Clcn1 (chloride voltage-gated channel 1) - Rat Genome Database

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Gene: Clcn1 (chloride voltage-gated channel 1) Ictidomys tridecemlineatus
Analyze
Symbol: Clcn1
Name: chloride voltage-gated channel 1
RGD ID: 12459753
Description: ENCODES a protein that exhibits voltage-gated chloride channel activity (ortholog); INVOLVED IN chloride transport (ortholog); ASSOCIATED WITH Becker disease (ortholog); cerebral palsy (ortholog); Charcot-Marie-Tooth disease intermediate type (ortholog); FOUND IN chloride channel complex (inferred); membrane (inferred); monoatomic ion channel complex (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: chloride channel protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511812,112,783 - 12,144,385 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936527759,047 - 790,670 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936527759,012 - 791,302 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Clcn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511812,112,783 - 12,144,385 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936527759,047 - 790,670 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936527759,012 - 791,302 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLCN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387143,316,111 - 143,352,083 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7143,316,111 - 143,352,083 (+)EnsemblGRCh38hg38GRCh38
GRCh377143,013,204 - 143,049,176 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367142,723,341 - 142,759,219 (+)NCBINCBI36Build 36hg18NCBI36
Build 347142,530,055 - 142,565,934NCBI
Celera7137,850,084 - 137,885,958 (+)NCBICelera
Cytogenetic Map7q34NCBI
HuRef7137,350,584 - 137,386,478 (+)NCBIHuRef
CHM1_17142,950,106 - 142,986,018 (+)NCBICHM1_1
T2T-CHM13v2.07144,671,527 - 144,707,513 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27142,415,337 - 142,451,223 (+)NCBI
Clcn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39642,263,552 - 42,292,693 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl642,263,619 - 42,292,690 (+)EnsemblGRCm39 Ensembl
GRCm38642,284,851 - 42,315,764 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl642,286,685 - 42,315,756 (+)EnsemblGRCm38mm10GRCm38
MGSCv37642,236,684 - 42,264,655 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36642,216,292 - 42,244,263 (+)NCBIMGSCv36mm8
Celera642,231,004 - 42,259,063 (+)NCBICelera
Cytogenetic Map6B2.1NCBI
cM Map620.57NCBI
Clcn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8472,138,739 - 72,168,113 (+)NCBIGRCr8
mRatBN7.2471,171,949 - 71,201,483 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl471,172,547 - 71,199,984 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx476,092,286 - 76,119,750 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0472,005,543 - 72,033,007 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0470,425,008 - 70,452,467 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0471,674,218 - 71,704,318 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl471,675,383 - 71,702,819 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04136,479,719 - 136,509,472 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4470,052,319 - 70,081,449 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1470,328,448 - 70,357,579 (+)NCBI
Celera466,103,038 - 66,130,477 (+)NCBICelera
RH 3.4 Map4433.61RGD
Cytogenetic Map4q24NCBI
Clcn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955494319,738 - 348,511 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955494318,137 - 349,568 (-)NCBIChiLan1.0ChiLan1.0
CLCN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26180,166,368 - 180,207,234 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1732,176,625 - 32,217,491 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07135,308,966 - 135,346,734 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17147,801,440 - 147,837,654 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7147,801,440 - 147,836,701 (+)Ensemblpanpan1.1panPan2
CLCN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1166,342,772 - 6,373,580 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl166,342,772 - 6,373,580 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha167,331,919 - 7,362,475 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0166,196,701 - 6,227,304 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl166,196,701 - 6,227,304 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1166,144,363 - 6,174,910 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0165,996,056 - 6,026,611 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0166,071,349 - 6,101,933 (-)NCBIUU_Cfam_GSD_1.0
CLCN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl186,902,542 - 6,940,449 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1186,902,540 - 6,941,530 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2187,143,450 - 7,181,431 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLCN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121112,196,136 - 112,237,836 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl21112,197,518 - 112,236,115 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660728,923,045 - 8,982,440 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clcn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480011,418,225 - 11,446,666 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480011,417,040 - 11,446,732 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005326614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAESOR010000177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSSTOT00000005075   ⟹   ENSSTOP00000004555
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_004936527759,047 - 790,670 (+)Ensembl
RefSeq Acc Id: XM_005326614   ⟹   XP_005326671
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440511812,112,783 - 12,144,385 (-)NCBI
SpeTri2.0NW_004936527759,012 - 791,302 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005326671 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000004555.3
GenBank Protein KAG3277313 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_005326671   ⟸   XM_005326614
- UniProtKB: I3M5F3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSSTOP00000004555   ⟸   ENSSTOT00000005075


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000005062 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000005075.3 UniProtKB/TrEMBL
Gene3D-CATH 3.10.580.10 UniProtKB/TrEMBL
  Clc chloride channel UniProtKB/TrEMBL
InterPro CBS_dom_sf UniProtKB/TrEMBL
  Cl-channel_core UniProtKB/TrEMBL
  Cl-channel_volt-gated UniProtKB/TrEMBL
  Cl_channel-1 UniProtKB/TrEMBL
  Cl_channel_volt-gated UniProtKB/TrEMBL
NCBI Gene Clcn1 ENTREZGENE
PANTHER CHLORIDE CHANNEL PROTEIN 1 UniProtKB/TrEMBL
  CHLORIDE CHANNEL PROTEIN 2 UniProtKB/TrEMBL
Pfam Voltage_CLC UniProtKB/TrEMBL
PRINTS CLCHANNEL UniProtKB/TrEMBL
  CLCHANNEL1 UniProtKB/TrEMBL
Superfamily-SCOP SSF54631 UniProtKB/TrEMBL
  SSF81340 UniProtKB/TrEMBL
UniProt I3M5F3 ENTREZGENE, UniProtKB/TrEMBL