Nalcn (sodium leak channel, non-selective) - Rat Genome Database

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Gene: Nalcn (sodium leak channel, non-selective) Rattus norvegicus
Analyze
Symbol: Nalcn
Name: sodium leak channel, non-selective
RGD ID: 628710
Description: Predicted to enable cation channel activity and leak channel activity. Predicted to be involved in inorganic cation transmembrane transport and regulation of resting membrane potential. Predicted to be integral component of membrane. Orthologous to human NALCN (sodium leak channel, non-selective); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: brain voltage-gated cation channel; four domain-type voltage-gated ion channel alpha-1 subunit; rb21-channel; sodium leak channel non-selective protein; Vgcnl1; voltage gated channel like 1; voltage gated channel-like protein 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
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.215100,398,615 - 100,712,283 (-)NCBI
Rnor_6.0 Ensembl15109,735,595 - 110,046,704 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.015109,734,092 - 110,046,729 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.015113,115,691 - 113,426,241 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415108,414,286 - 108,658,195 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.115108,430,065 - 108,673,975 (-)NCBI
Celera1599,154,725 - 99,456,878 (-)NCBICelera
Cytogenetic Map15q25NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12498692   PMID:17448995   PMID:33273469  


Genomics

Comparative Map Data
Nalcn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.215100,398,615 - 100,712,283 (-)NCBI
Rnor_6.0 Ensembl15109,735,595 - 110,046,704 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.015109,734,092 - 110,046,729 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.015113,115,691 - 113,426,241 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415108,414,286 - 108,658,195 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.115108,430,065 - 108,673,975 (-)NCBI
Celera1599,154,725 - 99,456,878 (-)NCBICelera
Cytogenetic Map15q25NCBI
NALCN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl13101,053,776 - 101,416,508 (-)EnsemblGRCh38hg38GRCh38
GRCh3813101,053,774 - 101,417,206 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3713101,706,128 - 102,068,859 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3613100,504,131 - 100,866,814 (-)NCBINCBI36hg18NCBI36
Build 3413100,505,600 - 100,866,707NCBI
Celera1382,551,415 - 82,911,536 (-)NCBI
Cytogenetic Map13q32.3-q33.1NCBI
HuRef1382,301,975 - 82,662,087 (-)NCBIHuRef
CHM1_113101,676,115 - 102,038,862 (-)NCBICHM1_1
Nalcn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914123,514,046 - 123,864,846 (-)NCBIGRCm39mm39
GRCm39 Ensembl14123,514,046 - 123,864,556 (-)Ensembl
GRCm3814123,275,678 - 123,627,330 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14123,276,634 - 123,627,144 (-)EnsemblGRCm38mm10GRCm38
MGSCv3714123,675,863 - 124,026,366 (-)NCBIGRCm37mm9NCBIm37
MGSCv3614122,434,608 - 122,762,324 (-)NCBImm8
Celera14121,838,270 - 121,890,033 (-)NCBICelera
Celera14122,811,564 - 123,084,265 (-)NCBICelera
Cytogenetic Map14E5NCBI
Nalcn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554049,603,562 - 9,895,817 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554049,603,567 - 9,894,688 (+)NCBIChiLan1.0ChiLan1.0
NALCN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113101,352,535 - 101,710,917 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13101,354,054 - 101,693,223 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01382,215,094 - 82,573,501 (-)NCBIMhudiblu_PPA_v0panPan3
NALCN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12250,821,983 - 51,142,000 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2250,823,478 - 51,141,644 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2250,601,806 - 50,922,190 (-)NCBI
ROS_Cfam_1.02251,265,000 - 51,586,596 (-)NCBI
UMICH_Zoey_3.12250,910,597 - 51,250,150 (-)NCBI
UNSW_CanFamBas_1.02250,941,445 - 51,259,292 (-)NCBI
UU_Cfam_GSD_1.02250,984,648 - 51,306,587 (-)NCBI
Nalcn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945186,162,530 - 186,450,079 (-)NCBI
SpeTri2.0NW_0049364729,502,054 - 9,789,714 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NALCN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1169,710,364 - 70,022,727 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11169,710,355 - 70,023,020 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
NALCN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1379,663,714 - 80,010,361 (-)NCBI
ChlSab1.1 Ensembl379,663,725 - 79,992,503 (-)Ensembl
Vero_WHO_p1.0NW_02366604636,176,805 - 36,522,145 (-)NCBI
Nalcn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247939,929,980 - 10,248,107 (+)NCBI

Position Markers
D14Mit107  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215100,704,919 - 100,705,094 (+)MAPPER
Rnor_6.015110,039,366 - 110,039,540NCBIRnor6.0
Rnor_5.015113,418,878 - 113,419,052UniSTSRnor5.0
RGSC_v3.415108,746,313 - 108,746,487UniSTSRGSC3.4
Celera1599,449,515 - 99,449,689UniSTS
Cytogenetic Map15q25UniSTS
PMC126259P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215100,400,189 - 100,400,264 (+)MAPPER
Rnor_6.015109,735,667 - 109,735,741NCBIRnor6.0
Rnor_5.015113,117,266 - 113,117,340UniSTSRnor5.0
RGSC_v3.415108,415,861 - 108,415,935UniSTSRGSC3.4
Celera1599,156,300 - 99,156,374UniSTS
Cytogenetic Map15q25UniSTS
RH130621  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215100,398,820 - 100,399,032 (+)MAPPER
Rnor_6.015109,734,298 - 109,734,509NCBIRnor6.0
Rnor_5.015113,115,897 - 113,116,108UniSTSRnor5.0
RGSC_v3.415108,414,492 - 108,414,703UniSTSRGSC3.4
Celera1599,154,931 - 99,155,142UniSTS
RH 3.4 Map15716.1UniSTS
Cytogenetic Map15q25UniSTS
BE113539  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215100,399,872 - 100,400,032 (+)MAPPER
Rnor_6.015109,735,350 - 109,735,509NCBIRnor6.0
Rnor_5.015113,116,949 - 113,117,108UniSTSRnor5.0
RGSC_v3.415108,415,544 - 108,415,703UniSTSRGSC3.4
Celera1599,155,983 - 99,156,142UniSTS
RH 3.4 Map15716.1UniSTS
Cytogenetic Map15q25UniSTS
RH136716  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215100,682,552 - 100,682,787 (+)MAPPER
Rnor_6.015110,017,848 - 110,018,082NCBIRnor6.0
Rnor_5.015113,397,362 - 113,397,596UniSTSRnor5.0
Celera1599,428,965 - 99,429,199UniSTS
Cytogenetic Map15q25UniSTS
RH138154  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215100,607,186 - 100,607,333 (+)MAPPER
Rnor_6.015109,942,414 - 109,942,560NCBIRnor6.0
Rnor_5.015113,323,215 - 113,323,361UniSTSRnor5.0
RGSC_v3.415108,629,836 - 108,629,982UniSTSRGSC3.4
Celera1599,353,846 - 99,353,992UniSTS
Cytogenetic Map15q25UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1565520564110520564Rat
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1575527634111246239Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1583947714111246239Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1584050550111246239Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1584050550111246239Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:153
Count of miRNA genes:96
Interacting mature miRNAs:107
Transcripts:ENSRNOT00000006624, ENSRNOT00000057404
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.


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 3 60
Low 3 7 1 4 1 7 7 14 35 5 7
Below cutoff 3 32 24 17 15 17 1 4 18 6 6 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006624   ⟹   ENSRNOP00000006624
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl15109,735,595 - 110,046,687 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000057404   ⟹   ENSRNOP00000054214
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl15109,735,595 - 110,046,687 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089695   ⟹   ENSRNOP00000069957
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl15109,735,595 - 110,046,704 (-)Ensembl
RefSeq Acc Id: NM_153630   ⟹   NP_705894
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.215100,398,615 - 100,712,283 (-)NCBI
Rnor_6.015109,734,092 - 110,046,729 (-)NCBI
Rnor_5.015113,115,691 - 113,426,241 (-)NCBI
RGSC_v3.415108,414,286 - 108,658,195 (-)RGD
Celera1599,154,725 - 99,456,878 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_705894   ⟸   NM_153630
- Sequence:
RefSeq Acc Id: ENSRNOP00000006624   ⟸   ENSRNOT00000006624
RefSeq Acc Id: ENSRNOP00000054214   ⟸   ENSRNOT00000057404
RefSeq Acc Id: ENSRNOP00000069957   ⟸   ENSRNOT00000089695
Protein Domains
Ion_trans

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)
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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:628710 AgrOrtholog
Ensembl Genes ENSRNOG00000004752 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006624 UniProtKB/TrEMBL
  ENSRNOP00000054214 UniProtKB/TrEMBL
  ENSRNOP00000069957 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006624 UniProtKB/TrEMBL
  ENSRNOT00000057404 UniProtKB/TrEMBL
  ENSRNOT00000089695 UniProtKB/TrEMBL
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NALCN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:266760 UniProtKB/Swiss-Prot
NCBI Gene 266760 ENTREZGENE
PANTHER PTHR46141 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nalcn PhenoGen
UniProt A0A0G2JWP2_RAT UniProtKB/TrEMBL
  F1LMW5_RAT UniProtKB/TrEMBL
  F1LS19_RAT UniProtKB/TrEMBL
  NALCN_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9Z165 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-25 Nalcn  sodium leak channel, non-selective  Vgcnl1  voltage gated channel like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Vgcnl1  voltage gated channel like 1      Symbol and Name status set to approved 1299863 APPROVED
2003-02-27 Vgcnl1  voltage gated channel like 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_evolution may have evolved from an ancestral four repeat ion channel structure prior to Ca+2 and Na+ channel divergence 634530