LCT (lactase) - Rat Genome Database

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Gene: LCT (lactase) Canis lupus familiaris
Analyze
Symbol: LCT
Name: lactase
RGD ID: 12148607
Description: ENCODES a protein that exhibits galactosylceramidase activity (ortholog); glucosylceramidase activity (ortholog); lactase activity (ortholog); INVOLVED IN glycosylceramide catabolic process (ortholog); response to estrogen (ortholog); response to ethanol (ortholog); PARTICIPATES IN galactose metabolic pathway; galactosemia pathway; lactose degradation pathway; ASSOCIATED WITH adult respiratory distress syndrome (ortholog); colitis (ortholog); congenital lactase deficiency (ortholog); FOUND IN brush border (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: lactase-phlorizin hydrolase
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11938,571,539 - 38,620,567 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1938,572,058 - 38,620,567 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1938,812,141 - 38,863,510 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01940,014,481 - 40,065,894 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1940,017,274 - 40,065,921 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11938,656,504 - 38,707,872 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01938,815,944 - 38,867,284 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01940,048,815 - 40,100,194 (-)NCBIUU_Cfam_GSD_1.0
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 Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
LCT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11938,571,539 - 38,620,567 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1938,572,058 - 38,620,567 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1938,812,141 - 38,863,510 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01940,014,481 - 40,065,894 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1940,017,274 - 40,065,921 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11938,656,504 - 38,707,872 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01938,815,944 - 38,867,284 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01940,048,815 - 40,100,194 (-)NCBIUU_Cfam_GSD_1.0
LCT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382135,787,850 - 135,837,184 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2135,787,850 - 135,837,184 (-)EnsemblGRCh38hg38GRCh38
GRCh372136,545,420 - 136,594,754 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362136,261,885 - 136,311,220 (-)NCBINCBI36Build 36hg18NCBI36
Build 342136,379,146 - 136,428,482NCBI
Celera2130,256,175 - 130,305,504 (-)NCBICelera
Cytogenetic Map2q21.3NCBI
HuRef2128,538,586 - 128,587,979 (-)NCBIHuRef
CHM1_12136,550,605 - 136,600,149 (-)NCBICHM1_1
T2T-CHM13v2.02136,228,325 - 136,281,636 (-)NCBIT2T-CHM13v2.0
Lct
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391128,212,493 - 128,256,055 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1128,212,493 - 128,256,055 (-)EnsemblGRCm39 Ensembl
GRCm381128,284,756 - 128,328,318 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1128,284,756 - 128,328,318 (-)EnsemblGRCm38mm10GRCm38
MGSCv371130,181,341 - 130,224,895 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361130,112,310 - 130,155,864 (-)NCBIMGSCv36mm8
Celera1130,912,375 - 130,955,221 (-)NCBICelera
Cytogenetic Map1E3NCBI
cM Map155.8NCBI
Lct
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81342,334,347 - 42,376,872 (-)NCBIGRCr8
mRatBN7.21339,781,929 - 39,824,456 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1339,781,929 - 39,824,456 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1342,375,821 - 42,418,341 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01343,663,926 - 43,706,446 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01340,917,951 - 40,960,284 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01344,998,414 - 45,040,593 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1344,998,414 - 45,040,593 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01350,083,769 - 50,125,203 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41340,990,315 - 41,043,388 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11341,017,068 - 41,018,494 (-)NCBI
Celera1340,155,673 - 40,198,507 (-)NCBICelera
Cytogenetic Map13q13NCBI
Lct
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554403,148,730 - 3,197,110 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554403,148,730 - 3,197,110 (-)NCBIChiLan1.0ChiLan1.0
LCT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21339,093,531 - 39,150,819 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B39,108,500 - 39,162,817 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B24,025,383 - 24,079,779 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B139,855,600 - 139,908,764 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B139,855,605 - 139,908,764 (-)Ensemblpanpan1.1panPan2
Lct
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303101,510,063 - 101,552,920 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493646940,064,822 - 40,107,447 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493646940,064,822 - 40,108,423 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100625897
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11516,094,277 - 16,154,467 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21518,486,673 - 18,544,563 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LCT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11019,994,398 - 20,049,325 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1019,994,384 - 20,049,097 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660612,414,641 - 2,469,654 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lct
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473235,125,287 - 35,175,062 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473235,125,995 - 35,177,055 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LCT
746 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium
Low 5 6 5
Below cutoff 5 5 17 6 6 6 6 6 6 8 5 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000008258   ⟹   ENSCAFP00000007651
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1938,572,058 - 38,620,567 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000062030   ⟹   ENSCAFP00000054003
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1938,572,058 - 38,620,567 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000062951   ⟹   ENSCAFP00000056231
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1938,572,058 - 38,620,567 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000064285   ⟹   ENSCAFP00000052455
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1938,572,058 - 38,620,567 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000064936   ⟹   ENSCAFP00000055452
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1938,572,058 - 38,620,567 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000075702   ⟹   ENSCAFP00000050359
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1938,572,058 - 38,620,567 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845017274   ⟹   ENSCAFP00845013463
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1940,017,274 - 40,065,921 (-)Ensembl
RefSeq Acc Id: XM_038425585   ⟹   XP_038281513
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01940,014,481 - 40,065,894 (-)NCBI
RefSeq Acc Id: XM_038454584   ⟹   XP_038310512
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha1938,812,141 - 38,863,510 (-)NCBI
RefSeq Acc Id: XM_038502279   ⟹   XP_038358207
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.11938,656,504 - 38,707,872 (-)NCBI
RefSeq Acc Id: XM_038564534   ⟹   XP_038420462
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01940,048,815 - 40,100,194 (-)NCBI
RefSeq Acc Id: XM_038628633   ⟹   XP_038484561
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.01938,815,944 - 38,867,284 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSCAFP00000052455   ⟸   ENSCAFT00000064285
RefSeq Acc Id: ENSCAFP00000055452   ⟸   ENSCAFT00000064936
RefSeq Acc Id: ENSCAFP00000054003   ⟸   ENSCAFT00000062030
RefSeq Acc Id: ENSCAFP00000056231   ⟸   ENSCAFT00000062951
RefSeq Acc Id: ENSCAFP00000007651   ⟸   ENSCAFT00000008258
RefSeq Acc Id: ENSCAFP00000050359   ⟸   ENSCAFT00000075702
RefSeq Acc Id: XP_038358207   ⟸   XM_038502279
RefSeq Acc Id: XP_038484561   ⟸   XM_038628633
RefSeq Acc Id: XP_038281513   ⟸   XM_038425585
- UniProtKB: A0A8C0SNV0 (UniProtKB/TrEMBL),   A0A8I3NDB4 (UniProtKB/TrEMBL),   A0A8C0KUQ1 (UniProtKB/TrEMBL),   A0A8C0NUM2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038310512   ⟸   XM_038454584
- UniProtKB: A0A8C0SNV0 (UniProtKB/TrEMBL),   A0A8I3NDB4 (UniProtKB/TrEMBL),   A0A8C0KUQ1 (UniProtKB/TrEMBL),   A0A8C0NUM2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038420462   ⟸   XM_038564534
- UniProtKB: A0A8I3NDB4 (UniProtKB/TrEMBL),   A0A8C0KUQ1 (UniProtKB/TrEMBL),   A0A8C0NUM2 (UniProtKB/TrEMBL),   A0A8C0SNV0 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845013463   ⟸   ENSCAFT00845017274


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000005126 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030018661 UniProtKB/TrEMBL
  ENSCAFG00040014568 UniProtKB/TrEMBL
  ENSCAFG00845009807 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000062030.2 UniProtKB/TrEMBL
  ENSCAFT00030034348.1 UniProtKB/TrEMBL
  ENSCAFT00040026846.1 UniProtKB/TrEMBL
  ENSCAFT00845017274 ENTREZGENE
  ENSCAFT00845017274.1 UniProtKB/TrEMBL
Gene3D-CATH Glycosidases UniProtKB/TrEMBL
InterPro Glyco_hydro_1 UniProtKB/TrEMBL
  Glyco_hydro_1_AS UniProtKB/TrEMBL
  Glyco_hydro_1_N_CS UniProtKB/TrEMBL
  Glycoside_hydrolase_SF UniProtKB/TrEMBL
NCBI Gene LCT ENTREZGENE
PANTHER LACTASE-LIKE PROTEIN UniProtKB/TrEMBL
  PTHR10353 UniProtKB/TrEMBL
Pfam Glyco_hydro_1 UniProtKB/TrEMBL
PRINTS GLHYDRLASE1 UniProtKB/TrEMBL
PROSITE GLYCOSYL_HYDROL_F1_1 UniProtKB/TrEMBL
  GLYCOSYL_HYDROL_F1_2 UniProtKB/TrEMBL
Superfamily-SCOP SSF51445 UniProtKB/TrEMBL
UniProt A0A8C0KUQ1 ENTREZGENE
  A0A8C0NUM2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0SNV0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NDB4 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:42616 ENTREZGENE