LRTM1 (leucine rich repeats and transmembrane domains 1) - Rat Genome Database

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Gene: LRTM1 (leucine rich repeats and transmembrane domains 1) Canis lupus familiaris
Analyze
Symbol: LRTM1
Name: leucine rich repeats and transmembrane domains 1
RGD ID: 12272704
Description: INVOLVED IN positive regulation of synapse assembly (ortholog); FOUND IN extracellular matrix (inferred); extracellular space (inferred); membrane (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: leucine-rich repeat and transmembrane domain-containing protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12035,220,954 - 35,236,425 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2035,221,951 - 35,231,943 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2035,151,325 - 35,162,968 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02035,494,882 - 35,506,518 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2035,496,155 - 35,508,172 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12034,937,103 - 34,948,750 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02035,296,361 - 35,308,008 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02035,511,795 - 35,523,447 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
LRTM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12035,220,954 - 35,236,425 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2035,221,951 - 35,231,943 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2035,151,325 - 35,162,968 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02035,494,882 - 35,506,518 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2035,496,155 - 35,508,172 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12034,937,103 - 34,948,750 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02035,296,361 - 35,308,008 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02035,511,795 - 35,523,447 (+)NCBIUU_Cfam_GSD_1.0
LRTM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38354,918,231 - 54,967,102 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl354,918,231 - 54,967,088 (-)EnsemblGRCh38hg38GRCh38
GRCh37354,952,258 - 55,001,129 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36354,927,400 - 54,937,112 (-)NCBINCBI36Build 36hg18NCBI36
Celera354,918,491 - 54,928,203 (-)NCBICelera
Cytogenetic Map3p14.3NCBI
HuRef355,001,810 - 55,011,526 (-)NCBIHuRef
CHM1_1354,903,712 - 54,913,435 (-)NCBICHM1_1
T2T-CHM13v2.0354,952,027 - 55,000,901 (-)NCBIT2T-CHM13v2.0
Lrtm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391428,740,165 - 28,755,599 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1428,740,165 - 28,755,602 (+)EnsemblGRCm39 Ensembl
GRCm381429,018,208 - 29,033,642 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1429,018,208 - 29,033,645 (+)EnsemblGRCm38mm10GRCm38
MGSCv371429,831,394 - 29,846,828 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361427,845,265 - 27,854,891 (+)NCBIMGSCv36mm8
Celera1425,271,616 - 25,287,049 (+)NCBICelera
Cytogenetic Map14A3NCBI
cM Map1416.8NCBI
Lrtm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8164,216,947 - 4,224,447 (+)NCBIGRCr8
mRatBN7.2164,210,343 - 4,217,843 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.0164,993,728 - 5,005,110 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl164,997,461 - 5,003,066 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0164,934,436 - 4,945,500 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4164,285,032 - 4,293,657 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1610,954,321 - 10,965,702 (-)NCBICelera
Cytogenetic Map16p16NCBI
Lrtm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554304,784,367 - 4,794,372 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554304,784,643 - 4,794,318 (-)NCBIChiLan1.0ChiLan1.0
LRTM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2254,911,383 - 54,921,629 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1354,916,154 - 54,926,400 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0354,858,452 - 54,868,183 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1356,078,743 - 56,127,798 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl356,078,764 - 56,085,634 (-)Ensemblpanpan1.1panPan2
Lrtm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118172,339,906 - 172,353,124 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364735,481,929 - 5,491,858 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364735,478,481 - 5,491,689 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRTM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1336,869,494 - 36,881,013 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11336,870,269 - 36,881,586 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21340,235,908 - 40,247,046 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LRTM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_023666041150,591,981 - 150,605,509 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lrtm1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248222,343,967 - 2,354,525 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248222,343,968 - 2,354,038 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LRTM1
155 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

endocrine system hemolymphoid system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium
Low 2 1
Below cutoff 11 1 5 4 9 7 4 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000013071   ⟹   ENSCAFP00000012094
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl2035,221,951 - 35,231,943 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845047783   ⟹   ENSCAFP00845037491
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl2035,496,155 - 35,508,172 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845047822   ⟹   ENSCAFP00845037522
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl2035,498,855 - 35,508,172 (+)Ensembl
RefSeq Acc Id: XM_022406584   ⟹   XP_022262292
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12035,220,954 - 35,236,425 (+)NCBI
Dog10K_Boxer_Tasha2035,151,325 - 35,162,968 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038427467   ⟹   XP_038283395
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.02035,494,882 - 35,506,518 (+)NCBI
RefSeq Acc Id: XM_038503176   ⟹   XP_038359104
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.12034,937,103 - 34,948,750 (+)NCBI
RefSeq Acc Id: XM_038566137   ⟹   XP_038422065
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.02035,511,795 - 35,523,447 (+)NCBI
RefSeq Acc Id: XM_038630293   ⟹   XP_038486221
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.02035,296,361 - 35,308,008 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_022262292   ⟸   XM_022406584
- UniProtKB: A0A8C0SXZ3 (UniProtKB/TrEMBL),   A0A8I3PRL3 (UniProtKB/TrEMBL),   A0A8I3PRL6 (UniProtKB/TrEMBL),   A0A8P0TJD0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000012094   ⟸   ENSCAFT00000013071
RefSeq Acc Id: XP_038359104   ⟸   XM_038503176
RefSeq Acc Id: XP_038486221   ⟸   XM_038630293
RefSeq Acc Id: XP_038283395   ⟸   XM_038427467
- UniProtKB: A0A8C0SXZ3 (UniProtKB/TrEMBL),   A0A8I3PRL3 (UniProtKB/TrEMBL),   A0A8I3PRL6 (UniProtKB/TrEMBL),   A0A8P0TJD0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038422065   ⟸   XM_038566137
- UniProtKB: A0A8C0SXZ3 (UniProtKB/TrEMBL),   A0A8I3PRL3 (UniProtKB/TrEMBL),   A0A8I3PRL6 (UniProtKB/TrEMBL),   A0A8P0TJD0 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845037491   ⟸   ENSCAFT00845047783
RefSeq Acc Id: ENSCAFP00845037522   ⟸   ENSCAFT00845047822
Protein Domains
LRRCT   LRRNT

Promoters
RGD ID:13686839
Promoter ID:EPDNEW_C4905
Type:multiple initiation site
Name:LRTM1_1
Description:leucine rich repeats and transmembrane domains 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12035,224,793 - 35,224,853EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000008232 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030025521 UniProtKB/TrEMBL
  ENSCAFG00040017270 UniProtKB/TrEMBL
  ENSCAFG00845027109 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000013071.5 UniProtKB/TrEMBL
  ENSCAFT00000108610.1 UniProtKB/TrEMBL
  ENSCAFT00030047140.1 UniProtKB/TrEMBL
  ENSCAFT00040031895.1 UniProtKB/TrEMBL
  ENSCAFT00845047783 ENTREZGENE
  ENSCAFT00845047783.1 UniProtKB/TrEMBL
  ENSCAFT00845047822.1 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro Cys-rich_flank_reg_C UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
NCBI Gene LRTM1 ENTREZGENE
PANTHER SLIT RELATED LEUCINE-RICH REPEAT NEURONAL PROTEIN UniProtKB/TrEMBL
  VASORIN UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/TrEMBL
PRINTS LEURICHRPT UniProtKB/TrEMBL
PROSITE LRR UniProtKB/TrEMBL
  PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
SMART LRR_BAC UniProtKB/TrEMBL
  LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt A0A8C0SXZ3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PRL3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PRL6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0TJD0 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:49805 ENTREZGENE