Lhfpl1 (LHFPL tetraspan subfamily member 1) - Rat Genome Database

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Gene: Lhfpl1 (LHFPL tetraspan subfamily member 1) Rattus norvegicus
Analyze
Symbol: Lhfpl1
Name: LHFPL tetraspan subfamily member 1
RGD ID: 727927
Description: Predicted to be active in membrane. Orthologous to human LHFPL1 (LHFPL tetraspan subfamily member 1); INTERACTS WITH 17beta-estradiol; acrylamide; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Lhfp; lipoma HMGIC fusion partner; lipoma HMGIC fusion partner-like 1; lipoma HMGIC fusion partner-like 1 protein; LOC300286
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
GRCr8X113,612,200 - 113,670,060 (-)NCBIGRCr8
mRatBN7.2X108,815,596 - 108,873,460 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX108,815,596 - 108,873,460 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX110,955,547 - 111,013,433 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X114,455,352 - 114,513,242 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X112,012,009 - 112,069,901 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X116,578,521 - 116,638,648 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX116,578,527 - 116,638,508 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X116,716,941 - 116,777,168 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X33,160,888 - 33,220,843 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X33,214,356 - 33,274,312 (+)NCBI
CeleraX108,198,021 - 108,255,504 (-)NCBICelera
Cytogenetic MapXq34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IBA)

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. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Lhfpl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X113,612,200 - 113,670,060 (-)NCBIGRCr8
mRatBN7.2X108,815,596 - 108,873,460 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX108,815,596 - 108,873,460 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX110,955,547 - 111,013,433 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X114,455,352 - 114,513,242 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X112,012,009 - 112,069,901 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X116,578,521 - 116,638,648 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX116,578,527 - 116,638,508 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X116,716,941 - 116,777,168 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X33,160,888 - 33,220,843 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X33,214,356 - 33,274,312 (+)NCBI
CeleraX108,198,021 - 108,255,504 (-)NCBICelera
Cytogenetic MapXq34NCBI
LHFPL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X112,630,648 - 112,679,938 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX112,630,648 - 112,680,054 (-)EnsemblGRCh38hg38GRCh38
GRCh37X111,873,876 - 111,923,166 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X111,760,535 - 111,810,031 (-)NCBINCBI36Build 36hg18NCBI36
CeleraX112,359,143 - 112,408,638 (-)NCBICelera
Cytogenetic MapXq23NCBI
HuRefX101,497,232 - 101,546,389 (-)NCBIHuRef
CHM1_1X111,785,057 - 111,834,527 (-)NCBICHM1_1
T2T-CHM13v2.0X111,081,595 - 111,130,884 (-)NCBIT2T-CHM13v2.0
Lhfpl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X144,073,355 - 144,155,388 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX144,073,355 - 144,132,085 (-)EnsemblGRCm39 Ensembl
GRCm38X145,290,359 - 145,372,392 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX145,290,359 - 145,349,089 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X141,724,902 - 141,783,437 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X140,536,727 - 140,595,262 (-)NCBIMGSCv36mm8
CeleraX129,239,006 - 129,295,143 (-)NCBICelera
Cytogenetic MapXF2NCBI
cM MapX66.54NCBI
Lhfpl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554903,156,323 - 3,216,037 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554903,156,323 - 3,215,925 (+)NCBIChiLan1.0ChiLan1.0
LHFPL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X112,116,907 - 112,173,064 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X112,120,514 - 112,176,672 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X101,739,343 - 101,797,855 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X112,202,054 - 112,254,096 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX112,202,054 - 112,254,096 (-)Ensemblpanpan1.1panPan2
LHFPL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X85,533,812 - 85,648,773 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX85,526,179 - 85,648,890 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX71,707,373 - 71,761,895 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X87,289,714 - 87,344,271 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX87,289,688 - 87,344,385 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X84,753,299 - 84,807,911 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X86,422,120 - 86,475,979 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X86,260,858 - 86,306,455 (-)NCBIUU_Cfam_GSD_1.0
Lhfpl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X84,862,211 - 84,912,018 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364992,745,825 - 2,795,721 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364992,745,825 - 2,795,691 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LHFPL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX92,422,918 - 92,481,761 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X92,422,913 - 92,542,291 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X106,788,151 - 106,907,178 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LHFPL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X100,225,777 - 100,405,628 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX100,355,574 - 100,405,518 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606525,696,554 - 25,758,776 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lhfpl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248032,725,695 - 2,785,166 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248032,725,695 - 2,785,183 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lhfpl1
105 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:82
Count of miRNA genes:67
Interacting mature miRNAs:75
Transcripts:ENSRNOT00000030400
Prediction methods:Microtar, 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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat


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
Low 3 14 4 4 6 6 28 34 41 11 6
Below cutoff 29 24 12 6 12 2 5 46 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000030400   ⟹   ENSRNOP00000037132
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX108,815,596 - 108,873,460 (-)Ensembl
Rnor_6.0 EnsemblX116,578,527 - 116,638,508 (-)Ensembl
RefSeq Acc Id: NM_181085   ⟹   NP_851599
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X113,612,200 - 113,670,060 (-)NCBI
mRatBN7.2X108,815,596 - 108,873,460 (-)NCBI
Rnor_6.0X116,579,571 - 116,638,493 (-)NCBI
Rnor_5.0X116,716,941 - 116,777,168 (-)NCBI
RGSC_v3.4X33,160,888 - 33,220,843 (+)RGD
CeleraX108,198,021 - 108,255,504 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_851599 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAP14356 (Get FASTA)   NCBI Sequence Viewer  
  EDL85180 (Get FASTA)   NCBI Sequence Viewer  
  EDL85181 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037132
  ENSRNOP00000037132.1
  ENSRNOP00055035950
  ENSRNOP00060026489
  ENSRNOP00065037966
GenBank Protein Q80WE5 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_851599   ⟸   NM_181085
- Peptide Label: precursor
- UniProtKB: Q80WE5 (UniProtKB/Swiss-Prot),   A6KG99 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000037132   ⟸   ENSRNOT00000030400

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q80WE5-F1-model_v2 AlphaFold Q80WE5 1-220 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:727927 AgrOrtholog
BioCyc Gene G2FUF-1472 BioCyc
Ensembl Genes ENSRNOG00000027601 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055025479 UniProtKB/Swiss-Prot
  ENSRNOG00060018837 UniProtKB/Swiss-Prot
  ENSRNOG00065026834 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000030400 ENTREZGENE
  ENSRNOT00000030400.3 UniProtKB/Swiss-Prot
  ENSRNOT00055043966 UniProtKB/Swiss-Prot
  ENSRNOT00060032479 UniProtKB/Swiss-Prot
  ENSRNOT00065046287 UniProtKB/Swiss-Prot
InterPro LHFPL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:300286 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 300286 ENTREZGENE
PANTHER LHFPL TETRASPAN SUBFAMILY MEMBER 1 PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIPOMA HMGIC FUSION PARTNER-LIKE PROTEIN UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
Pfam L_HMGIC_fpl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lhfpl1 PhenoGen
RatGTEx ENSRNOG00000027601 RatGTEx
  ENSRNOG00055025479 RatGTEx
  ENSRNOG00060018837 RatGTEx
  ENSRNOG00065026834 RatGTEx
UniProt A6KG99 ENTREZGENE, UniProtKB/TrEMBL
  LHPL1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-07-05 Lhfpl1  LHFPL tetraspan subfamily member 1  Lhfpl1  lipoma HMGIC fusion partner-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-09-18 Lhfpl1  lipoma HMGIC fusion partner-like 1  Lhfp  lipoma HMGIC fusion partner  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2004-02-11 Lhfp  A kinase (PRKA) anchor protein 13  LOC300286  lipoma HMGIC fusion partner  Symbol updated to reflect Human and Mouse nomenclature 625702 APPROVED