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Center for Computational Systems Medicine
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Protein Summary

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AS Summary

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Protein Functional Features

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Gene Isoform Structures and Expression Levels

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Protein Structures

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pLDDT Score Distribution

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Ramachandran Plot of Protein Structures

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Potential Active Site Information

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Protein Structure and Feature Comparision

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Protein-Protein Interaction

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Related Drugs

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Related Diseases

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Clinically Important Variants

Protein:HPSE

Protein Summary

check button Gene summary
Gene name: HPSE
ASpdb.0 ID: 10855
Gene
Gene symbol

HPSE

Gene ID

10855

Gene nameheparanase
SynonymsHPA|HPA1|HPR1|HPSE1|HSE1
Cytomap

4q21.23

Type of geneprotein-coding
Descriptionheparanaseendo-glucoronidaseheparanase-1
Modification date20240305
UniProtAcc

Q9Y251


check button Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
GeneHPSE

GO:0005634

nucleus

20309870

GeneHPSE

GO:0005654

nucleoplasm

-

GeneHPSE

GO:0005764

lysosome

15126626

GeneHPSE

GO:0007160

cell-matrix adhesion

12773484

GeneHPSE

GO:0010575

positive regulation of vascular endothelial growth factor production

16452201

GeneHPSE

GO:0030194

positive regulation of blood coagulation

20634491

GeneHPSE

GO:0030200

heparan sulfate proteoglycan catabolic process

12213822

GeneHPSE

GO:0030305

heparanase activity

12213822

GeneHPSE

GO:0033690

positive regulation of osteoblast proliferation

20309870

GeneHPSE

GO:0043231

intracellular membrane-bounded organelle

-

GeneHPSE

GO:0045545

syndecan binding

15292202

GeneHPSE

GO:0051797

regulation of hair follicle development

18557927

GeneHPSE

GO:0051897

positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction

15044433



AS Summary

check button Information of the canonical protein with experimentally identified structure from PDB (2023).
UniProt AccFile namePDB IDMethodResolutionChainStartEnd
Q9Y251-1Q9Y251-1_5la4_A.pdb5LA4X-ray1.9A36543

check button ASpdb's canonical and alternatively spliced isoform information.
accession_idgene_namecanonical_idalternative_idcanonical_lengthalternative_lengthcanonical_startcanonical_endtypeoriginalSEQvariationSEQalternative_startalternative_end
Q9Y251HPSEQ9Y251-1Q9Y251-2543485167225SubstitutionRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEK167167
Q9Y251HPSEQ9Y251-1Q9Y251-3543469329402Deletionnonenone328328
Q9Y251HPSEQ9Y251-1Q9Y251-4543380365380SubstitutionWLDKLGLSARMGIEVVIIGYLFCSRNWWAPRC365380
Q9Y251HPSEQ9Y251-1Q9Y251-4543380381543Deletionnonenone380380

check buttonMultiple sequence alignment of our canonical and alternatively spliced HPSE

check button Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of HPSE
UniProt-idENSGENSTENSP
Q9Y251-1ENSG00000173083.16ENST00000311412.10ENSP00000308107.5
Q9Y251-1ENSG00000173083.16ENST00000405413.6ENSP00000384262.2
Q9Y251-2ENSG00000173083.16ENST00000513463.1ENSP00000421365.1
Q9Y251-3ENSG00000173083.16ENST00000512196.5ENSP00000423265.1
Q9Y251-4ENSG00000173083.16ENST00000509906.5ENSP00000421038.1

UniProt-idNM IDNP ID
Q9Y251-1NM_001098540.2NP_001092010.1
Q9Y251-1NM_006665.5NP_006656.2
Q9Y251-2NM_001199830.1NP_001186759.1
Q9Y251-3NM_001166498.2NP_001159970.1

check buttonAmino acid sequences of our canonical and alternatively spliced HPSE
accession_idProtein sequence
Q9Y251-1MLLRSKPALPPPLMLLLLGPLGPLSPGALPRPAQAQDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPA
YLRFGGTKTDFLIFDPKKESTFEERSYWQSQVNQDICKYGSIPPDVEEKLRLEWPYQEQLLLREHYQKKFKNSTYSRSSVDVLYTFANCS
GLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQ
PRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATKEDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFA
AGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDL
TLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVA
Q9Y251-2MLLRSKPALPPPLMLLLLGPLGPLSPGALPRPAQAQDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPA
YLRFGGTKTDFLIFDPKKESTFEERSYWQSQVNQDICKYGSIPPDVEEKLRLEWPYQEQLLLREHYQKKFKNSTYSKPNSFLKKADIFIN
GSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATKEDFLNPDVLDIFISSVQKVFQ
VVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKV
LMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTL
Q9Y251-3MLLRSKPALPPPLMLLLLGPLGPLSPGALPRPAQAQDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPA
YLRFGGTKTDFLIFDPKKESTFEERSYWQSQVNQDICKYGSIPPDVEEKLRLEWPYQEQLLLREHYQKKFKNSTYSRSSVDVLYTFANCS
GLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQ
PRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATKEDFLNPDVLDIFISSVQKVFQDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVY
LHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGL
Q9Y251-4MLLRSKPALPPPLMLLLLGPLGPLSPGALPRPAQAQDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPA
YLRFGGTKTDFLIFDPKKESTFEERSYWQSQVNQDICKYGSIPPDVEEKLRLEWPYQEQLLLREHYQKKFKNSTYSRSSVDVLYTFANCS
GLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQ
PRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATKEDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFA

Protein Functional Features

check buttonMain function of this protein. (from UniProt)
HPSE (go to UniProt):Q9Y251

check buttonRetention 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

download page

* Minus value of BPloci means that the break pointn is located before the CDS.
- Retained protein feature among the 13 regional features.
Accession_idSubsectionStartEndFuncitonal featureSplicing information
Q9Y251Region288417Note=Required for heterodimerization with the heparanase 8 kDa subunit;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12927802;Dbxref=PMID:12927802Type=Deletion;Start=329;End=402
Q9Y251Region288417Note=Required for heterodimerization with the heparanase 8 kDa subunit;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12927802;Dbxref=PMID:12927802Type=Substitution;Start=365;End=380
Q9Y251Region288417Note=Required for heterodimerization with the heparanase 8 kDa subunit;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12927802;Dbxref=PMID:12927802Type=Deletion;Start=381;End=543
Q9Y251Region527543Note=Required for transferring proheparanase to the Golgi apparatus%2C secretion and subsequent enzyme activity and for enhancement of PKB/AKT1 phosphorylationType=Deletion;Start=381;End=543


Gene Isoform Structures and Expression Levels for HPSE

check buttonGene 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.
gene isoform structure of HPSE

check button Expression levels of gene isoforms across GTEx.
gtex expression

check button Expression levels of gene isoforms across TCGA.
tcga expression


Protein Structures

check button 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

check button 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 Q9Y251-1
all structure
pLDDT distribution across the protein length of Q9Y251-2
all structure
pLDDT distribution across the protein length of Q9Y251-3
all structure
pLDDT distribution across the protein length of Q9Y251-4
all structure


Ramachandran Plot of Protein Structures


check button 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
all structure
Ramachandran plot of Q9Y251-3
all structure

Potential Active Site Information


check button The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.
UniProt-idSite scoreSizeD scoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues
Q9Y251-11.0511670.97517.2440.5270.7741.0520.3541.3330.2650.6962,64,96,97,98,151,152,154,155,156,158,160,224,225
,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
Q9Y251-21.052091.018541.5970.4940.7731.0130.6481.1830.5480.30862,64,96,97,98,151,152,154,155,156,158,160,167,168
,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
Q9Y251-31.0783491.1451477.3010.6680.7110.7991.1480.681.690.59557,58,59,60,61,62,64,65,75,80,83,84,87,91,92,93,95
,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
Q9Y251-41.0782581.102534.3940.3890.7921.0441.2060.9631.2530.57550,51,52,53,55,56,57,58,59,60,91,93,185,221,294,32
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


check button Protein Structure Comparision Using Template Modeling Scores (TM-score).
all structure

check button 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

check button 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

check button 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

check button Protein Feature Comparison of the protein sequendary structures among the protiens.
./stats/secondary_structure/figure/Q9Y251-1_vs_Q9Y251-2.png
all structure<
./stats/secondary_structure/figure/Q9Y251-1_vs_Q9Y251-3.png
all structure<
./stats/secondary_structure/figure/Q9Y251-1_vs_Q9Y251-4.png
all structure<

check button Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.
./stats/relative_asa/Q9Y251-1_vs_Q9Y251-2.png
all structure<
./stats/relative_asa/Q9Y251-1_vs_Q9Y251-3.png
all structure<
./stats/relative_asa/Q9Y251-1_vs_Q9Y251-4.png
all structure<


Protein-Protein Interaction


check button Interactors from UniProt.
Accession_idSubsectionStartEndFuncitonal featureSplicing information


check button Interactors from STRING.
Gene nameInteractors


Related Drugs to HPSE


check button Drugs targeting this gene/protein.
(DrugBank)
UniProt accessionGene nameDrugBank IDDrug nameDrug groupActions

Related Diseases to HPSE


check button Previous studies relating to the alternative splicing of HPSE and disease information from the MeSH term (PubMed)
GenePMIDTitleAbstractMeSH IDMeSH term
HPSE22363633Small 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.D009361Neoplasm Invasiveness
HPSE22363633Small 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.D009362Neoplasm Metastasis
HPSE22363633Small 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.D009369Neoplasms
HPSE22363633Small 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.D009389Neovascularization, Pathologic


Clinically important variants in HPSE


check button (ClinVar, 04/20/2024)
accession_iduniprot_idgene_nameTypeVariantClinical_significance