Human Gene LHFPL1 (ENST00000371968.8) from GENCODE V44
  Description: Homo sapiens LHFPL tetraspan subfamily member 1 (LHFPL1), mRNA. (from RefSeq NM_178175)
RefSeq Summary (NM_178175): This gene is a member of the lipoma HMGIC fusion partner (LHFP) gene family, which is a subset of the superfamily of tetraspan transmembrane protein encoding genes. Mutations in one LHFP-like gene result in deafness in humans and mice, and a second LHFP-like gene is fused to a high-mobility group gene in a translocation-associated lipoma. Alternatively spliced transcript variants have been found, but their biological validity has not been determined. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000371968.8
Gencode Gene: ENSG00000182508.14
Transcript (Including UTRs)
   Position: hg38 chrX:112,630,648-112,679,938 Size: 49,291 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg38 chrX:112,631,420-112,671,390 Size: 39,971 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:112,630,648-112,679,938)mRNA (may differ from genome)Protein (220 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHGNC
HPRDLynxMGIneXtProtOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LHPL1_HUMAN
DESCRIPTION: RecName: Full=Lipoma HMGIC fusion partner-like 1 protein; Flags: Precursor;
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
TISSUE SPECIFICITY: Widely expressed. Expressed at high levels in lung, thymus, skeletal muscle, colon and ovary.
SIMILARITY: Belongs to the LHFP family.
SEQUENCE CAUTION: Sequence=AAQ88575.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.45 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 11.55 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -26.00124-0.210 Picture PostScript Text
3' UTR -214.80772-0.278 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019372 - Lipome_HGMIC_fus_partner-like

Pfam Domains:
PF10242 - Lipoma HMGIC fusion partner-like protein

ModBase Predicted Comparative 3D Structure on Q86WI0
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  LP896582 - Sequence 1446 from Patent EP3253886.
AY358208 - Homo sapiens clone DNA145556 VTYC5824 (UNQ5824) mRNA, complete cds.
AY217350 - Homo sapiens lipoma HMGIC fusion partner-like 1 (LHFPL1) mRNA, complete cds.
JD110843 - Sequence 91867 from Patent EP1572962.
JD554438 - Sequence 535462 from Patent EP1572962.
JD348204 - Sequence 329228 from Patent EP1572962.
JD350382 - Sequence 331406 from Patent EP1572962.
AK289946 - Homo sapiens cDNA FLJ76001 complete cds, highly similar to Homo sapiens lipoma HMGIC fusion partner-like 1 (LHFPL1), mRNA.
JD149952 - Sequence 130976 from Patent EP1572962.
BC100785 - Homo sapiens lipoma HMGIC fusion partner-like 1, mRNA (cDNA clone MGC:118798 IMAGE:40000445), complete cds.
BC100786 - Homo sapiens lipoma HMGIC fusion partner-like 1, mRNA (cDNA clone MGC:118800 IMAGE:40000448), complete cds.
BC100787 - Homo sapiens lipoma HMGIC fusion partner-like 1, mRNA (cDNA clone IMAGE:40000449), complete cds.
JD483143 - Sequence 464167 from Patent EP1572962.
JD235017 - Sequence 216041 from Patent EP1572962.
JD380390 - Sequence 361414 from Patent EP1572962.
JD456360 - Sequence 437384 from Patent EP1572962.
JD481017 - Sequence 462041 from Patent EP1572962.
JD077148 - Sequence 58172 from Patent EP1572962.
KJ896083 - Synthetic construct Homo sapiens clone ccsbBroadEn_05477 LHFPL1 gene, encodes complete protein.
KJ904208 - Synthetic construct Homo sapiens clone ccsbBroadEn_13602 LHFPL1 gene, encodes complete protein.
JD421161 - Sequence 402185 from Patent EP1572962.
JD448725 - Sequence 429749 from Patent EP1572962.
JD176010 - Sequence 157034 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K1N1, ENST00000371968.1, ENST00000371968.2, ENST00000371968.3, ENST00000371968.4, ENST00000371968.5, ENST00000371968.6, ENST00000371968.7, LHPL1_HUMAN, NM_178175, Q496M9, Q496N0, Q6UXU2, Q86WI0, uc004epq.1, uc004epq.2, uc004epq.3, uc004epq.4, uc004epq.5, UNQ5824/PRO19643
UCSC ID: ENST00000371968.8
RefSeq Accession: NM_178175
Protein: Q86WI0 (aka LHPL1_HUMAN)
CCDS: CCDS14562.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.