Human Gene PKHD1L1 (ENST00000378402.10_4) from GENCODE V47lift37
  Description: PKHD1 like 1 (from RefSeq NM_177531.6)
Gencode Transcript: ENST00000378402.10_4
Gencode Gene: ENSG00000205038.12_10
Transcript (Including UTRs)
   Position: hg19 chr8:110,374,690-110,549,436 Size: 174,747 Total Exon Count: 78 Strand: +
Coding Region
   Position: hg19 chr8:110,374,810-110,542,319 Size: 167,510 Coding Exon Count: 78 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:110,374,690-110,549,436)mRNA (may differ from genome)Protein (4243 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PKHL1_HUMAN
DESCRIPTION: RecName: Full=Fibrocystin-L; AltName: Full=Polycystic kidney and hepatic disease 1-like protein 1; Short=PKHD1-like protein 1; Flags: Precursor;
SUBCELLULAR LOCATION: Membrane; Single-pass membrane protein (Potential).
TISSUE SPECIFICITY: Ubiquitous. Expressed in spleen and thymus as well as in activated T-cells and B-lymphoblasts.
SIMILARITY: Contains 2 G8 domains.
SIMILARITY: Contains 14 IPT/TIG domains.
SIMILARITY: Contains 9 PbH1 repeats.
SEQUENCE CAUTION: Sequence=AAH93096.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

-  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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 28.53 RPKM in Thyroid
Total median expression: 55.00 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 -46.00120-0.383 Picture PostScript Text
3' UTR -1895.907117-0.266 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
IPR008972 - Cupredoxin
IPR019316 - G8_domain
IPR013783 - Ig-like_fold
IPR014756 - Ig_E-set
IPR002909 - IPT_TIG_rcpt
IPR011658 - PA14
IPR006626 - PbH1
IPR011050 - Pectin_lyase_fold/virulence

Pfam Domains:
PF01833 - IPT/TIG domain
PF07691 - PA14 domain
PF10162 - G8 domain

SCOP Domains:
48726 - Immunoglobulin
81296 - E set domains
49503 - Cupredoxins
51126 - Pectin lyase-like
51338 - Composite domain of metallo-dependent hydrolases
56988 - Anthrax protective antigen

ModBase Predicted Comparative 3D Structure on Q86WI1
FrontTopSide
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0038023 signaling receptor activity

Biological Process:
GO:0006955 immune response
GO:0007165 signal transduction

Cellular Component:
GO:0005615 extracellular space
GO:0005829 cytosol
GO:0005929 cilium
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AY219181 - Homo sapiens fibrocystin L mRNA, complete cds.
AK131338 - Homo sapiens cDNA FLJ16352 fis, clone TESTI4000155.
JD404809 - Sequence 385833 from Patent EP1572962.
BC093096 - Homo sapiens polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1, mRNA (cDNA clone IMAGE:30330124), partial cds.
AK128617 - Homo sapiens cDNA FLJ46776 fis, clone TRACH3026650, highly similar to Actin cross-linking family protein 7.
JD296807 - Sequence 277831 from Patent EP1572962.
AL133640 - Homo sapiens mRNA; cDNA DKFZp586C1021 (from clone DKFZp586C1021).
JD154633 - Sequence 135657 from Patent EP1572962.
JD434215 - Sequence 415239 from Patent EP1572962.
JD349755 - Sequence 330779 from Patent EP1572962.
JD509072 - Sequence 490096 from Patent EP1572962.
JD553889 - Sequence 534913 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000378402.1, ENST00000378402.2, ENST00000378402.3, ENST00000378402.4, ENST00000378402.5, ENST00000378402.6, ENST00000378402.7, ENST00000378402.8, ENST00000378402.9, NM_177531, PKHL1_HUMAN, Q567P2, Q86WI1, Q9UF27, uc318ogm.1, uc318ogm.2
UCSC ID: ENST00000378402.10_4
RefSeq Accession: NM_177531.6
Protein: Q86WI1 (aka PKHL1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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