Laptm4a (lysosomal protein transmembrane 4 alpha) - Rat Genome Database

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Gene: Laptm4a (lysosomal protein transmembrane 4 alpha) Rattus norvegicus
Analyze
Symbol: Laptm4a
Name: lysosomal protein transmembrane 4 alpha
RGD ID: 735179
Description: Predicted to be located in Golgi apparatus and late endosome membrane. Predicted to be active in lysosomal membrane. Orthologous to human LAPTM4A (lysosomal protein transmembrane 4 alpha); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2-methoxyethanol; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: lysosomal-associated protein transmembrane 4 alpha; lysosomal-associated protein transmembrane 4A; lysosomal-associated transmembrane protein 4A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8637,438,503 - 37,456,238 (+)NCBIGRCr8
mRatBN7.2631,719,287 - 31,737,023 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl631,718,976 - 31,737,020 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx632,011,285 - 32,029,021 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0632,327,147 - 32,344,883 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0631,801,757 - 31,819,494 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0634,042,132 - 34,059,960 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl634,028,936 - 34,059,961 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0643,823,229 - 43,841,057 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4632,410,289 - 32,427,917 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1632,413,241 - 32,430,870 (+)NCBI
Celera631,167,791 - 31,185,419 (+)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
Golgi apparatus  (IEA,ISO)
late endosome membrane  (IEA,ISO,ISS)
lysosomal membrane  (IBA,IEA,ISO,ISS)
membrane  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Lysosome-associated protein transmembrane 4 alpha (LAPTM4 alpha) requires two tandemly arranged tyrosine-based signals for sorting to lysosomes. Hogue DL, etal., Biochem J 2002 Aug 1;365(Pt 3):721-30.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:10942595   PMID:15489334   PMID:20080761   PMID:22096579   PMID:22871113  


Genomics

Comparative Map Data
Laptm4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8637,438,503 - 37,456,238 (+)NCBIGRCr8
mRatBN7.2631,719,287 - 31,737,023 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl631,718,976 - 31,737,020 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx632,011,285 - 32,029,021 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0632,327,147 - 32,344,883 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0631,801,757 - 31,819,494 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0634,042,132 - 34,059,960 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl634,028,936 - 34,059,961 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0643,823,229 - 43,841,057 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4632,410,289 - 32,427,917 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1632,413,241 - 32,430,870 (+)NCBI
Celera631,167,791 - 31,185,419 (+)NCBICelera
Cytogenetic Map6q14NCBI
LAPTM4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38220,032,650 - 20,051,628 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl220,032,650 - 20,051,628 (-)EnsemblGRCh38hg38GRCh38
GRCh37220,232,411 - 20,251,389 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36220,095,894 - 20,114,926 (-)NCBINCBI36Build 36hg18NCBI36
Build 34220,154,040 - 20,173,073NCBI
Celera220,094,750 - 20,114,129 (-)NCBICelera
Cytogenetic Map2p24.1NCBI
HuRef219,989,688 - 20,009,087 (-)NCBIHuRef
CHM1_1220,161,760 - 20,181,158 (-)NCBICHM1_1
T2T-CHM13v2.0220,066,155 - 20,085,173 (-)NCBIT2T-CHM13v2.0
Laptm4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39128,972,072 - 8,988,742 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl128,971,598 - 8,988,742 (+)EnsemblGRCm39 Ensembl
GRCm38128,921,307 - 8,938,742 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl128,921,664 - 8,938,742 (+)EnsemblGRCm38mm10GRCm38
MGSCv37128,928,113 - 8,945,548 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36128,947,419 - 8,964,736 (+)NCBIMGSCv36mm8
Celera129,304,882 - 9,322,098 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
cM Map123.96NCBI
Laptm4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554692,604,464 - 2,627,043 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554692,604,464 - 2,626,835 (-)NCBIChiLan1.0ChiLan1.0
LAPTM4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v212106,473,385 - 106,495,128 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A106,477,357 - 106,499,100 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A20,019,774 - 20,038,289 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A20,135,960 - 20,154,667 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A20,135,960 - 20,154,667 (-)Ensemblpanpan1.1panPan2
LAPTM4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11715,066,326 - 15,081,562 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1715,066,885 - 15,080,752 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1715,026,395 - 15,043,908 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01715,214,034 - 15,231,554 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1715,214,035 - 15,231,476 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11715,067,635 - 15,085,234 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01715,074,180 - 15,091,684 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01715,105,848 - 15,123,371 (-)NCBIUU_Cfam_GSD_1.0
Laptm4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629259,503,393 - 59,519,963 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493649311,319,923 - 11,336,204 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LAPTM4A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3118,152,587 - 118,170,278 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13118,151,866 - 118,170,279 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23126,183,059 - 126,201,156 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LAPTM4A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11487,668,955 - 87,688,080 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1487,668,710 - 87,690,467 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604524,539,687 - 24,558,540 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Laptm4a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247382,763,165 - 2,790,289 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247382,763,287 - 2,790,244 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Laptm4a
29 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:77
Count of miRNA genes:60
Interacting mature miRNAs:75
Transcripts:ENSRNOT00000009665
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat

Markers in Region
BI292974  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2631,734,314 - 31,734,509 (+)MAPPERmRatBN7.2
Rnor_6.0634,057,268 - 34,057,462NCBIRnor6.0
Rnor_5.0643,838,365 - 43,838,559UniSTSRnor5.0
RGSC_v3.4632,425,225 - 32,425,419UniSTSRGSC3.4
Celera631,182,727 - 31,182,921UniSTS
Cytogenetic Map6q14UniSTS


Sequence


Ensembl Acc Id: ENSRNOT00000009665   ⟹   ENSRNOP00000009665
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl631,719,339 - 31,737,004 (+)Ensembl
Rnor_6.0 Ensembl634,042,130 - 34,059,960 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000085797   ⟹   ENSRNOP00000070019
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl631,718,976 - 31,736,260 (+)Ensembl
Rnor_6.0 Ensembl634,028,936 - 34,059,961 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000091651   ⟹   ENSRNOP00000075537
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl631,718,976 - 31,737,020 (+)Ensembl
Rnor_6.0 Ensembl634,030,620 - 34,059,961 (+)Ensembl
RefSeq Acc Id: NM_199384   ⟹   NP_955416
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8637,438,503 - 37,456,238 (+)NCBI
mRatBN7.2631,719,287 - 31,737,023 (+)NCBI
Rnor_6.0634,042,132 - 34,059,960 (+)NCBI
Rnor_5.0643,823,229 - 43,841,057 (+)NCBI
RGSC_v3.4632,410,289 - 32,427,917 (+)RGD
Celera631,167,791 - 31,185,419 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_955416 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH63179 (Get FASTA)   NCBI Sequence Viewer  
  EDM03082 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009665.5
  ENSRNOP00000070019.2
  ENSRNOP00000075537.2
GenBank Protein Q6P501 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_955416   ⟸   NM_199384
- UniProtKB: Q6P501 (UniProtKB/Swiss-Prot),   A0A0G2JWU5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000070019   ⟸   ENSRNOT00000085797
Ensembl Acc Id: ENSRNOP00000009665   ⟸   ENSRNOT00000009665
Ensembl Acc Id: ENSRNOP00000075537   ⟸   ENSRNOT00000091651

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6P501-F1-model_v2 AlphaFold Q6P501 1-233 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13694486
Promoter ID:EPDNEW_R5011
Type:initiation region
Name:Laptm4a_1
Description:lysosomal protein transmembrane 4 alpha
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0634,042,098 - 34,042,158EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735179 AgrOrtholog
BioCyc Gene G2FUF-38173 BioCyc
Ensembl Genes ENSRNOG00000006865 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009665.7 UniProtKB/Swiss-Prot
  ENSRNOT00000085797.2 UniProtKB/TrEMBL
  ENSRNOT00000091651.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6890564 IMAGE-MGC_LOAD
InterPro LAPTM4/5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LAPTM_4A/5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LAPTM_transporter UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:298875 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72951 IMAGE-MGC_LOAD
NCBI Gene 298875 ENTREZGENE
PANTHER LYSOSOMAL-ASSOCIATED TRANSMEMBRANE PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LYSOSOMAL-ASSOCIATED TRANSMEMBRANE PROTEIN 4A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Mtp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Laptm4a PhenoGen
RatGTEx ENSRNOG00000006865 RatGTEx
UniProt A0A0G2JWU5 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2KAV0_RAT UniProtKB/TrEMBL
  A6HAM7_RAT UniProtKB/TrEMBL
  LAP4A_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-11-11 Laptm4a  lysosomal protein transmembrane 4 alpha  Laptm4a  lysosomal-associated protein transmembrane 4A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Laptm4a  lysosomal-associated protein transmembrane 4A    lysosomal-associated protein transmembrane 4 alpha  Name updated 1299863 APPROVED