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

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Gene: Nalcn (sodium leak channel, non-selective) Mus musculus
Analyze
Symbol: Nalcn
Name: sodium leak channel, non-selective
RGD ID: 1621205
MGI Page MGI
Description: Enables cation channel activity and leak channel activity. Involved in inorganic cation transmembrane transport and regulation of resting membrane potential. Predicted to be located in membrane. Predicted to be integral component of membrane. Is expressed in central nervous system. Orthologous to human NALCN (sodium leak channel, non-selective); INTERACTS WITH 2,2',4,4',5,5'-hexachlorobiphenyl; 2,2',5,5'-tetrachlorobiphenyl; 2,3',4,4',5-Pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: A530023G15Rik; AI849508; sodium leak channel non-selective protein; Vgc; Vgcnl1; voltage gated channel like 1; voltage gated channel-like protein 1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
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
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:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:16141072   PMID:16141073   PMID:17448995   PMID:19092807   PMID:19575010   PMID:21040849  
PMID:21099296   PMID:21177381   PMID:21267068   PMID:21677750   PMID:22508057   PMID:26276633   PMID:27177420   PMID:27488637   PMID:27806374   PMID:28392070   PMID:30556810   PMID:31601786  
PMID:32325033   PMID:32620897   PMID:33176139   PMID:33766679  


Genomics

Comparative Map Data
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
(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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.215100,398,615 - 100,712,283 (-)NCBImRatBN7.2
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
(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
AI849508  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3814123,276,870 - 123,276,984UniSTSGRCm38
MGSCv3714123,676,092 - 123,676,206UniSTSGRCm37
Celera14121,838,499 - 121,838,613UniSTS
Cytogenetic Map14E5UniSTS
Whitehead/MRC_RH141290.99UniSTS
D14Mit107  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3814123,595,892 - 123,596,041UniSTSGRCm38
MGSCv3714123,995,114 - 123,995,263UniSTSGRCm37
Celera14123,050,340 - 123,050,513UniSTS
Cytogenetic Map14E5UniSTS
cM Map1463.0UniSTS
Whitehead Genetic1469.9UniSTS
D14Mit107.1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3814123,596,070 - 123,596,201UniSTSGRCm38
MGSCv3714123,995,292 - 123,995,423UniSTSGRCm37
Celera14123,050,542 - 123,050,673UniSTS
Cytogenetic Map14E5UniSTS
cM Map1463.0UniSTS
cM Map14 UniSTS
Whitehead Genetic1469.9UniSTS
PMC126259P1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Celera14121,839,869 - 121,839,943UniSTS
Cytogenetic Map14E5UniSTS
Nalcn  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map14E5UniSTS
cM Map14 UniSTS
D14Mit248  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3814123,450,189 - 123,450,377UniSTSGRCm38
MGSCv3714123,849,411 - 123,849,599UniSTSGRCm37
Celera14122,905,852 - 122,906,034UniSTS
Cytogenetic Map14E5UniSTS
cM Map1460.0UniSTS
UniSTS:536239  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3814123,624,444 - 123,625,997UniSTSGRCm38
Celera14123,081,565 - 123,083,118UniSTS
Cytogenetic Map14E5UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755523Hgb2_mhemoglobin 2 (mouse)14105647242124902244Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:460
Count of miRNA genes:308
Interacting mature miRNAs:365
Transcripts:ENSMUST00000000201
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


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_177393 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011245094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017316066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_030247866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036158681 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036158682 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036158683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036158684 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036158685 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036158686 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC102783 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC124818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC154677 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK036122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK039034 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK040761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK043071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK044431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK143219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK161382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CD802755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CT010566 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000000201   ⟹   ENSMUSP00000000201
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl14123,276,634 - 123,627,144 (-)Ensembl
RefSeq Acc Id: ENSMUST00000226617
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl14123,485,655 - 123,627,136 (-)Ensembl
RefSeq Acc Id: ENSMUST00000227541
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl14123,368,769 - 123,371,075 (-)Ensembl
RefSeq Acc Id: ENSMUST00000227818
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl14123,299,686 - 123,626,876 (-)Ensembl
RefSeq Acc Id: ENSMUST00000228766
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl14123,591,460 - 123,626,961 (-)Ensembl
RefSeq Acc Id: ENSMUST00000228789
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl14123,568,991 - 123,626,961 (-)Ensembl
RefSeq Acc Id: ENSMUST00000228860
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl14123,299,428 - 123,627,144 (-)Ensembl
RefSeq Acc Id: NM_177393   ⟹   NP_796367
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914123,514,053 - 123,864,556 (-)NCBI
GRCm3814123,276,641 - 123,627,144 (-)NCBI
MGSCv3714123,675,863 - 124,026,366 (-)RGD
Celera14121,838,270 - 121,890,033 (-)NCBI
Celera14122,811,564 - 123,084,265 (-)RGD
cM Map14 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_011245094   ⟹   XP_011243396
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914123,514,046 - 123,864,846 (-)NCBI
GRCm3814123,275,678 - 123,627,330 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017316066   ⟹   XP_017171555
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914123,536,732 - 123,864,782 (-)NCBI
GRCm3814123,299,318 - 123,603,833 (-)NCBI
Sequence:
RefSeq Acc Id: XM_030247866   ⟹   XP_030103726
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914123,514,046 - 123,864,846 (-)NCBI
GRCm3814123,275,678 - 123,627,245 (-)NCBI
Sequence:
RefSeq Acc Id: XM_036158681   ⟹   XP_036014574
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914123,514,046 - 123,864,782 (-)NCBI
RefSeq Acc Id: XM_036158682   ⟹   XP_036014575
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914123,514,046 - 123,864,782 (-)NCBI
RefSeq Acc Id: XM_036158683   ⟹   XP_036014576
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914123,514,046 - 123,864,782 (-)NCBI
RefSeq Acc Id: XM_036158684   ⟹   XP_036014577
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914123,514,046 - 123,864,782 (-)NCBI
RefSeq Acc Id: XM_036158685   ⟹   XP_036014578
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914123,514,046 - 123,864,782 (-)NCBI
RefSeq Acc Id: XM_036158686   ⟹   XP_036014579
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914123,514,046 - 123,864,782 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_796367   ⟸   NM_177393
- UniProtKB: Q8BXR5 (UniProtKB/Swiss-Prot),   E9QLE4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011243396   ⟸   XM_011245094
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017171555   ⟸   XM_017316066
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_030103726   ⟸   XM_030247866
- Peptide Label: isoform X5
RefSeq Acc Id: ENSMUSP00000000201   ⟸   ENSMUST00000000201
RefSeq Acc Id: XP_036014579   ⟸   XM_036158686
- Peptide Label: isoform X8
RefSeq Acc Id: XP_036014578   ⟸   XM_036158685
- Peptide Label: isoform X7
RefSeq Acc Id: XP_036014577   ⟸   XM_036158684
- Peptide Label: isoform X6
RefSeq Acc Id: XP_036014575   ⟸   XM_036158682
- Peptide Label: isoform X3
RefSeq Acc Id: XP_036014576   ⟸   XM_036158683
- Peptide Label: isoform X4
RefSeq Acc Id: XP_036014574   ⟸   XM_036158681
- Peptide Label: isoform X1
Protein Domains
Ion_trans

Promoters
RGD ID:8683288
Promoter ID:EPDNEW_M19674
Type:initiation region
Name:Nalcn_1
Description:Mus musculus sodium leak channel, non-selective , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3814123,627,101 - 123,627,161EPDNEW
RGD ID:6825546
Promoter ID:MM_KWN:17891
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain,   ES_Cell
Transcripts:ENSMUST00000072254,   NM_177393,   UC007VBR.1,   UC007VBS.1,   UC007VBT.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3614124,025,836 - 124,026,336 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2444306 AgrOrtholog
Ensembl Genes ENSMUSG00000000197 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000000201 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000000201 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000228860 ENTREZGENE
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 mmu:338370 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:2444306 ENTREZGENE
NCBI Gene 338370 ENTREZGENE
PANTHER PTHR46141 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nalcn PhenoGen
UniProt E9QLE4 ENTREZGENE, UniProtKB/TrEMBL
  NALCN_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q8BYM2 UniProtKB/Swiss-Prot