Protein:PTPRO |
Protein Summary |
 Gene summary |
| Gene name: PTPRO | ASpdb.0 ID: 5800 | Gene | Gene symbol | PTPRO | Gene ID | 5800 |
| Gene name | protein tyrosine phosphatase receptor type O |
| Synonyms | GLEPP1|NPHS6|PTP-OC|PTP-U2|PTPROT|PTPU2|R-PTP-O |
| Cytomap | 12p12.3|12p13-p12 |
| Type of gene | protein-coding |
| Description | receptor-type tyrosine-protein phosphatase OPTP phiPTPase U2glomerular epithelial protein 1osteoclastic transmembrane protein-tyrosine phosphatasephosphotyrosine phosphatase U2protein tyrosine phosphatase PTP-U2 |
| Modification date | 20240403 |
| UniProtAcc | Q16827 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | PTPRO | GO:0004725 | protein tyrosine phosphatase activity | 19167335 |
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 |
| Q16827-1 | Q16827-1_2gjt_A.pdb | 2GJT | X-ray | 2.15 | A | 916 | 1208 |
| 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 |
| Q16827 | PTPRO | Q16827-1 | Q16827-3 | 1216 | 405 | 1 | 811 | Deletion | none | none | 0 | 0 |
| Q16827 | PTPRO | Q16827-1 | Q16827-4 | 1216 | 377 | 1 | 811 | Deletion | none | none | 0 | 0 |
| Q16827 | PTPRO | Q16827-1 | Q16827-4 | 1216 | 377 | 876 | 903 | Deletion | none | none | 64 | 64 |
| Q16827 | PTPRO | Q16827-1 | Q16827-5 | 1216 | 597 | 594 | 597 | Substitution | RIAN | VIFP | 594 | 597 |
| Q16827 | PTPRO | Q16827-1 | Q16827-5 | 1216 | 597 | 598 | 1216 | Deletion | none | none | 597 | 597 |
| Multiple sequence alignment of our canonical and alternatively spliced PTPRO |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PTPRO |
| UniProt-id | ENSG | ENST | ENSP |
| Q16827-1 | ENSG00000151490.15 | ENST00000281171.9 | ENSP00000281171.4 |
| Q16827-1 | ENSG00000151490.15 | ENST00000674261.1 | ENSP00000501538.1 |
| Q16827-1 | ENSG00000151490.15 | ENST00000674316.1 | ENSP00000501352.1 |
| Q16827-3 | ENSG00000151490.15 | ENST00000442921.7 | ENSP00000404188.2 |
| Q16827-3 | ENSG00000151490.15 | ENST00000445537.6 | ENSP00000393449.2 |
| Q16827-3 | ENSG00000151490.15 | ENST00000674388.1 | ENSP00000501494.1 |
| Q16827-4 | ENSG00000151490.15 | ENST00000542557.5 | ENSP00000437571.1 |
| Q16827-4 | ENSG00000151490.15 | ENST00000544244.5 | ENSP00000439234.1 |
| Q16827-5 | ENSG00000151490.15 | ENST00000543886.6 | ENSP00000444173.1 |
| UniProt-id | NM ID | NP ID |
| Q16827-1 | NM_030667.2 | NP_109592.1 |
| Q16827-3 | NM_030669.2 | NP_109594.1 |
| Q16827-3 | NM_030671.2 | NP_109596.1 |
| Q16827-4 | NM_030668.2 | NP_109593.1 |
| Q16827-4 | NM_030670.2 | NP_109595.1 |
| Amino acid sequences of our canonical and alternatively spliced PTPRO |
| accession_id | Protein sequence |
| Q16827-1 | MGHLPTGIHGARRLLPLLWLFVLFKNATAFHVTVQDDNNIVVSLEASDVISPASVYVVKITGESKNYFFEFEEFNSTLPPPVIFKASYHG LYYIITLVVVNGNVVTKPSRSITVLTKPLPVTSVSIYDYKPSPETGVLFEIHYPEKYNVFTRVNISYWEGKDFRTMLYKDFFKGKTVFNH WLPGMCYSNITFQLVSEATFNKSTLVEYSGVSHEPKQHRTAPYPPQNISVRIVNLNKNNWEEQSGNFPEESFMRSQDTIGKEKLFHFTEE TPEIPSGNISSGWPDFNSSDYETTSQPYWWDSASAAPESEDEFVSVLPMEYENNSTLSETEKSTSGSFSFFPVQMILTWLPPKPPTAFDG FHIHIEREENFTEYLMVDEEAHEFVAELKEPGKYKLSVTTFSSSGSCETRKSQSAKSLSFYISPSGEWIEELTEKPQHVSVHVLSSTTAL MSWTSSQENYNSTIVSVVSLTCQKQKESQRLEKQYCTQVNSSKPIIENLVPGAQYQVVIYLRKGPLIGPPSDPVTFAIVPTGIKDLMLYP LGPTAVVLSWTRPYLGVFRKYVVEMFYFNPATMTSEWTTYYEIAATVSLTASVRIANLLPAWYYNFRVTMVTWGDPELSCCDSSTISFIT APVAPEITSVEYFNSLLYISWTYGDDTTDLSHSRMLHWMVVAEGKKKIKKSVTRNVMTAILSLPPGDIYNLSVTACTERGSNTSMLRLVK LEPAPPKSLFAVNKTQTSVTLLWVEEGVADFFEVFCQQVGSSQKTKLQEPVAVSSHVVTISSLLPATAYNCSVTSFSHDSPSVPTFIAVS TMVTEMNPNVVVISVLAILSTLLIGLLLVTLIILRKKHLQMARECGAGTFVNFASLERDGKLPYNWRRSIFAFLTLLPSCLWTDYLLAFY INPWSKNGLKKRKLTNPVQLDDFDAYIKDMAKDSDYKFSLQFEELKLIGLDIPHFAADLPLNRCKNRYTNILPYDFSRVRLVSMNEEEGA DYINANYIPGYNSPQEYIATQGPLPETRNDFWKMVLQQKSQIIVMLTQCNEKRRVKCDHYWPFTEEPIAYGDITVEMISEEEQDDWACRH FRINYADEMQDVMHFNYTAWPDHGVPTANAAESILQFVHMVRQQATKSKGPMIIHCSAGVGRTGTFIALDRLLQHIRDHEFVDILGLVSE |
| Q16827-3 | MVTEMNPNVVVISVLAILSTLLIGLLLVTLIILRKKHLQMARECGAGTFVNFASLERDGKLPYNWRRSIFAFLTLLPSCLWTDYLLAFYI NPWSKNGLKKRKLTNPVQLDDFDAYIKDMAKDSDYKFSLQFEELKLIGLDIPHFAADLPLNRCKNRYTNILPYDFSRVRLVSMNEEEGAD YINANYIPGYNSPQEYIATQGPLPETRNDFWKMVLQQKSQIIVMLTQCNEKRRVKCDHYWPFTEEPIAYGDITVEMISEEEQDDWACRHF RINYADEMQDVMHFNYTAWPDHGVPTANAAESILQFVHMVRQQATKSKGPMIIHCSAGVGRTGTFIALDRLLQHIRDHEFVDILGLVSEM |
| Q16827-4 | MVTEMNPNVVVISVLAILSTLLIGLLLVTLIILRKKHLQMARECGAGTFVNFASLERDGKLPYNWSKNGLKKRKLTNPVQLDDFDAYIKD MAKDSDYKFSLQFEELKLIGLDIPHFAADLPLNRCKNRYTNILPYDFSRVRLVSMNEEEGADYINANYIPGYNSPQEYIATQGPLPETRN DFWKMVLQQKSQIIVMLTQCNEKRRVKCDHYWPFTEEPIAYGDITVEMISEEEQDDWACRHFRINYADEMQDVMHFNYTAWPDHGVPTAN AAESILQFVHMVRQQATKSKGPMIIHCSAGVGRTGTFIALDRLLQHIRDHEFVDILGLVSEMRSYRMSMVQTEEQYIFIHQCVQLMWMKK |
| Q16827-5 | MGHLPTGIHGARRLLPLLWLFVLFKNATAFHVTVQDDNNIVVSLEASDVISPASVYVVKITGESKNYFFEFEEFNSTLPPPVIFKASYHG LYYIITLVVVNGNVVTKPSRSITVLTKPLPVTSVSIYDYKPSPETGVLFEIHYPEKYNVFTRVNISYWEGKDFRTMLYKDFFKGKTVFNH WLPGMCYSNITFQLVSEATFNKSTLVEYSGVSHEPKQHRTAPYPPQNISVRIVNLNKNNWEEQSGNFPEESFMRSQDTIGKEKLFHFTEE TPEIPSGNISSGWPDFNSSDYETTSQPYWWDSASAAPESEDEFVSVLPMEYENNSTLSETEKSTSGSFSFFPVQMILTWLPPKPPTAFDG FHIHIEREENFTEYLMVDEEAHEFVAELKEPGKYKLSVTTFSSSGSCETRKSQSAKSLSFYISPSGEWIEELTEKPQHVSVHVLSSTTAL MSWTSSQENYNSTIVSVVSLTCQKQKESQRLEKQYCTQVNSSKPIIENLVPGAQYQVVIYLRKGPLIGPPSDPVTFAIVPTGIKDLMLYP |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| PTPRO (go to UniProt):Q16827 |
| 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 |
| Q16827 | Topological domain | 30 | 822 | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=1;End=811 |
| Q16827 | Topological domain | 30 | 822 | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=1;End=811 |
| Q16827 | Topological domain | 30 | 822 | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Substitution;Start=594;End=597 |
| Q16827 | Topological domain | 30 | 822 | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=598;End=1216 |
| Q16827 | Transmembrane | 823 | 843 | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=598;End=1216 |
| Q16827 | Topological domain | 844 | 1216 | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=876;End=903 |
| Q16827 | Topological domain | 844 | 1216 | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=598;End=1216 |
| Q16827 | Domain | 50 | 124 | Note=Fibronectin type-III 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 50 | 124 | Note=Fibronectin type-III 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 142 | 211 | Note=Fibronectin type-III 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 142 | 211 | Note=Fibronectin type-III 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 246 | 306 | Note=Fibronectin type-III 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 246 | 306 | Note=Fibronectin type-III 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 329 | 425 | Note=Fibronectin type-III 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 329 | 425 | Note=Fibronectin type-III 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 435 | 531 | Note=Fibronectin type-III 5;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 435 | 531 | Note=Fibronectin type-III 5;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 532 | 628 | Note=Fibronectin type-III 6;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 532 | 628 | Note=Fibronectin type-III 6;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 532 | 628 | Note=Fibronectin type-III 6;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Substitution;Start=594;End=597 |
| Q16827 | Domain | 532 | 628 | Note=Fibronectin type-III 6;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=598;End=1216 |
| Q16827 | Domain | 631 | 724 | Note=Fibronectin type-III 7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 631 | 724 | Note=Fibronectin type-III 7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 631 | 724 | Note=Fibronectin type-III 7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=598;End=1216 |
| Q16827 | Domain | 725 | 817 | Note=Fibronectin type-III 8;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 725 | 817 | Note=Fibronectin type-III 8;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=1;End=811 |
| Q16827 | Domain | 725 | 817 | Note=Fibronectin type-III 8;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 | Type=Deletion;Start=598;End=1216 |
| Q16827 | Domain | 938 | 1195 | Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160 | Type=Deletion;Start=598;End=1216 |
Gene Isoform Structures and Expression Levels for PTPRO |
| Gene structures of our canonical and alternative spliced genes of PTPRO * 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 Q16827-1 |
| 3D view using mol* of Q16827-3 |
| 3D view using mol* of Q16827-4 |
| 3D view using mol* of Q16827-5 |
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 Q16827-1 |
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| pLDDT distribution across the protein length of Q16827-3 |
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| pLDDT distribution across the protein length of Q16827-4 |
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| pLDDT distribution across the protein length of Q16827-5 |
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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 Q16827-1 |
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| Ramachandran plot of Q16827-3 |
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| Ramachandran plot of Q16827-5 |
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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 |
| Q16827-1 | 1.011 | 138 | 0.911 | 505.239 | 0.617 | 0.715 | 0.865 | 0.107 | 1.404 | 0.077 | 0.373 | 289,290,291,293,942,946,948,949,950,954,968,970,97 1,974,1037,1044,1046,1100,1101,1102,1103,1104,1136 ,1137,1138,1141,1142,1172,1176,1177,1180,1181,1182 ,1183,1184 |
| Q16827-3 | 0.985 | 118 | 1.032 | 302.869 | 0.631 | 0.625 | 0.829 | 0.66 | 0.867 | 0.761 | 1.09 | 190,191,192,194,195,219,220,221,301,304,305,308,31 1,312,314,315,317,318,319,320,321,342,343,345,346, 384,387,388,391 |
| Q16827-4 | 1.023 | 132 | 1.082 | 568.694 | 0.709 | 0.652 | 0.779 | 0.603 | 0.763 | 0.789 | 1.524 | 47,50,52,61,62,63,64,65,66,67,72,73,74,75,76,77,78 ,79,80,83,91,98,101,102,105,108,109,110,111,112,11 3,326,330,331,334 |
| Q16827-5 | 0.99 | 105 | 1.043 | 414.344 | 0.73 | 0.623 | 0.733 | 0.476 | 0.831 | 0.573 | 0.638 | 470,471,474,475,479,481,502,504,530,531,532,533,53 6,548,552,553,556,557,558,559,560,561,562,563,564, 585,586 |
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 Q16827-1_Q16827-1_2gjt_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 Q16827-1_2gjt_A_Q16827-3.pdb |
| 3D view using mol* of Q16827-1_2gjt_A_Q16827-4.pdb |
| 3D view using mol* of Q16827-1_2gjt_A_Q16827-5.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q16827-1_Q16827-3.pdb |
| 3D view using mol* of Q16827-1_Q16827-4.pdb |
| 3D view using mol* of Q16827-1_Q16827-5.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q16827-1_vs_Q16827-3.png |
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| ./stats/secondary_structure/figure/Q16827-1_vs_Q16827-4.png |
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| ./stats/secondary_structure/figure/Q16827-1_vs_Q16827-5.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q16827-1_vs_Q16827-3.png |
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| ./stats/relative_asa/Q16827-1_vs_Q16827-4.png |
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| ./stats/relative_asa/Q16827-1_vs_Q16827-5.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 PTPRO |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to PTPRO |
| Previous studies relating to the alternative splicing of PTPRO and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| PTPRO | 12949066 | Expression of a structurally unique osteoclastic protein-tyrosine phosphatase is driven by an alternative intronic, cell type-specific promoter. | An osteoclastic protein-tyrosine phosphatase (PTP-oc), essential for osteoclast activity, shows sequence identity with the intracellular domain of GLEPP1, a renal receptor-like transmembrane PTP. PTP-oc has been assumed to be a truncated variant of GLEPP1, resulting from alternative splicing. However, the 5'-untranslated region sequence of PTP-oc mRNA contains 217 bp from an intron of GLEPP1. There are no splicing acceptor sites at the PTP-oc transcription site. The intronic sequence flanking the 5' end of the PTP-oc transcription start site contains potential promoter elements essential for transcriptional initiation. To test the hypothesis that the PTP-oc gene has an alternative, tissue-specific, intronic promoter, the promoter activity of a 1.3-kb PCR fragment covering the 5'-flanking region of the PTP-oc gene was measured. The putative PTP-oc promoter fragment showed strong promoter activity in U937 cells. Mutation of the putative TATA box within the PTP-oc promoter abolished 60-90% of its promoter activity. The PTP-oc promoter fragment showed strong promoter activity in cells that express PTP-oc (U937 cells and RAW264.7 cells) but not in cells that do not express the enzyme (skin fibroblasts, TE85 cells, and HEK293 cells). These findings strongly support the conclusion that the 1.3-kb intronic fragment contains the tissue-specific, PTP-oc proximal promoter. Deletion and functional analyses indicate that the proximal 5' sequence flanking the TATA box of the PTP-oc contains potential repressor elements. The removal of the putative repressor elements led to the apparent loss of tissue specificity. In summary, we conclude that an intronic promoter within the GLEPP1 gene drives the expression of the PTP-oc in a cell type-specific manner. This GLEPP1/PTP-oc gene system is one of the very few systems in which two important tissue-specific enzymes are derived from the same gene by the use of alternative intronic promoters. | D015479 | Leukemia, Myelomonocytic, Acute |
Clinically important variants in PTPRO |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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