Limch1 (LIM and calponin homology domains 1) - Rat Genome Database

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Gene: Limch1 (LIM and calponin homology domains 1) Heterocephalus glaber
Analyze
Symbol: Limch1
Name: LIM and calponin homology domains 1
RGD ID: 18912921
Description: ENCODES a protein that exhibits actin binding (inferred); metal ion binding (inferred); myosin II head/neck binding (inferred); INVOLVED IN cytoplasmic actin-based contraction involved in cell motility (ortholog); negative regulation of cell migration (ortholog); positive regulation of protein phosphorylation (ortholog); ASSOCIATED WITH Hyperglycinemia, Lactic Acidosis, and Seizures (ortholog); malignant mesothelioma (ortholog); substance-related disorder (ortholog); FOUND IN myosin II complex (ortholog); stress fiber (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LIM and calponin homology domains-containing protein 1; LIM and calponin-like protein domains-containing protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476125,382,274 - 25,578,503 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476125,375,501 - 25,706,756 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:21993625   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Limch1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476125,382,274 - 25,578,503 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476125,375,501 - 25,706,756 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
LIMCH1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38441,359,607 - 41,700,044 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl441,359,607 - 41,700,044 (+)EnsemblGRCh38hg38GRCh38
GRCh37441,361,624 - 41,702,061 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36441,057,561 - 41,395,767 (+)NCBINCBI36Build 36hg18NCBI36
Celera441,806,095 - 42,146,075 (+)NCBICelera
Cytogenetic Map4p13NCBI
HuRef440,684,478 - 41,024,427 (+)NCBIHuRef
CHM1_1441,363,356 - 41,702,595 (+)NCBICHM1_1
T2T-CHM13v2.0441,333,394 - 41,673,808 (+)NCBIT2T-CHM13v2.0
Limch1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39566,903,232 - 67,214,502 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl566,903,170 - 67,214,501 (+)EnsemblGRCm39 Ensembl
GRCm38566,745,889 - 67,057,159 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl566,745,827 - 67,057,158 (+)EnsemblGRCm38mm10GRCm38
MGSCv37567,137,079 - 67,448,398 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36567,025,084 - 67,335,232 (+)NCBIMGSCv36mm8
Celera564,048,465 - 64,361,964 (+)NCBICelera
Cytogenetic Map5C3.1NCBI
cM Map535.95NCBI
Limch1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81441,466,433 - 41,779,477 (-)NCBIGRCr8
mRatBN7.21441,112,579 - 41,425,001 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1441,114,803 - 41,425,191 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1441,458,625 - 41,770,890 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01442,758,712 - 43,070,966 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01441,239,523 - 41,551,800 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01442,760,363 - 43,072,976 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1442,762,587 - 43,072,843 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01442,558,732 - 42,868,387 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41443,722,254 - 44,049,555 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11443,681,141 - 44,052,100 (-)NCBI
Celera1440,270,045 - 40,579,190 (-)NCBICelera
Cytogenetic Map14p11NCBI
Limch1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554435,983,842 - 6,305,014 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554435,984,027 - 6,305,014 (-)NCBIChiLan1.0ChiLan1.0
LIMCH1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2341,545,334 - 41,884,903 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1441,738,614 - 42,078,297 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0435,685,904 - 36,025,582 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1441,533,508 - 41,873,694 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl441,533,560 - 41,873,694 (+)Ensemblpanpan1.1panPan2
LIMCH1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11338,518,653 - 38,816,804 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1338,518,644 - 38,814,369 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1338,495,198 - 38,793,400 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01339,008,734 - 39,307,552 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1339,008,727 - 39,306,490 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11338,699,406 - 38,997,408 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01338,809,648 - 39,105,367 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01339,284,402 - 39,582,653 (+)NCBIUU_Cfam_GSD_1.0
Limch1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528537,365,504 - 37,677,692 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364828,620,858 - 8,930,495 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364828,620,543 - 8,932,731 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIMCH1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl832,433,318 - 32,792,546 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1832,433,035 - 32,792,553 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2834,048,380 - 34,408,111 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LIMCH1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1278,656,502 - 8,994,669 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl278,653,600 - 8,994,634 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604754,972,000 - 55,314,409 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSHGLT00000011755   ⟹   ENSHGLP00000011627
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_00462476125,382,274 - 25,578,503 (-)Ensembl
RefSeq Acc Id: ENSHGLT00000011756   ⟹   ENSHGLP00000011628
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_00462476125,382,274 - 25,578,503 (-)Ensembl
RefSeq Acc Id: ENSHGLT00000011757   ⟹   ENSHGLP00000011629
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_00462476125,382,274 - 25,458,515 (-)Ensembl
RefSeq Acc Id: XM_021262418   ⟹   XP_021118077
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462476125,375,501 - 25,706,756 (-)NCBI
Protein Sequences
Protein RefSeqs XP_021118077 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EHA98556 (Get FASTA)   NCBI Sequence Viewer  
  JAN98130 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_021118077   ⟸   XM_021262418
- UniProtKB: G5ANE6 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSHGLP00000011628   ⟸   ENSHGLT00000011756
RefSeq Acc Id: ENSHGLP00000011629   ⟸   ENSHGLT00000011757
RefSeq Acc Id: ENSHGLP00000011627   ⟸   ENSHGLT00000011755


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000008342 Ensembl
Gene3D-CATH 1.10.418.10 UniProtKB/TrEMBL
  Cysteine Rich Protein UniProtKB/TrEMBL
  P-loop containing nucleotide triphosphate hydrolases UniProtKB/TrEMBL
InterPro Calponin/LIMCH1 UniProtKB/TrEMBL
  CH-domain UniProtKB/TrEMBL
  CH_dom_sf UniProtKB/TrEMBL
  DUF4757 UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  SM22_calponin UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
NCBI Gene Limch1 ENTREZGENE
PANTHER LIM DOMAIN ONLY 7 UniProtKB/TrEMBL
  PTHR15551:SF3 UniProtKB/TrEMBL
Pfam DUF4757 UniProtKB/TrEMBL
  LIM UniProtKB/TrEMBL
  PF00307 UniProtKB/TrEMBL
PRINTS CALPONIN UniProtKB/TrEMBL
  SM22CALPONIN UniProtKB/TrEMBL
PROSITE LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
  PS50021 UniProtKB/TrEMBL
SMART LIM UniProtKB/TrEMBL
  SM00033 UniProtKB/TrEMBL
Superfamily-SCOP SSF47576 UniProtKB/TrEMBL
UniProt A0A0P6JUG7_HETGA UniProtKB/TrEMBL
  G5ANE6 ENTREZGENE, UniProtKB/TrEMBL