Protein:PKD2L1 |
Protein Summary |
 Gene summary |
| Gene name: PKD2L1 | ASpdb.0 ID: 9033 | Gene | Gene symbol | PKD2L1 | Gene ID | 9033 |
| Gene name | polycystin 2 like 1, transient receptor potential cation channel |
| Synonyms | PCL|PKD2L|PKDL|TRPP3 |
| Cytomap | 10q24.31 |
| Type of gene | protein-coding |
| Description | polycystin-2-like protein 1polycystic kidney disease 2-like 1 proteinpolycystin-2 homologpolycystin-2L1polycystin-Lpolycystin-L1transient receptor potential cation channel, subfamily P, member 3 |
| Modification date | 20240305 |
| UniProtAcc | Q9P0L9 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | PKD2L1 | GO:0005227 | calcium-activated cation channel activity | 10517637|11959145 |
| Gene | PKD2L1 | GO:0005261 | monoatomic cation channel activity | 17944866|30004384 |
| Gene | PKD2L1 | GO:0005262 | calcium channel activity | 24336289 |
| Gene | PKD2L1 | GO:0005272 | sodium channel activity | 10517637 |
| Gene | PKD2L1 | GO:0005509 | calcium ion binding | 22193359 |
| Gene | PKD2L1 | GO:0005829 | cytosol | - |
| Gene | PKD2L1 | GO:0005886 | plasma membrane | 20538909 |
| Gene | PKD2L1 | GO:0015269 | calcium-activated potassium channel activity | 10517637 |
| Gene | PKD2L1 | GO:0015629 | actin cytoskeleton | - |
| Gene | PKD2L1 | GO:0016020 | membrane | 19812697 |
| Gene | PKD2L1 | GO:0034704 | calcium channel complex | 24336289 |
| Gene | PKD2L1 | GO:0035725 | sodium ion transmembrane transport | 10517637 |
| Gene | PKD2L1 | GO:0043231 | intracellular membrane-bounded organelle | 17944866 |
| Gene | PKD2L1 | GO:0051289 | protein homotetramerization | 30004384 |
| Gene | PKD2L1 | GO:0071805 | potassium ion transmembrane transport | 10517637 |
| Gene | PKD2L1 | GO:0097730 | non-motile cilium | 24336289 |
| Gene | PKD2L1 | GO:0098662 | inorganic cation transmembrane transport | 30004384 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| Q9P0L9-1 | Q9P0L9-1_6du8_A.pdb | 6DU8 | EM | 3.11 | A | 101 | 561 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| Q9P0L9 | PKD2L1 | Q9P0L9-1 | Q9P0L9-2 | 805 | 760 | 751 | 760 | Substitution | KEQAIWKHPQ | RFPIKEKRKP | 751 | 760 |
| Q9P0L9 | PKD2L1 | Q9P0L9-1 | Q9P0L9-2 | 805 | 760 | 761 | 805 | Deletion | none | none | 760 | 760 |
| Q9P0L9 | PKD2L1 | Q9P0L9-1 | Q9P0L9-3 | 805 | 730 | 245 | 319 | Deletion | none | none | 244 | 244 |
| Q9P0L9 | PKD2L1 | Q9P0L9-1 | Q9P0L9-4 | 805 | 685 | 225 | 344 | Deletion | none | none | 224 | 224 |
| Q9P0L9 | PKD2L1 | Q9P0L9-1 | Q9P0L9-5 | 805 | 776 | 638 | 666 | Deletion | none | none | 637 | 637 |
| Multiple sequence alignment of our canonical and alternatively spliced PKD2L1 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PKD2L1 |
| UniProt-id | ENSG | ENST | ENSP |
| Q9P0L9-1 | ENSG00000107593.17 | ENST00000318222.4 | ENSP00000325296.3 |
| UniProt-id | NM ID | NP ID |
| Q9P0L9-1 | NM_016112.2 | NP_057196.2 |
| Amino acid sequences of our canonical and alternatively spliced PKD2L1 |
| accession_id | Protein sequence |
| Q9P0L9-1 | MNAVGSPEGQELQKLGSGAWDNPAYSGPPSPHGTLRVCTISSTGPLQPQPKKPEDEPQETAYRTQVSSCCLHICQGIRGLWGTTLTENTA ENRELYIKTTLRELLVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDTGVSFQAISSMADFWDFAQGPLLDSLYWTKWYNNQSL GHGSHSFIYYENMLLGVPRLRQLKVRNDSCVVHEDFREDILSCYDVYSPDKEEQLPFGPFNGTAWTYHSQDELGGFSHWGRLTSYSGGGY YLDLPGSRQGSAEALRALQEGLWLDRGTRVVFIDFSVYNANINLFCVLRLVVEFPATGGAIPSWQIRTVKLIRYVSNWDFFIVGCEVIFC VFIFYYVVEEILELHIHRLRYLSSIWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPNTYADFEFLAFWQTQYNNMNAVNLFFAW IKIFKYISFNKTMTQLSSTLARCAKDILGFAVMFFIVFFAYAQLGYLLFGTQVENFSTFIKCIFTQFRIILGDFDYNAIDNANRILGPAY FVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDELQLSDLLKQGYNKTLLRLRLRKERVSDVQKVLQGGEQEIQFEDFTNTLRELGH AEHEITELTATFTKFDRDGNRILDEKEQEKMRQDLEEERVALNTEIEKLGRSIVSSPQGKSGPEAARAGGWVSGEEFYMLTRRVLQLETV |
| Q9P0L9-2 | MNAVGSPEGQELQKLGSGAWDNPAYSGPPSPHGTLRVCTISSTGPLQPQPKKPEDEPQETAYRTQVSSCCLHICQGIRGLWGTTLTENTA ENRELYIKTTLRELLVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDTGVSFQAISSMADFWDFAQGPLLDSLYWTKWYNNQSL GHGSHSFIYYENMLLGVPRLRQLKVRNDSCVVHEDFREDILSCYDVYSPDKEEQLPFGPFNGTAWTYHSQDELGGFSHWGRLTSYSGGGY YLDLPGSRQGSAEALRALQEGLWLDRGTRVVFIDFSVYNANINLFCVLRLVVEFPATGGAIPSWQIRTVKLIRYVSNWDFFIVGCEVIFC VFIFYYVVEEILELHIHRLRYLSSIWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPNTYADFEFLAFWQTQYNNMNAVNLFFAW IKIFKYISFNKTMTQLSSTLARCAKDILGFAVMFFIVFFAYAQLGYLLFGTQVENFSTFIKCIFTQFRIILGDFDYNAIDNANRILGPAY FVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDELQLSDLLKQGYNKTLLRLRLRKERVSDVQKVLQGGEQEIQFEDFTNTLRELGH AEHEITELTATFTKFDRDGNRILDEKEQEKMRQDLEEERVALNTEIEKLGRSIVSSPQGKSGPEAARAGGWVSGEEFYMLTRRVLQLETV |
| Q9P0L9-3 | MNAVGSPEGQELQKLGSGAWDNPAYSGPPSPHGTLRVCTISSTGPLQPQPKKPEDEPQETAYRTQVSSCCLHICQGIRGLWGTTLTENTA ENRELYIKTTLRELLVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDTGVSFQAISSMADFWDFAQGPLLDSLYWTKWYNNQSL GHGSHSFIYYENMLLGVPRLRQLKVRNDSCVVHEDFREDILSCYDVYSPDKEEQLPFGPFNGTALVVEFPATGGAIPSWQIRTVKLIRYV SNWDFFIVGCEVIFCVFIFYYVVEEILELHIHRLRYLSSIWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPNTYADFEFLAFWQ TQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAVMFFIVFFAYAQLGYLLFGTQVENFSTFIKCIFTQFRIILGDFD YNAIDNANRILGPAYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDELQLSDLLKQGYNKTLLRLRLRKERVSDVQKVLQGGEQE IQFEDFTNTLRELGHAEHEITELTATFTKFDRDGNRILDEKEQEKMRQDLEEERVALNTEIEKLGRSIVSSPQGKSGPEAARAGGWVSGE EFYMLTRRVLQLETVLEGVVSQIDAVGSKLKMLERKGWLAPSPGVKEQAIWKHPQPAPAVTPDPWGVQGGQESEVPYKREEEALEERRLS |
| Q9P0L9-4 | MNAVGSPEGQELQKLGSGAWDNPAYSGPPSPHGTLRVCTISSTGPLQPQPKKPEDEPQETAYRTQVSSCCLHICQGIRGLWGTTLTENTA ENRELYIKTTLRELLVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDTGVSFQAISSMADFWDFAQGPLLDSLYWTKWYNNQSL GHGSHSFIYYENMLLGVPRLRQLKVRNDSCVVHEDFREDILSCYVSNWDFFIVGCEVIFCVFIFYYVVEEILELHIHRLRYLSSIWNILD LVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPNTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGF AVMFFIVFFAYAQLGYLLFGTQVENFSTFIKCIFTQFRIILGDFDYNAIDNANRILGPAYFVTYVFFVFFVLLNMFLAIINDTYSEVKEE LAGQKDELQLSDLLKQGYNKTLLRLRLRKERVSDVQKVLQGGEQEIQFEDFTNTLRELGHAEHEITELTATFTKFDRDGNRILDEKEQEK MRQDLEEERVALNTEIEKLGRSIVSSPQGKSGPEAARAGGWVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGSKLKMLERKGWLAPSPGV |
| Q9P0L9-5 | MNAVGSPEGQELQKLGSGAWDNPAYSGPPSPHGTLRVCTISSTGPLQPQPKKPEDEPQETAYRTQVSSCCLHICQGIRGLWGTTLTENTA ENRELYIKTTLRELLVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDTGVSFQAISSMADFWDFAQGPLLDSLYWTKWYNNQSL GHGSHSFIYYENMLLGVPRLRQLKVRNDSCVVHEDFREDILSCYDVYSPDKEEQLPFGPFNGTAWTYHSQDELGGFSHWGRLTSYSGGGY YLDLPGSRQGSAEALRALQEGLWLDRGTRVVFIDFSVYNANINLFCVLRLVVEFPATGGAIPSWQIRTVKLIRYVSNWDFFIVGCEVIFC VFIFYYVVEEILELHIHRLRYLSSIWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPNTYADFEFLAFWQTQYNNMNAVNLFFAW IKIFKYISFNKTMTQLSSTLARCAKDILGFAVMFFIVFFAYAQLGYLLFGTQVENFSTFIKCIFTQFRIILGDFDYNAIDNANRILGPAY FVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDELQLSDLLKQGYNKTLLRLRLRKERVSDVQKVLQGGEQEIQFEDFTNTLRELGH AEHEITEEERVALNTEIEKLGRSIVSSPQGKSGPEAARAGGWVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGSKLKMLERKGWLAPSPG |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| PKD2L1 (go to UniProt):Q9P0L9 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Q9P0L9 | Topological domain | 125 | 356 | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:30004384;Dbxref=PMID:30004384 | Type=Deletion;Start=245;End=319 |
| Q9P0L9 | Topological domain | 125 | 356 | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:30004384;Dbxref=PMID:30004384 | Type=Deletion;Start=225;End=344 |
| Q9P0L9 | Topological domain | 558 | 805 | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:30004384;Dbxref=PMID:30004384 | Type=Substitution;Start=751;End=760 |
| Q9P0L9 | Topological domain | 558 | 805 | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:30004384;Dbxref=PMID:30004384 | Type=Deletion;Start=761;End=805 |
| Q9P0L9 | Topological domain | 558 | 805 | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:30004384;Dbxref=PMID:30004384 | Type=Deletion;Start=638;End=666 |
| Q9P0L9 | Domain | 633 | 668 | Note=EF-hand;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=638;End=666 |
| Q9P0L9 | Region | 704 | 763 | Note=Required for homooligomerization | Type=Substitution;Start=751;End=760 |
| Q9P0L9 | Region | 704 | 763 | Note=Required for homooligomerization | Type=Deletion;Start=761;End=805 |
| Q9P0L9 | Region | 759 | 805 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Substitution;Start=751;End=760 |
| Q9P0L9 | Region | 759 | 805 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=761;End=805 |
| Q9P0L9 | Coiled coil | 650 | 686 | Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=638;End=666 |
| Q9P0L9 | Compositional bias | 779 | 799 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=761;End=805 |
Gene Isoform Structures and Expression Levels for PKD2L1 |
| Gene structures of our canonical and alternative spliced genes of PKD2L1 * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of Q9P0L9-1 |
| 3D view using mol* of Q9P0L9-2 |
| 3D view using mol* of Q9P0L9-3 |
| 3D view using mol* of Q9P0L9-4 |
| 3D view using mol* of Q9P0L9-5 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of Q9P0L9-1 |
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| pLDDT distribution across the protein length of Q9P0L9-2 |
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| pLDDT distribution across the protein length of Q9P0L9-3 |
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| pLDDT distribution across the protein length of Q9P0L9-4 |
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| pLDDT distribution across the protein length of Q9P0L9-5 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of Q9P0L9-1 |
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| Ramachandran plot of Q9P0L9-3 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| Q9P0L9-1 | 1.146 | 80 | 1.228 | 134.456 | 0.424 | 0.831 | 1.181 | 3.935 | 0.343 | 11.482 | 0.59 | 114,117,118,121,343,353,356,357,359,360,396,397,40 0,401,404,438,439,441,442,445 |
| Q9P0L9-2 | 1.065 | 69 | 1.153 | 120.05 | 0.555 | 0.75 | 0.976 | 3.398 | 0.241 | 14.117 | 0.699 | 114,117,118,121,356,357,359,360,400,401,404,438,44 2,445 |
| Q9P0L9-3 | 1.097 | 346 | 1.154 | 1376.802 | 0.542 | 0.754 | 0.877 | 1.161 | 0.733 | 1.585 | 0.722 | 129,133,137,148,154,157,160,161,165,166,169,170,18 8,192,193,194,195,196,197,198,199,200,201,202,203, 204,205,224,225,226,227,237,242,243,244,245,246,24 7,248,249,250,251,260,261,262,263,264,266,343,350, 351,352,353,354,356,357,358 |
| Q9P0L9-4 | 1.101 | 76 | 1.172 | 119.021 | 0.476 | 0.807 | 1.067 | 3.552 | 0.404 | 8.785 | 0.79 | 114,117,118,121,236,237,239,240,280,281,284,318,32 2,325 |
| Q9P0L9-5 | 1.042 | 455 | 1.062 | 1113.035 | 0.537 | 0.751 | 0.962 | 0.855 | 1.009 | 0.848 | 1.035 | 13,15,16,17,18,19,20,21,22,23,24,25,26,27,28,80,82 ,83,84,85,87,88,89,90,93,96,97,99,100,102,103,106, 107,110,365,366,369,370,373,377,380,381,383,384,38 5,386,387,389,390,393,394,451,452,454,455,456,457, 458,459,461,463,464,466,467,468,469,470,471,472,47 5,476,560,564,571,574,575,576,577,578,580 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of Q9P0L9-1_Q9P0L9-1_6du8_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q9P0L9-1_6du8_A_Q9P0L9-2.pdb |
| 3D view using mol* of Q9P0L9-1_6du8_A_Q9P0L9-3.pdb |
| 3D view using mol* of Q9P0L9-1_6du8_A_Q9P0L9-4.pdb |
| 3D view using mol* of Q9P0L9-1_6du8_A_Q9P0L9-5.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q9P0L9-1_Q9P0L9-2.pdb |
| 3D view using mol* of Q9P0L9-1_Q9P0L9-3.pdb |
| 3D view using mol* of Q9P0L9-1_Q9P0L9-4.pdb |
| 3D view using mol* of Q9P0L9-1_Q9P0L9-5.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q9P0L9-1_vs_Q9P0L9-2.png |
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| ./stats/secondary_structure/figure/Q9P0L9-1_vs_Q9P0L9-3.png |
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| ./stats/secondary_structure/figure/Q9P0L9-1_vs_Q9P0L9-4.png |
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| ./stats/secondary_structure/figure/Q9P0L9-1_vs_Q9P0L9-5.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q9P0L9-1_vs_Q9P0L9-2.png |
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| ./stats/relative_asa/Q9P0L9-1_vs_Q9P0L9-3.png |
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| ./stats/relative_asa/Q9P0L9-1_vs_Q9P0L9-4.png |
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| ./stats/relative_asa/Q9P0L9-1_vs_Q9P0L9-5.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to PKD2L1 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to PKD2L1 |
| Previous studies relating to the alternative splicing of PKD2L1 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| PKD2L1 | 10602992 | The human polycystic kidney disease 2-like (PKDL) gene: exon/intron structure and evidence for a novel splicing mechanism. | Polycystin-L is a member of the expanding family of polycystins. Mutations in polycystin-1 or -2 cause human autosomal dominant polycystic kidney disease (ADPKD). The mouse ortholog of PKDL, Pkdl, is deleted in a mouse line with renal and retinal defects. We recently have shown that polycystin-L has calcium channel properties. In the current study, we determined the exon/intron organization of the PKDL gene and its alternative splicing. We show that PKDL has 16 exons. All splice acceptor/donor sites for these exons conform to the GT-AG rule. The positions of introns and the sizes of exons in the PKDL gene are very similar to those of PKD2, except for the last two 3' end exons. RT-PCR demonstrates the existence of at least three polycystin-L splice variants: PKDL(Delta5), PKDL(Delta456), and PKDL(Delta15) that are expressed in a tissue-specific manner. In addition, we have localized polymorphic marker D10S603 to intron 4 and exon 5 of PKDL. Elucidation of the gene structure, exact location, and alternative splicing patterns of PKDL will facilitate its evaluation as a candidate gene in cystic or other genetic disorders. | D016891 | Polycystic Kidney, Autosomal Dominant |
Clinically important variants in PKD2L1 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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