Protein:PTPRN |
Protein Summary |
 Gene summary |
| Gene name: PTPRN | ASpdb.0 ID: 5798 | Gene | Gene symbol | PTPRN | Gene ID | 5798 |
| Gene name | protein tyrosine phosphatase receptor type N |
| Synonyms | IA-2|IA-2/PTP|IA2|ICA512|R-PTP-N |
| Cytomap | 2q35 |
| Type of gene | protein-coding |
| Description | receptor-type tyrosine-protein phosphatase-like NICA 512PTP IA-2insulinoma-associated tyrosine-phosphatase-like proteinislet cell antigen 2islet cell antigen 512islet cell autoantigen 3protein tyrosine phosphatase-like N |
| Modification date | 20240411 |
| UniProtAcc | Q16849 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | PTPRN | GO:0000302 | response to reactive oxygen species | 18048354 |
| Gene | PTPRN | GO:0005634 | nucleus | 15596545 |
| Gene | PTPRN | GO:0008134 | transcription factor binding | 16622421 |
| Gene | PTPRN | GO:0044389 | ubiquitin-like protein ligase binding | 15596545 |
| Gene | PTPRN | GO:0045944 | positive regulation of transcription by RNA polymerase II | 15596545 |
| Gene | PTPRN | GO:1904692 | positive regulation of type B pancreatic cell proliferation | 18178618 |
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 |
| Q16849-1 | Q16849-1_2i1y_B.pdb | 2I1Y | X-ray | 2.23 | B | 687 | 976 |
| 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 |
| Q16849 | PTPRN | Q16849-1 | Q16849-2 | 979 | 950 | 479 | 508 | Substitution | KPLSLAAGVKLLEILAEHVHMSSGSFINIS | N | 479 | 479 |
| Q16849 | PTPRN | Q16849-1 | Q16849-3 | 979 | 889 | 1 | 90 | Deletion | none | none | 0 | 0 |
| Multiple sequence alignment of our canonical and alternatively spliced PTPRN |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PTPRN |
| UniProt-id | ENSG | ENST | ENSP |
| Q16849-1 | ENSG00000054356.14 | ENST00000295718.7 | ENSP00000295718.2 |
| Q16849-2 | ENSG00000054356.14 | ENST00000409251.7 | ENSP00000386638.3 |
| Q16849-3 | ENSG00000054356.14 | ENST00000423636.6 | ENSP00000392598.2 |
| UniProt-id | NM ID | NP ID |
| Q16849-1 | NM_002846.3 | NP_002837.1 |
| Q16849-2 | NM_001199763.1 | NP_001186692.1 |
| Q16849-3 | NM_001199764.1 | NP_001186693.1 |
| Amino acid sequences of our canonical and alternatively spliced PTPRN |
| accession_id | Protein sequence |
| Q16849-1 | MRRPRRPGGLGGSGGLRLLLCLLLLSSRPGGCSAVSAHGCLFDRRLCSHLEVCIQDGLFGQCQVGVGQARPLLQVTSPVLQRLQGVLRQL MSQGLSWHDDLTQYVISQEMERIPRLRPPEPRPRDRSGLAPKRPGPAGELLLQDIPTGSAPAAQHRLPQPPVGKGGAGASSSLSPLQAEL LPPLLEHLLLPPQPPHPSLSYEPALLQPYLFHQFGSRDGSRVSEGSPGMVSVGPLPKAEAPALFSRTASKGIFGDHPGHSYGDLPGPSPA QLFQDSGLLYLAQELPAPSRARVPRLPEQGSSSRAEDSPEGYEKEGLGDRGEKPASPAVQPDAALQRLAAVLAGYGVELRQLTPEQLSTL LTLLQLLPKGAGRNPGGVVNVGADIKKTMEGPVEGRDTAELPARTSPMPGHPTASPTSSEVQQVPSPVSSEPPKAARPPVTPVLLEKKSP LGQSQPTVAGQPSARPAAEEYGYIVTDQKPLSLAAGVKLLEILAEHVHMSSGSFINISVVGPALTFRIRHNEQNLSLADVTQQAGLVKSE LEAQTGLQILQTGVGQREEAAAVLPQTAHSTSPMRSVLLTLVALAGVAGLLVALAVALCVRQHARQQDKERLAALGPEGAHGDTTFEYQD LCRQHMATKSLFNRAEGPPEPSRVSSVSSQFSDAAQASPSSHSSTPSWCEEPAQANMDISTGHMILAYMEDHLRNRDRLAKEWQALCAYQ AEPNTCATAQGEGNIKKNRHPDFLPYDHARIKLKVESSPSRSDYINASPIIEHDPRMPAYIATQGPLSHTIADFWQMVWESGCTVIVMLT PLVEDGVKQCDRYWPDEGASLYHVYEVNLVSEHIWCEDFLVRSFYLKNVQTQETRTLTQFHFLSWPAEGTPASTRPLLDFRRKVNKCYRG |
| Q16849-2 | MRRPRRPGGLGGSGGLRLLLCLLLLSSRPGGCSAVSAHGCLFDRRLCSHLEVCIQDGLFGQCQVGVGQARPLLQVTSPVLQRLQGVLRQL MSQGLSWHDDLTQYVISQEMERIPRLRPPEPRPRDRSGLAPKRPGPAGELLLQDIPTGSAPAAQHRLPQPPVGKGGAGASSSLSPLQAEL LPPLLEHLLLPPQPPHPSLSYEPALLQPYLFHQFGSRDGSRVSEGSPGMVSVGPLPKAEAPALFSRTASKGIFGDHPGHSYGDLPGPSPA QLFQDSGLLYLAQELPAPSRARVPRLPEQGSSSRAEDSPEGYEKEGLGDRGEKPASPAVQPDAALQRLAAVLAGYGVELRQLTPEQLSTL LTLLQLLPKGAGRNPGGVVNVGADIKKTMEGPVEGRDTAELPARTSPMPGHPTASPTSSEVQQVPSPVSSEPPKAARPPVTPVLLEKKSP LGQSQPTVAGQPSARPAAEEYGYIVTDQNVVGPALTFRIRHNEQNLSLADVTQQAGLVKSELEAQTGLQILQTGVGQREEAAAVLPQTAH STSPMRSVLLTLVALAGVAGLLVALAVALCVRQHARQQDKERLAALGPEGAHGDTTFEYQDLCRQHMATKSLFNRAEGPPEPSRVSSVSS QFSDAAQASPSSHSSTPSWCEEPAQANMDISTGHMILAYMEDHLRNRDRLAKEWQALCAYQAEPNTCATAQGEGNIKKNRHPDFLPYDHA RIKLKVESSPSRSDYINASPIIEHDPRMPAYIATQGPLSHTIADFWQMVWESGCTVIVMLTPLVEDGVKQCDRYWPDEGASLYHVYEVNL VSEHIWCEDFLVRSFYLKNVQTQETRTLTQFHFLSWPAEGTPASTRPLLDFRRKVNKCYRGRSCPIIVHCSDGAGRTGTYILIDMVLNRM |
| Q16849-3 | MSQGLSWHDDLTQYVISQEMERIPRLRPPEPRPRDRSGLAPKRPGPAGELLLQDIPTGSAPAAQHRLPQPPVGKGGAGASSSLSPLQAEL LPPLLEHLLLPPQPPHPSLSYEPALLQPYLFHQFGSRDGSRVSEGSPGMVSVGPLPKAEAPALFSRTASKGIFGDHPGHSYGDLPGPSPA QLFQDSGLLYLAQELPAPSRARVPRLPEQGSSSRAEDSPEGYEKEGLGDRGEKPASPAVQPDAALQRLAAVLAGYGVELRQLTPEQLSTL LTLLQLLPKGAGRNPGGVVNVGADIKKTMEGPVEGRDTAELPARTSPMPGHPTASPTSSEVQQVPSPVSSEPPKAARPPVTPVLLEKKSP LGQSQPTVAGQPSARPAAEEYGYIVTDQKPLSLAAGVKLLEILAEHVHMSSGSFINISVVGPALTFRIRHNEQNLSLADVTQQAGLVKSE LEAQTGLQILQTGVGQREEAAAVLPQTAHSTSPMRSVLLTLVALAGVAGLLVALAVALCVRQHARQQDKERLAALGPEGAHGDTTFEYQD LCRQHMATKSLFNRAEGPPEPSRVSSVSSQFSDAAQASPSSHSSTPSWCEEPAQANMDISTGHMILAYMEDHLRNRDRLAKEWQALCAYQ AEPNTCATAQGEGNIKKNRHPDFLPYDHARIKLKVESSPSRSDYINASPIIEHDPRMPAYIATQGPLSHTIADFWQMVWESGCTVIVMLT PLVEDGVKQCDRYWPDEGASLYHVYEVNLVSEHIWCEDFLVRSFYLKNVQTQETRTLTQFHFLSWPAEGTPASTRPLLDFRRKVNKCYRG |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| PTPRN (go to UniProt):Q16849 |
| 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 |
| Q16849 | Topological domain | 35 | 575 | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Substitution;Start=479;End=508 |
| Q16849 | Topological domain | 35 | 575 | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=1;End=90 |
| Q16849 | Region | 35 | 131 | Note=RESP18 homology domain | Type=Deletion;Start=1;End=90 |
| Q16849 | Region | 449 | 575 | Note=Sufficient for dimerization of proICA512;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25561468;Dbxref=PMID:25561468 | Type=Substitution;Start=479;End=508 |
Gene Isoform Structures and Expression Levels for PTPRN |
| Gene structures of our canonical and alternative spliced genes of PTPRN * 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 Q16849-1 |
| 3D view using mol* of Q16849-2 |
| 3D view using mol* of Q16849-3 |
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 Q16849-1 |
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| pLDDT distribution across the protein length of Q16849-2 |
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| pLDDT distribution across the protein length of Q16849-3 |
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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 Q16849-1 |
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| Ramachandran plot of Q16849-2 |
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| Ramachandran plot of Q16849-3 |
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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 |
| Q16849-1 | 1.097 | 102 | 1.157 | 439.04 | 0.566 | 0.746 | 0.93 | 1.339 | 0.706 | 1.896 | 1.257 | 82,86,89,90,93,95,101,104,105,108,109,112,206,209, 483,484,485,487,488,490,491,501,502,504,505,507 |
| Q16849-2 | 1.037 | 77 | 1.087 | 255.535 | 0.557 | 0.76 | 1.013 | 2.805 | 0.595 | 4.712 | 0.779 | 171,173,177,180,181,184,185,337,338,340,341,342,36 0,363,364,365,367,368,369,370 |
| Q16849-3 | 1.099 | 143 | 1.175 | 322.077 | 0.493 | 0.721 | 0.996 | 2.286 | 0.605 | 3.776 | 1.201 | 81,82,83,84,86,87,90,91,94,95,98,243,244,247,248,2 51,252,270,273,274,275,276,277,278,279,280 |
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 Q16849-1_Q16849-1_2i1y_B.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q16849-1_2i1y_B_Q16849-2.pdb |
| 3D view using mol* of Q16849-1_2i1y_B_Q16849-3.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q16849-1_Q16849-2.pdb |
| 3D view using mol* of Q16849-1_Q16849-3.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q16849-1_vs_Q16849-2.png |
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| ./stats/secondary_structure/figure/Q16849-1_vs_Q16849-3.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q16849-1_vs_Q16849-2.png |
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| ./stats/relative_asa/Q16849-1_vs_Q16849-3.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 PTPRN |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to PTPRN |
| Previous studies relating to the alternative splicing of PTPRN and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| PTPRN | 11289059 | Differential splicing of the IA-2 mRNA in pancreas and lymphoid organs as a permissive genetic mechanism for autoimmunity against the IA-2 type 1 diabetes autoantigen. | Type 1 diabetes results from the autoimmune destruction of pancreatic beta-cells in genetically susceptible individuals. Growing evidence suggests that genetically determined variation in the expression of self-antigens in thymus may affect the shaping of the T-cell repertoire and susceptibility to autoimmunity. For example, both allelic variation and parent-of-origin effects influence the thymic expression of insulin (a known type 1 diabetes autoantigen), and insulin gene transcription levels in thymus inversely correlate with susceptibility in both humans and transgenic models. It is unclear why patients lose tolerance to IA-2 (insulinoma-associated tyrosine phosphatase-like protein, or islet cell antigen 512 [ICA512]), especially because IA-2 polymorphisms are not associated with type 1 diabetes. We report that alternative splicing determines differential IA-2 expression in islets compared with thymus and spleen. Islets express full-length mRNA and two alternatively spliced transcripts, whereas thymus and spleen exclusively express an alternatively spliced transcript lacking exon 13. This encodes for the transmembrane (TM) and juxta-membrane (JM) domains that comprise several type 1 diabetes target epitopes, supporting the concept that tolerance to IA-2 epitopes not expressed in lymphoid organs may not be achieved. We propose differential splicing as a regulatory mechanism of gene expression playing a permissive role in the development of autoimmune responses to IA-2. Our findings also show that candidate gene expression studies can help in dissecting the complex genetic determinants of a multifactorial disease such as type 1 diabetes. | D003922 | Diabetes Mellitus, Type 1 |
Clinically important variants in PTPRN |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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