Protein:HPSE |
Protein Summary |
Gene summary |
| Gene name: HPSE | ASpdb.0 ID: 10855 | Gene | Gene symbol | HPSE | Gene ID | 10855 |
| Gene name | heparanase |
| Synonyms | HPA|HPA1|HPR1|HPSE1|HSE1 |
| Cytomap | 4q21.23 |
| Type of gene | protein-coding |
| Description | heparanaseendo-glucoronidaseheparanase-1 |
| Modification date | 20240305 |
| UniProtAcc | Q9Y251 |
Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | HPSE | GO:0005634 | nucleus | 20309870 |
| Gene | HPSE | GO:0005654 | nucleoplasm | - |
| Gene | HPSE | GO:0005764 | lysosome | 15126626 |
| Gene | HPSE | GO:0007160 | cell-matrix adhesion | 12773484 |
| Gene | HPSE | GO:0010575 | positive regulation of vascular endothelial growth factor production | 16452201 |
| Gene | HPSE | GO:0030194 | positive regulation of blood coagulation | 20634491 |
| Gene | HPSE | GO:0030200 | heparan sulfate proteoglycan catabolic process | 12213822 |
| Gene | HPSE | GO:0030305 | heparanase activity | 12213822 |
| Gene | HPSE | GO:0033690 | positive regulation of osteoblast proliferation | 20309870 |
| Gene | HPSE | GO:0043231 | intracellular membrane-bounded organelle | - |
| Gene | HPSE | GO:0045545 | syndecan binding | 15292202 |
| Gene | HPSE | GO:0051797 | regulation of hair follicle development | 18557927 |
| Gene | HPSE | GO:0051897 | positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction | 15044433 |
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 |
| Q9Y251-1 | Q9Y251-1_5la4_A.pdb | 5LA4 | X-ray | 1.9 | A | 36 | 543 |
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 |
| Q9Y251 | HPSE | Q9Y251-1 | Q9Y251-2 | 543 | 485 | 167 | 225 | Substitution | RSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNE | K | 167 | 167 |
| Q9Y251 | HPSE | Q9Y251-1 | Q9Y251-3 | 543 | 469 | 329 | 402 | Deletion | none | none | 328 | 328 |
| Q9Y251 | HPSE | Q9Y251-1 | Q9Y251-4 | 543 | 380 | 365 | 380 | Substitution | WLDKLGLSARMGIEVV | IIGYLFCSRNWWAPRC | 365 | 380 |
| Q9Y251 | HPSE | Q9Y251-1 | Q9Y251-4 | 543 | 380 | 381 | 543 | Deletion | none | none | 380 | 380 |
Multiple sequence alignment of our canonical and alternatively spliced HPSE |
Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of HPSE |
| UniProt-id | ENSG | ENST | ENSP |
| Q9Y251-1 | ENSG00000173083.16 | ENST00000311412.10 | ENSP00000308107.5 |
| Q9Y251-1 | ENSG00000173083.16 | ENST00000405413.6 | ENSP00000384262.2 |
| Q9Y251-2 | ENSG00000173083.16 | ENST00000513463.1 | ENSP00000421365.1 |
| Q9Y251-3 | ENSG00000173083.16 | ENST00000512196.5 | ENSP00000423265.1 |
| Q9Y251-4 | ENSG00000173083.16 | ENST00000509906.5 | ENSP00000421038.1 |
| UniProt-id | NM ID | NP ID |
| Q9Y251-1 | NM_001098540.2 | NP_001092010.1 |
| Q9Y251-1 | NM_006665.5 | NP_006656.2 |
| Q9Y251-2 | NM_001199830.1 | NP_001186759.1 |
| Q9Y251-3 | NM_001166498.2 | NP_001159970.1 |
Amino acid sequences of our canonical and alternatively spliced HPSE |
| accession_id | Protein sequence |
| Q9Y251-1 | MLLRSKPALPPPLMLLLLGPLGPLSPGALPRPAQAQDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPA YLRFGGTKTDFLIFDPKKESTFEERSYWQSQVNQDICKYGSIPPDVEEKLRLEWPYQEQLLLREHYQKKFKNSTYSRSSVDVLYTFANCS GLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQ PRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATKEDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFA AGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDL TLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVA |
| Q9Y251-2 | MLLRSKPALPPPLMLLLLGPLGPLSPGALPRPAQAQDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPA YLRFGGTKTDFLIFDPKKESTFEERSYWQSQVNQDICKYGSIPPDVEEKLRLEWPYQEQLLLREHYQKKFKNSTYSKPNSFLKKADIFIN GSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATKEDFLNPDVLDIFISSVQKVFQ VVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKV LMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTL |
| Q9Y251-3 | MLLRSKPALPPPLMLLLLGPLGPLSPGALPRPAQAQDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPA YLRFGGTKTDFLIFDPKKESTFEERSYWQSQVNQDICKYGSIPPDVEEKLRLEWPYQEQLLLREHYQKKFKNSTYSRSSVDVLYTFANCS GLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQ PRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATKEDFLNPDVLDIFISSVQKVFQDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVY LHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGL |
| Q9Y251-4 | MLLRSKPALPPPLMLLLLGPLGPLSPGALPRPAQAQDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPA YLRFGGTKTDFLIFDPKKESTFEERSYWQSQVNQDICKYGSIPPDVEEKLRLEWPYQEQLLLREHYQKKFKNSTYSRSSVDVLYTFANCS GLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQ PRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATKEDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFA |
Protein Functional Features |
Main function of this protein. (from UniProt) |
| HPSE (go to UniProt):Q9Y251 |
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 |
| Q9Y251 | Region | 288 | 417 | Note=Required for heterodimerization with the heparanase 8 kDa subunit;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12927802;Dbxref=PMID:12927802 | Type=Deletion;Start=329;End=402 |
| Q9Y251 | Region | 288 | 417 | Note=Required for heterodimerization with the heparanase 8 kDa subunit;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12927802;Dbxref=PMID:12927802 | Type=Substitution;Start=365;End=380 |
| Q9Y251 | Region | 288 | 417 | Note=Required for heterodimerization with the heparanase 8 kDa subunit;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12927802;Dbxref=PMID:12927802 | Type=Deletion;Start=381;End=543 |
| Q9Y251 | Region | 527 | 543 | Note=Required for transferring proheparanase to the Golgi apparatus%2C secretion and subsequent enzyme activity and for enhancement of PKB/AKT1 phosphorylation | Type=Deletion;Start=381;End=543 |
Gene Isoform Structures and Expression Levels for HPSE |
Gene structures of our canonical and alternative spliced genes of HPSE* 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. |
Expression levels of gene isoforms across TCGA. |
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 Q9Y251-1 |
| 3D view using mol* of Q9Y251-2 |
| 3D view using mol* of Q9Y251-3 |
| 3D view using mol* of Q9Y251-4 |
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. |
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 Q9Y251-1 |
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| Ramachandran plot of Q9Y251-3 |
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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 |
| Q9Y251-1 | 1.051 | 167 | 0.97 | 517.244 | 0.527 | 0.774 | 1.052 | 0.354 | 1.333 | 0.265 | 0.69 | 62,64,96,97,98,151,152,154,155,156,158,160,224,225 ,226,227,228,229,230,231,232,236,238,239,240,269,2 70,272,274,275,277,278,281,296,298,303,343,348,349 ,350,383,388,391 |
| Q9Y251-2 | 1.05 | 209 | 1.018 | 541.597 | 0.494 | 0.773 | 1.013 | 0.648 | 1.183 | 0.548 | 0.308 | 62,64,96,97,98,151,152,154,155,156,158,160,167,168 ,169,170,171,172,173,174,178,179,180,181,211,212,2 14,215,216,217,219,220,223,238,240,243,245,285,290 ,291,292,325,330,333 |
| Q9Y251-3 | 1.078 | 349 | 1.145 | 1477.301 | 0.668 | 0.711 | 0.799 | 1.148 | 0.68 | 1.69 | 0.595 | 57,58,59,60,61,62,64,65,75,80,83,84,87,91,92,93,95 ,96,97,144,148,151,152,154,155,156,158,160,176,182 ,185,221,224,225,227,228,231,232,264,269,270,272,2 75,294,295,296,297,298,299,300,301,302,303,305,307 ,310,311,315,316,319,325,326,327,328,329,330,332,3 33,337,381,382,383,406,407,408,414,415,416,419,452 ,453,454,455 |
| Q9Y251-4 | 1.078 | 258 | 1.102 | 534.394 | 0.389 | 0.792 | 1.044 | 1.206 | 0.963 | 1.253 | 0.575 | 50,51,52,53,55,56,57,58,59,60,91,93,185,221,294,32 7,330,331,335,336,337,338,339,340,341,342,343,344, 345,346,365,368,369,372,373,375,376 |
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 Q9Y251-1_Q9Y251-1_5la4_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 Q9Y251-1_5la4_A_Q9Y251-2.pdb |
| 3D view using mol* of Q9Y251-1_5la4_A_Q9Y251-3.pdb |
| 3D view using mol* of Q9Y251-1_5la4_A_Q9Y251-4.pdb |
Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q9Y251-1_Q9Y251-2.pdb |
| 3D view using mol* of Q9Y251-1_Q9Y251-3.pdb |
| 3D view using mol* of Q9Y251-1_Q9Y251-4.pdb |
Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q9Y251-1_vs_Q9Y251-2.png |
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| ./stats/secondary_structure/figure/Q9Y251-1_vs_Q9Y251-3.png |
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| ./stats/secondary_structure/figure/Q9Y251-1_vs_Q9Y251-4.png |
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Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q9Y251-1_vs_Q9Y251-2.png |
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| ./stats/relative_asa/Q9Y251-1_vs_Q9Y251-3.png |
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| ./stats/relative_asa/Q9Y251-1_vs_Q9Y251-4.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 HPSE |
Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to HPSE |
Previous studies relating to the alternative splicing of HPSE and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| HPSE | 22363633 | Small RNAs targeting transcription start site induce heparanase silencing through interference with transcription initiation in human cancer cells. | Heparanase (HPA), an endo-h-D-glucuronidase that cleaves the heparan sulfate chain of heparan sulfate proteoglycans, is overexpressed in majority of human cancers. Recent evidence suggests that small interfering RNA (siRNA) induces transcriptional gene silencing (TGS) in human cells. In this study, transfection of siRNA against -9/+10 bp (siH3), but not -174/-155 bp (siH1) or -134/-115 bp (siH2) region relative to transcription start site (TSS) locating at 101 bp upstream of the translation start site, resulted in TGS of heparanase in human prostate cancer, bladder cancer, and gastric cancer cells in a sequence-specific manner. Methylation-specific PCR and bisulfite sequencing revealed no DNA methylation of CpG islands within heparanase promoter in siH3-transfected cells. The TGS of heparanase did not involve changes of epigenetic markers histone H3 lysine 9 dimethylation (H3K9me2), histone H3 lysine 27 trimethylation (H3K27me3) or active chromatin marker acetylated histone H3 (AcH3). The regulation of alternative splicing was not involved in siH3-mediated TGS. Instead, siH3 interfered with transcription initiation via decreasing the binding of both RNA polymerase II and transcription factor II B (TFIIB), but not the binding of transcription factors Sp1 or early growth response 1, on the heparanase promoter. Moreover, Argonaute 1 and Argonaute 2 facilitated the decreased binding of RNA polymerase II and TFIIB on heparanase promoter, and were necessary in siH3-induced TGS of heparanase. Stable transfection of the short hairpin RNA construct targeting heparanase TSS (-9/+10 bp) into cancer cells, resulted in decreased proliferation, invasion, metastasis and angiogenesis of cancer cells in vitro and in athymic mice models. These results suggest that small RNAs targeting TSS can induce TGS of heparanase via interference with transcription initiation, and significantly suppress the tumor growth, invasion, metastasis and angiogenesis of cancer cells. | D009361 | Neoplasm Invasiveness |
| HPSE | 22363633 | Small RNAs targeting transcription start site induce heparanase silencing through interference with transcription initiation in human cancer cells. | Heparanase (HPA), an endo-h-D-glucuronidase that cleaves the heparan sulfate chain of heparan sulfate proteoglycans, is overexpressed in majority of human cancers. Recent evidence suggests that small interfering RNA (siRNA) induces transcriptional gene silencing (TGS) in human cells. In this study, transfection of siRNA against -9/+10 bp (siH3), but not -174/-155 bp (siH1) or -134/-115 bp (siH2) region relative to transcription start site (TSS) locating at 101 bp upstream of the translation start site, resulted in TGS of heparanase in human prostate cancer, bladder cancer, and gastric cancer cells in a sequence-specific manner. Methylation-specific PCR and bisulfite sequencing revealed no DNA methylation of CpG islands within heparanase promoter in siH3-transfected cells. The TGS of heparanase did not involve changes of epigenetic markers histone H3 lysine 9 dimethylation (H3K9me2), histone H3 lysine 27 trimethylation (H3K27me3) or active chromatin marker acetylated histone H3 (AcH3). The regulation of alternative splicing was not involved in siH3-mediated TGS. Instead, siH3 interfered with transcription initiation via decreasing the binding of both RNA polymerase II and transcription factor II B (TFIIB), but not the binding of transcription factors Sp1 or early growth response 1, on the heparanase promoter. Moreover, Argonaute 1 and Argonaute 2 facilitated the decreased binding of RNA polymerase II and TFIIB on heparanase promoter, and were necessary in siH3-induced TGS of heparanase. Stable transfection of the short hairpin RNA construct targeting heparanase TSS (-9/+10 bp) into cancer cells, resulted in decreased proliferation, invasion, metastasis and angiogenesis of cancer cells in vitro and in athymic mice models. These results suggest that small RNAs targeting TSS can induce TGS of heparanase via interference with transcription initiation, and significantly suppress the tumor growth, invasion, metastasis and angiogenesis of cancer cells. | D009362 | Neoplasm Metastasis |
| HPSE | 22363633 | Small RNAs targeting transcription start site induce heparanase silencing through interference with transcription initiation in human cancer cells. | Heparanase (HPA), an endo-h-D-glucuronidase that cleaves the heparan sulfate chain of heparan sulfate proteoglycans, is overexpressed in majority of human cancers. Recent evidence suggests that small interfering RNA (siRNA) induces transcriptional gene silencing (TGS) in human cells. In this study, transfection of siRNA against -9/+10 bp (siH3), but not -174/-155 bp (siH1) or -134/-115 bp (siH2) region relative to transcription start site (TSS) locating at 101 bp upstream of the translation start site, resulted in TGS of heparanase in human prostate cancer, bladder cancer, and gastric cancer cells in a sequence-specific manner. Methylation-specific PCR and bisulfite sequencing revealed no DNA methylation of CpG islands within heparanase promoter in siH3-transfected cells. The TGS of heparanase did not involve changes of epigenetic markers histone H3 lysine 9 dimethylation (H3K9me2), histone H3 lysine 27 trimethylation (H3K27me3) or active chromatin marker acetylated histone H3 (AcH3). The regulation of alternative splicing was not involved in siH3-mediated TGS. Instead, siH3 interfered with transcription initiation via decreasing the binding of both RNA polymerase II and transcription factor II B (TFIIB), but not the binding of transcription factors Sp1 or early growth response 1, on the heparanase promoter. Moreover, Argonaute 1 and Argonaute 2 facilitated the decreased binding of RNA polymerase II and TFIIB on heparanase promoter, and were necessary in siH3-induced TGS of heparanase. Stable transfection of the short hairpin RNA construct targeting heparanase TSS (-9/+10 bp) into cancer cells, resulted in decreased proliferation, invasion, metastasis and angiogenesis of cancer cells in vitro and in athymic mice models. These results suggest that small RNAs targeting TSS can induce TGS of heparanase via interference with transcription initiation, and significantly suppress the tumor growth, invasion, metastasis and angiogenesis of cancer cells. | D009369 | Neoplasms |
| HPSE | 22363633 | Small RNAs targeting transcription start site induce heparanase silencing through interference with transcription initiation in human cancer cells. | Heparanase (HPA), an endo-h-D-glucuronidase that cleaves the heparan sulfate chain of heparan sulfate proteoglycans, is overexpressed in majority of human cancers. Recent evidence suggests that small interfering RNA (siRNA) induces transcriptional gene silencing (TGS) in human cells. In this study, transfection of siRNA against -9/+10 bp (siH3), but not -174/-155 bp (siH1) or -134/-115 bp (siH2) region relative to transcription start site (TSS) locating at 101 bp upstream of the translation start site, resulted in TGS of heparanase in human prostate cancer, bladder cancer, and gastric cancer cells in a sequence-specific manner. Methylation-specific PCR and bisulfite sequencing revealed no DNA methylation of CpG islands within heparanase promoter in siH3-transfected cells. The TGS of heparanase did not involve changes of epigenetic markers histone H3 lysine 9 dimethylation (H3K9me2), histone H3 lysine 27 trimethylation (H3K27me3) or active chromatin marker acetylated histone H3 (AcH3). The regulation of alternative splicing was not involved in siH3-mediated TGS. Instead, siH3 interfered with transcription initiation via decreasing the binding of both RNA polymerase II and transcription factor II B (TFIIB), but not the binding of transcription factors Sp1 or early growth response 1, on the heparanase promoter. Moreover, Argonaute 1 and Argonaute 2 facilitated the decreased binding of RNA polymerase II and TFIIB on heparanase promoter, and were necessary in siH3-induced TGS of heparanase. Stable transfection of the short hairpin RNA construct targeting heparanase TSS (-9/+10 bp) into cancer cells, resulted in decreased proliferation, invasion, metastasis and angiogenesis of cancer cells in vitro and in athymic mice models. These results suggest that small RNAs targeting TSS can induce TGS of heparanase via interference with transcription initiation, and significantly suppress the tumor growth, invasion, metastasis and angiogenesis of cancer cells. | D009389 | Neovascularization, Pathologic |
Clinically important variants in HPSE |
(ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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