Lmbr1 (limb development membrane protein 1) - Rat Genome Database

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Gene: Lmbr1 (limb development membrane protein 1) Rattus norvegicus
Analyze
Symbol: Lmbr1
Name: limb development membrane protein 1
RGD ID: 1563910
Description: Predicted to enable transmembrane signaling receptor activity. Predicted to be involved in signal transduction. Predicted to act upstream of or within embryonic digit morphogenesis. Predicted to be located in membrane. Human ortholog(s) of this gene implicated in Laurin-Sandrow syndrome; acheiropody; and syndactyly type 4. Orthologous to human LMBR1 (limb development membrane protein 1); INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: limb region 1; limb region 1 homolog; limb region 1 homolog (mouse); limb region 1 protein homolog; LOC362295; RGD1563910; similar to Lmbr1 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr846,649,824 - 6,820,525 (+)NCBIGRCr8
mRatBN7.245,974,687 - 6,146,348 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl45,974,750 - 6,146,368 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx410,964,561 - 11,104,689 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.046,778,789 - 6,918,931 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.045,124,942 - 5,265,085 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.042,116,094 - 2,274,111 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl42,116,094 - 2,201,749 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.042,172,459 - 2,330,391 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.441,177,941 - 1,344,583 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera44,186,584 - 4,352,183 (-)NCBICelera
Cytogenetic Map4q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. Acheiropodia is caused by a genomic deletion in C7orf2, the human orthologue of the Lmbr1 gene. Ianakiev P, etal., Am J Hum Genet. 2001 Jan;68(1):38-45. Epub 2000 Nov 22.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:11606546  


Genomics

Comparative Map Data
Lmbr1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr846,649,824 - 6,820,525 (+)NCBIGRCr8
mRatBN7.245,974,687 - 6,146,348 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl45,974,750 - 6,146,368 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx410,964,561 - 11,104,689 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.046,778,789 - 6,918,931 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.045,124,942 - 5,265,085 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.042,116,094 - 2,274,111 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl42,116,094 - 2,201,749 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.042,172,459 - 2,330,391 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.441,177,941 - 1,344,583 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera44,186,584 - 4,352,183 (-)NCBICelera
Cytogenetic Map4q11NCBI
LMBR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387156,669,012 - 156,893,183 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7156,668,946 - 156,893,216 (-)EnsemblGRCh38hg38GRCh38
GRCh377156,461,706 - 156,685,877 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367156,166,331 - 156,378,663 (-)NCBINCBI36Build 36hg18NCBI36
Build 347155,975,109 - 156,185,317NCBI
Celera7150,900,771 - 151,113,109 (-)NCBICelera
Cytogenetic Map7q36.3NCBI
HuRef7150,206,410 - 150,418,614 (-)NCBIHuRef
CHM1_17156,482,285 - 156,694,637 (-)NCBICHM1_1
T2T-CHM13v2.07157,856,727 - 158,080,951 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27155,702,965 - 155,915,305 (-)NCBI
Lmbr1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39529,434,800 - 29,583,414 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl529,481,000 - 29,485,295 (-)EnsemblGRCm39 Ensembl
GRCm39 Ensembl529,434,800 - 29,583,388 (-)EnsemblGRCm39 Ensembl
GRCm38529,229,802 - 29,378,421 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl529,229,802 - 29,378,390 (-)EnsemblGRCm38mm10GRCm38
MGSCv37529,556,342 - 29,704,930 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36529,563,850 - 29,708,979 (-)NCBIMGSCv36mm8
Celera526,746,188 - 26,894,229 (-)NCBICelera
Cytogenetic Map5B1NCBI
cM Map514.81NCBI
Lmbr1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554919,171,462 - 9,217,996 (-)NCBIChiLan1.0ChiLan1.0
LMBR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26193,126,963 - 193,338,373 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1745,138,039 - 45,348,637 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07148,301,263 - 148,512,407 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17159,995,236 - 160,151,025 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7159,999,389 - 160,152,858 (-)Ensemblpanpan1.1panPan2
LMBR1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11619,295,235 - 19,442,390 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1619,296,149 - 19,442,369 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1619,926,402 - 20,073,017 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01621,024,102 - 21,171,034 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1621,025,016 - 21,171,045 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11619,393,417 - 19,539,921 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01619,975,284 - 20,122,102 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01620,027,644 - 20,174,745 (-)NCBIUU_Cfam_GSD_1.0
Lmbr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244051181,986,679 - 2,145,004 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936797745,845 - 868,632 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936797745,851 - 873,388 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LMBR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl181,795,497 - 1,934,947 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1181,795,462 - 1,934,951 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2181,941,562 - 1,997,710 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LMBR1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121124,819,580 - 125,032,058 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl21124,819,887 - 124,981,008 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607221,034,422 - 21,261,773 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lmbr1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248001,494,192 - 1,648,978 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248001,494,183 - 1,648,978 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lmbr1
433 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:138
Count of miRNA genes:112
Interacting mature miRNAs:125
Transcripts:ENSRNOT00000007189
Prediction methods:Miranda
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
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4131934116Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat

Markers in Region
RH138859  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.246,144,311 - 6,144,447 (-)MAPPERmRatBN7.2
Rnor_6.042,117,052 - 2,117,187NCBIRnor6.0
Rnor_5.042,173,417 - 2,173,552UniSTSRnor5.0
RGSC_v3.441,343,490 - 1,343,625UniSTSRGSC3.4
Celera44,187,542 - 4,187,677UniSTS
Cytogenetic Map4q11UniSTS


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 renal system reproductive system respiratory system appendage
High
Medium 12 13 6 17 6 74 26 36 10
Low 3 31 44 35 2 35 8 11 9 5 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000089327   ⟹   ENSRNOP00000072977
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl45,974,750 - 6,145,405 (+)Ensembl
Rnor_6.0 Ensembl42,116,094 - 2,201,749 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102591   ⟹   ENSRNOP00000084962
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl45,974,750 - 6,146,368 (+)Ensembl
RefSeq Acc Id: NM_001191858   ⟹   NP_001178787
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr846,649,881 - 6,820,523 (+)NCBI
mRatBN7.245,974,750 - 6,145,405 (+)NCBI
Rnor_6.042,116,094 - 2,274,111 (-)NCBI
Rnor_5.042,172,459 - 2,330,391 (-)NCBI
Celera44,186,584 - 4,352,183 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107740   ⟹   XP_038963668
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr846,687,925 - 6,820,525 (+)NCBI
mRatBN7.246,012,808 - 6,146,348 (+)NCBI
RefSeq Acc Id: XM_063286221   ⟹   XP_063142291
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr846,649,824 - 6,820,525 (+)NCBI
RefSeq Acc Id: XR_010065654
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr846,649,824 - 6,817,348 (+)NCBI
RefSeq Acc Id: XR_010065655
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr846,649,824 - 6,783,397 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001178787 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963668 (Get FASTA)   NCBI Sequence Viewer  
  XP_063142291 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL86424 (Get FASTA)   NCBI Sequence Viewer  
  EDL86425 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000072977
  ENSRNOP00000072977.2
  ENSRNOP00000084962.1
Reference Protein Sequences
RefSeq Acc Id: NP_001178787   ⟸   NM_001191858
- UniProtKB: A0A0G2K4B6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072977   ⟸   ENSRNOT00000089327
RefSeq Acc Id: XP_038963668   ⟸   XM_039107740
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZY94 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000084962   ⟸   ENSRNOT00000102591
RefSeq Acc Id: XP_063142291   ⟸   XM_063286221
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K4B6-F1-model_v2 AlphaFold A0A0G2K4B6 1-389 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563910 AgrOrtholog
BioCyc Gene G2FUF-46164 BioCyc
Ensembl Genes ENSRNOG00000059589 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000089327 ENTREZGENE
  ENSRNOT00000089327.2 UniProtKB/TrEMBL
  ENSRNOT00000102591.1 UniProtKB/TrEMBL
InterPro Lipcalin_1_rcpt UniProtKB/TrEMBL
  LMBR1-like_membr_prot UniProtKB/TrEMBL
KEGG Report rno:362295 UniProtKB/TrEMBL
NCBI Gene 362295 ENTREZGENE
PANTHER LIMB REGION 1 PROTEIN HOMOLOG UniProtKB/TrEMBL
  PTHR12625 UniProtKB/TrEMBL
Pfam LMBR1 UniProtKB/TrEMBL
PhenoGen Lmbr1 PhenoGen
PRINTS LIPOCALINIMR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000059589 RatGTEx
UniProt A0A0G2K4B6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZY94 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-14 Lmbr1  limb development membrane protein 1  Lmbr1  limb region 1 homolog (mouse)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-17 Lmbr1  limb region 1 homolog (mouse)  Lmbr1  limb region 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Lmbr1  limb region 1  RGD1563910_predicted  similar to Lmbr1 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563910_predicted  similar to Lmbr1 protein (predicted)  LOC362295  similar to Lmbr1 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC362295  similar to Lmbr1 protein      Symbol and Name status set to provisional 70820 PROVISIONAL