptor nicotinic delta subunit); PARTICIPATES IN acetylcholine signaling pathway via nicotinic acetylcholine receptor; INTERACTS WITH 3H-1,2-dithiole-3-thione; acetylcholine; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: acetylcholine receptor subunit delta; cholinergic receptor, nicotinic delta; cholinergic receptor, nicotinic, delta; cholinergic receptor, nicotinic, delta (muscle); cholinergic receptor, nicotinic, delta polypeptide; nicotinic acetylcholine receptor delta-subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2987,862,417 - 87,870,833 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl987,862,407 - 87,870,833 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx996,286,713 - 96,295,119 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.09101,422,491 - 101,430,928 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0999,790,669 - 99,799,093 (+)NCBIRnor_WKY
Rnor_6.0994,286,550 - 94,294,968 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl994,286,550 - 94,294,968 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0994,010,107 - 94,018,572 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4985,996,421 - 86,004,839 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1986,179,839 - 86,188,258 (+)NCBI
Celera985,275,482 - 85,284,297 (+)NCBICelera
Cytogenetic Map9q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Multiple inhibitory actions of lidocaine on Torpedo nicotinic acetylcholine receptors transplanted to Xenopus oocytes. Alberola-Die A, etal., J Neurochem. 2011 Jun;117(6):1009-19. doi: 10.1111/j.1471-4159.2011.07271.x. Epub 2011 May 10.
2. Mammalian nicotinic acetylcholine receptors: from structure to function. Albuquerque EX, etal., Physiol Rev. 2009 Jan;89(1):73-120. doi: 10.1152/physrev.00015.2008.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. Online Mendelian Inheritance in Man, OMIM (TM). Online Mendelian Inheritance in Man, OMIM (TM).
9. A novel mode-of-action mediated by the fetal muscle nicotinic acetylcholine receptor resulting in developmental toxicity in rats. Rasoulpour RJ, etal., Toxicol Sci. 2012 Jun;127(2):522-34. doi: 10.1093/toxsci/kfs118. Epub 2012 Mar 29.
10. GOA pipeline RGD automated data pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
14. Refined structure of the nicotinic acetylcholine receptor at 4A resolution. Unwin N, J Mol Biol. 2005 Mar 4;346(4):967-89. doi: 10.1016/j.jmb.2004.12.031. Epub 2005 Jan 25.
15. Primary structure and functional expression of the alpha-, beta-, gamma-, delta- and epsilon-subunits of the acetylcholine receptor from rat muscle. Witzemann V, etal., Eur J Biochem 1990 Dec 12;194(2):437-48.
16. The neuromuscular junction: selective remodeling of synaptic regulators at the nerve/muscle interface. Witzemann V, etal., Mech Dev. 2013 Jun-Aug;130(6-8):402-11. doi: 10.1016/j.mod.2012.09.004. Epub 2012 Sep 29.
Additional References at PubMed
PMID:1638981   PMID:2383398   PMID:4781450   PMID:8798466   PMID:8910344   PMID:10201407   PMID:11435464   PMID:12388596   PMID:18252226  


Genomics

Comparative Map Data
Chrnd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2987,862,417 - 87,870,833 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl987,862,407 - 87,870,833 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx996,286,713 - 96,295,119 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.09101,422,491 - 101,430,928 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0999,790,669 - 99,799,093 (+)NCBIRnor_WKY
Rnor_6.0994,286,550 - 94,294,968 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl994,286,550 - 94,294,968 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0994,010,107 - 94,018,572 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4985,996,421 - 86,004,839 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1986,179,839 - 86,188,258 (+)NCBI
Celera985,275,482 - 85,284,297 (+)NCBICelera
Cytogenetic Map9q35NCBI
CHRND
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382232,526,160 - 232,536,664 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2232,525,993 - 232,536,667 (+)EnsemblGRCh38hg38GRCh38
GRCh372233,390,870 - 233,401,374 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362233,099,166 - 233,108,449 (+)NCBINCBI36Build 36hg18NCBI36
Build 342233,216,426 - 233,225,710NCBI
Celera2227,155,237 - 227,164,520 (+)NCBICelera
Cytogenetic Map2q37.1NCBI
HuRef2225,241,762 - 225,252,266 (+)NCBIHuRef
CHM1_12233,396,959 - 233,407,466 (+)NCBICHM1_1
T2T-CHM13v2.02233,012,979 - 233,023,446 (+)NCBIT2T-CHM13v2.0
Chrnd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39187,118,319 - 87,127,792 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl187,118,329 - 87,127,792 (+)EnsemblGRCm39 Ensembl
GRCm38187,190,597 - 87,200,070 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl187,190,607 - 87,200,070 (+)EnsemblGRCm38mm10GRCm38
MGSCv37189,087,227 - 89,096,645 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36189,021,808 - 89,030,277 (+)NCBIMGSCv36mm8
Celera190,163,639 - 90,173,135 (+)NCBICelera
Cytogenetic Map1C5NCBI
cM Map144.07NCBI
Chrnd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554533,433,341 - 3,440,269 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554533,433,915 - 3,440,534 (-)NCBIChiLan1.0ChiLan1.0
CHRND
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B238,676,495 - 238,686,987 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B238,676,495 - 238,686,987 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B119,757,722 - 119,768,254 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CHRND
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12544,166,089 - 44,175,047 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2544,165,819 - 44,174,216 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2544,660,579 - 44,668,126 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02544,423,511 - 44,430,928 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2544,423,053 - 44,431,615 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12544,349,791 - 44,356,777 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02544,194,650 - 44,202,069 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02544,349,780 - 44,357,201 (+)NCBIUU_Cfam_GSD_1.0
Chrnd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303186,371,088 - 186,379,436 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365254,561,507 - 4,568,409 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365254,560,293 - 4,568,431 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHRND
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15133,040,340 - 133,048,829 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115133,040,310 - 133,047,839 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215146,939,779 - 146,947,258 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHRND
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110118,546,408 - 118,556,343 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10118,546,464 - 118,554,993 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604080,945,213 - 80,955,904 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chrnd
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248435,287,169 - 5,293,593 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248435,287,362 - 5,293,507 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chrnd
67 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:132
Count of miRNA genes:114
Interacting mature miRNAs:119
Transcripts:ENSRNOT00000026504
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)97927151191616855Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)98636963192058970Rat


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 2 2 2
Low 14 2 2 2 6 9 4 18 4 6
Below cutoff 1 17 8 5 4 5 4 10 13 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026504   ⟹   ENSRNOP00000026504
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl987,862,407 - 87,870,833 (+)Ensembl
Rnor_6.0 Ensembl994,286,550 - 94,294,968 (+)Ensembl
RefSeq Acc Id: NM_019298   ⟹   NP_062171
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2987,862,417 - 87,870,833 (+)NCBI
Rnor_6.0994,286,550 - 94,294,968 (+)NCBI
Rnor_5.0994,010,107 - 94,018,572 (+)NCBI
RGSC_v3.4985,996,421 - 86,004,839 (+)RGD
Celera985,275,482 - 85,284,297 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062171   ⟸   NM_019298
- Peptide Label: precursor
- UniProtKB: P25110 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026504   ⟸   ENSRNOT00000026504

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P25110-F1-model_v2 AlphaFold P25110 1-517 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2352 AgrOrtholog
BioCyc Gene G2FUF-26850 BioCyc
Ensembl Genes ENSRNOG00000019527 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000026504 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026504 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.58.390 UniProtKB/Swiss-Prot
  2.70.170.10 UniProtKB/Swiss-Prot
InterPro Neur_chan_lig-bd UniProtKB/Swiss-Prot
  Neur_chan_lig-bd_sf UniProtKB/Swiss-Prot
  Neur_channel UniProtKB/Swiss-Prot
  Neuro-gated_channel_TM_sf UniProtKB/Swiss-Prot
  Neuro_actylchol_rec UniProtKB/Swiss-Prot
  Neurotrans-gated_channel_TM UniProtKB/Swiss-Prot
  Neurotransmitter_ion_chnl_CS UniProtKB/Swiss-Prot
  Nicotinic_acetylcholine_rcpt UniProtKB/Swiss-Prot
KEGG Report rno:54240 UniProtKB/Swiss-Prot
NCBI Gene 54240 ENTREZGENE
PANTHER PTHR18945 UniProtKB/Swiss-Prot
Pfam Neur_chan_LBD UniProtKB/Swiss-Prot
  Neur_chan_memb UniProtKB/Swiss-Prot
PhenoGen Chrnd PhenoGen
PRINTS NICOTINICR UniProtKB/Swiss-Prot
  NRIONCHANNEL UniProtKB/Swiss-Prot
PROSITE NEUROTR_ION_CHANNEL UniProtKB/Swiss-Prot
Superfamily-SCOP SSF63712 UniProtKB/Swiss-Prot
  SSF90112 UniProtKB/Swiss-Prot
TIGR TC221601
TIGRFAMs LIC UniProtKB/Swiss-Prot
UniProt ACHD_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Chrnd  cholinergic receptor nicotinic delta subunit  Chrnd  cholinergic receptor, nicotinic delta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-12-09 Chrnd  cholinergic receptor, nicotinic delta  Chrnd  cholinergic receptor, nicotinic, delta (muscle)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Chrnd  cholinergic receptor, nicotinic, delta (muscle)  Chrnd  cholinergic receptor, nicotinic, delta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-29 Chrnd  cholinergic receptor, nicotinic, delta  Chrnd  cholinergic receptor, nicotinic, delta polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Chrnd  cholinergic receptor, nicotinic, delta polypeptide      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in muscle 68734