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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:SHPRH

Protein Summary

check button Gene summary
Gene name: SHPRH
ASpdb.0 ID: 257218
Gene
Gene symbol

SHPRH

Gene ID

257218

Gene nameSNF2 histone linker PHD RING helicase
SynonymsRAD5|bA545I5.2
Cytomap

6q24.3

Type of geneprotein-coding
DescriptionE3 ubiquitin-protein ligase SHPRH2610103K11RikRING-type E3 ubiquitin transferase SHPRHSNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligaseSNF2, histone-linker, PHD and RING finger domain-containing helicase
Modification date20240407
UniProtAcc

Q149N8


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

GO:0000209

protein polyubiquitination

17108083

GeneSHPRH

GO:0004842

ubiquitin-protein transferase activity

17108083

GeneSHPRH

GO:0006974

DNA damage response

25023518

GeneSHPRH

GO:0031625

ubiquitin protein ligase binding

25023518



AS Summary

check button Information of the canonical protein with experimentally identified structure from PDB (2023).
UniProt AccFile namePDB IDMethodResolutionChainStartEnd
Q149N8-1Q149N8-1_4qn1_A.pdb4QN1X-ray2.48A10001418

check button ASpdb's canonical and alternatively spliced isoform information.
accession_idgene_namecanonical_idalternative_idcanonical_lengthalternative_lengthcanonical_startcanonical_endtypeoriginalSEQvariationSEQalternative_startalternative_end
Q149N8SHPRHQ149N8-1Q149N8-2168392946156Deletionnonenone4545
Q149N8SHPRHQ149N8-1Q149N8-2168392910391040SubstitutionEYRR928929
Q149N8SHPRHQ149N8-1Q149N8-2168392910411683Deletionnonenone929929
Q149N8SHPRHQ149N8-1Q149N8-416831659996996SubstitutionKKSFEQSTFSF9961005
Q149N8SHPRHQ149N8-1Q149N8-41683165911831187Deletionnonenone11911191
Q149N8SHPRHQ149N8-1Q149N8-41683165916531655SubstitutionHTNIYI16571659
Q149N8SHPRHQ149N8-1Q149N8-41683165916561683Deletionnonenone16591659
Q149N8SHPRHQ149N8-1Q149N8-51683471442471SubstitutionTRVMILTAVKEMNGKKGVSILSIYKYVSSIYPFTFSYTCDDTDSCERNEWKKRSVHPFHL442471
Q149N8SHPRHQ149N8-1Q149N8-516834714721683Deletionnonenone471471

check buttonMultiple sequence alignment of our canonical and alternatively spliced SHPRH

check button Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of SHPRH
UniProt-idENSGENSTENSP
Q149N8-1ENSG00000146414.17ENST00000275233.12ENSP00000275233.7
Q149N8-1ENSG00000146414.17ENST00000367505.6ENSP00000356475.2
Q149N8-2ENSG00000146414.17ENST00000519632.5ENSP00000430528.1
Q149N8-4ENSG00000146414.17ENST00000438092.6ENSP00000412797.2

UniProt-idNM IDNP ID
Q149N8-1NM_001042683.2NP_001036148.2
Q149N8-4NM_173082.3NP_775105.1

check buttonAmino acid sequences of our canonical and alternatively spliced SHPRH
accession_idProtein sequence
Q149N8-1MSSRRKRAPPVRVDEEKRQQLHWNMHEDRRNEPIIISDDDEQPCPGSDTSSAHYIILSDSLKEEVAHRDKKRCSKVVSFSKPIEKEETVG
IFSPLSVKLNIVISPYHFDNSWKAFLGELTLQLLPAQSLIENFSERSITLMSSESSNQFLIYVHSKGEDVEKQKKEPMSICDKGILVESS
FSGEMLEDLGWLQKKRRIKLYQKPEGNHIIKVGIYLLEAGLAKLDFLSDANSRMKKFNQLMKKVMEKLHNSIIPDVLEEDEDDPESEPEG
QDIDELYHFVKQTHQQETQSIQVDVQHPALIPVLRPYQREAVNWMLQQECFRSSPATESALHFLWREIVTSEGLKLYYNPYTGCIIREYP
NSGPQLLGGILADEMGLGKTVEVLALILTHTRQDVKQDALTLPEGKVVNYFIPSHYFGGKLKKTEIQNIEFEPKEKVQCPPTRVMILTAV
KEMNGKKGVSILSIYKYVSSIYRYDVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTFTLGKNYKEEDICDKTKKQAVGSPRKIQKETRK
SGNKDTDSEYLPSDTSDDDDDPYYYYYKSRRNRSKLRKKLVPSTKKGKSQPFINPDSQGHCPATSDSGITDVAMSKSTCISEFNQEHETE
DCAESLNHADSDVPPSNTMSPFNTSDYRFECICGELDQIDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKPFYCPHCLVAMEPVSTRATLI
ISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDGFLQPHFLAEQDIVIITYDVLRSELNYVDIPHSNSEDGRRLRNQKRYMAIPSPLVA
VEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFLGIEPYCVKHWWVRLLYRPYCKKNPQHLYSFIAKIL
WRSAKKDVIDQIQIPPQTEEIHWLHFSPVERHFYHRQHEVCCQDVVVKLRKISDWALKLSSLDRRTVTSILYPLLRLRQACCHPQAVRGE
FLPLQKSTMTMEELLTSLQKKCGTECEEAHRQLVCALNGLAGIHIIKGEYALAAELYREVLRSSEEHKGKLKTDSLQRLHATHNLMELLI
ARHPGIPPTLRDGRLEEEAKQLREHYMSKCNTEVAEAQQALYPVQQTIHELQRKIHSNSPWWLNVIHRAIEFTIDEELVQRVRNEITSNY
KQQTGKLSMSEKFRDCRGLQFLLTTQMEELNKCQKLVREAVKNLEGPPSRNVIESATVCHLRPARLPLNCCVFCKADELFTEYESKLFSN
TVKGQTAIFEEMIEDEEGLVDDRAPTTTRGLWAISETERSMKAILSFAKSHRFDVEFVDEGSTSMDLFEAWKKEYKLLHEYWMALRNRVS
AVDELAMATERLRVRDPREPKPNPPVLHIIEPHEVEQNRIKLLNDKAVATSQLQKKLGQLLYLTNLEKSQDKTSGGVNPEPCPICARQLG
KQWAVLTCGHCFCNECISIIIEQYSVGSHRSSIKCAICRQTTSHKEISYVFTSEKANQEEDIPVKGSHSTKVEAVVRTLMKIQLRDPGAK
ALVFSTWQDVLDIISKALTDNNMEFAQISRVKTFQENLSAFKRDPQINILLLPLHTGSNGLTIIEATHVLLVEPILNPAHELQAIGRVHR
Q149N8-2MSSRRKRAPPVRVDEEKRQQLHWNMHEDRRNEPIIISDDDEQPCPGEDVEKQKKEPMSICDKGILVESSFSGEMLEDLGWLQKKRRIKLY
QKPEGNHIIKVGIYLLEAGLAKLDFLSDANSRMKKFNQLMKKVMEKLHNSIIPDVLEEDEDDPESEPEGQDIDELYHFVKQTHQQETQSI
QVDVQHPALIPVLRPYQREAVNWMLQQECFRSSPATESALHFLWREIVTSEGLKLYYNPYTGCIIREYPNSGPQLLGGILADEMGLGKTV
EVLALILTHTRQDVKQDALTLPEGKVVNYFIPSHYFGGKLKKTEIQNIEFEPKEKVQCPPTRVMILTAVKEMNGKKGVSILSIYKYVSSI
YRYDVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTFTLGKNYKEEDICDKTKKQAVGSPRKIQKETRKSGNKDTDSEYLPSDTSDDDDD
PYYYYYKSRRNRSKLRKKLVPSTKKGKSQPFINPDSQGHCPATSDSGITDVAMSKSTCISEFNQEHETEDCAESLNHADSDVPPSNTMSP
FNTSDYRFECICGELDQIDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKPFYCPHCLVAMEPVSTRATLIISPSSICHQWVDEINRHVRSS
SLRVLVYQGVKKDGFLQPHFLAEQDIVIITYDVLRSELNYVDIPHSNSEDGRRLRNQKRYMAIPSPLVAVEWWRICLDEAQMVECPTVKA
AEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFLGIEPYCVKHWWVRLLYRPYCKKNPQHLYSFIAKILWRSAKKDVIDQIQIPPQTEEI
HWLHFSPVERHFYHRQHEVCCQDVVVKLRKISDWALKLSSLDRRTVTSILYPLLRLRQACCHPQAVRGEFLPLQKSTMTMEELLTSLQKK
Q149N8-4MSSRRKRAPPVRVDEEKRQQLHWNMHEDRRNEPIIISDDDEQPCPGSDTSSAHYIILSDSLKEEVAHRDKKRCSKVVSFSKPIEKEETVG
IFSPLSVKLNIVISPYHFDNSWKAFLGELTLQLLPAQSLIENFSERSITLMSSESSNQFLIYVHSKGEDVEKQKKEPMSICDKGILVESS
FSGEMLEDLGWLQKKRRIKLYQKPEGNHIIKVGIYLLEAGLAKLDFLSDANSRMKKFNQLMKKVMEKLHNSIIPDVLEEDEDDPESEPEG
QDIDELYHFVKQTHQQETQSIQVDVQHPALIPVLRPYQREAVNWMLQQECFRSSPATESALHFLWREIVTSEGLKLYYNPYTGCIIREYP
NSGPQLLGGILADEMGLGKTVEVLALILTHTRQDVKQDALTLPEGKVVNYFIPSHYFGGKLKKTEIQNIEFEPKEKVQCPPTRVMILTAV
KEMNGKKGVSILSIYKYVSSIYRYDVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTFTLGKNYKEEDICDKTKKQAVGSPRKIQKETRK
SGNKDTDSEYLPSDTSDDDDDPYYYYYKSRRNRSKLRKKLVPSTKKGKSQPFINPDSQGHCPATSDSGITDVAMSKSTCISEFNQEHETE
DCAESLNHADSDVPPSNTMSPFNTSDYRFECICGELDQIDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKPFYCPHCLVAMEPVSTRATLI
ISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDGFLQPHFLAEQDIVIITYDVLRSELNYVDIPHSNSEDGRRLRNQKRYMAIPSPLVA
VEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFLGIEPYCVKHWWVRLLYRPYCKKNPQHLYSFIAKIL
WRSAKKDVIDQIQIPPQTEEIHWLHFSPVERHFYHRQHEVCCQDVVVKLRKISDWALKLSSLDRRTVTSILYPLLRLRQACCHPQAVRGE
FLPLQKSFEQSTFSFSTMTMEELLTSLQKKCGTECEEAHRQLVCALNGLAGIHIIKGEYALAAELYREVLRSSEEHKGKLKTDSLQRLHA
THNLMELLIARHPGIPPTLRDGRLEEEAKQLREHYMSKCNTEVAEAQQALYPVQQTIHELQRKIHSNSPWWLNVIHRAIEFTIDEELVQR
VRNEITSNYKQQTGKLSMSEKGLQFLLTTQMEELNKCQKLVREAVKNLEGPPSRNVIESATVCHLRPARLPLNCCVFCKADELFTEYESK
LFSNTVKGQTAIFEEMIEDEEGLVDDRAPTTTRGLWAISETERSMKAILSFAKSHRFDVEFVDEGSTSMDLFEAWKKEYKLLHEYWMALR
NRVSAVDELAMATERLRVRDPREPKPNPPVLHIIEPHEVEQNRIKLLNDKAVATSQLQKKLGQLLYLTNLEKSQDKTSGGVNPEPCPICA
RQLGKQWAVLTCGHCFCNECISIIIEQYSVGSHRSSIKCAICRQTTSHKEISYVFTSEKANQEEDIPVKGSHSTKVEAVVRTLMKIQLRD
PGAKALVFSTWQDVLDIISKALTDNNMEFAQISRVKTFQENLSAFKRDPQINILLLPLHTGSNGLTIIEATHVLLVEPILNPAHELQAIG
Q149N8-5MSSRRKRAPPVRVDEEKRQQLHWNMHEDRRNEPIIISDDDEQPCPGSDTSSAHYIILSDSLKEEVAHRDKKRCSKVVSFSKPIEKEETVG
IFSPLSVKLNIVISPYHFDNSWKAFLGELTLQLLPAQSLIENFSERSITLMSSESSNQFLIYVHSKGEDVEKQKKEPMSICDKGILVESS
FSGEMLEDLGWLQKKRRIKLYQKPEGNHIIKVGIYLLEAGLAKLDFLSDANSRMKKFNQLMKKVMEKLHNSIIPDVLEEDEDDPESEPEG
QDIDELYHFVKQTHQQETQSIQVDVQHPALIPVLRPYQREAVNWMLQQECFRSSPATESALHFLWREIVTSEGLKLYYNPYTGCIIREYP
NSGPQLLGGILADEMGLGKTVEVLALILTHTRQDVKQDALTLPEGKVVNYFIPSHYFGGKLKKTEIQNIEFEPKEKVQCPPYPFTFSYTC

Protein Functional Features

check buttonMain function of this protein. (from UniProt)
SHPRH (go to UniProt):Q149N8

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
Q149N8Domain438512Note=H15;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00837Type=Substitution;Start=442;End=471
Q149N8Domain438512Note=H15;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00837Type=Deletion;Start=472;End=1683
Q149N8Domain710868Note=Helicase ATP-binding%3B second part;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541Type=Deletion;Start=472;End=1683
Q149N8Domain15141672Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542Type=Deletion;Start=1041;End=1683
Q149N8Domain15141672Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542Type=Substitution;Start=1653;End=1655
Q149N8Domain15141672Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542Type=Deletion;Start=1656;End=1683
Q149N8Domain15141672Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542Type=Deletion;Start=472;End=1683
Q149N8Zinc finger658709Note=PHD-typeType=Deletion;Start=472;End=1683
Q149N8Zinc finger14321479Note=RING-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00175Type=Deletion;Start=1041;End=1683
Q149N8Zinc finger14321479Note=RING-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00175Type=Deletion;Start=472;End=1683
Q149N8Region525607Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=472;End=1683
Q149N8Motif819822Note=DEAQ boxType=Deletion;Start=472;End=1683
Q149N8Compositional bias525551Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=472;End=1683
Q149N8Compositional bias570584Note=Basic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=472;End=1683
Q149N8Compositional bias587607Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=472;End=1683


Gene Isoform Structures and Expression Levels for SHPRH

check buttonGene structures of our canonical and alternative spliced genes of SHPRH
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
gene isoform structure of SHPRH

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 Q149N8-1
3D view using mol* of Q149N8-2
3D view using mol* of Q149N8-4
3D view using mol* of Q149N8-5


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 Q149N8-1
all structure
pLDDT distribution across the protein length of Q149N8-2
all structure
pLDDT distribution across the protein length of Q149N8-4
all structure
pLDDT distribution across the protein length of Q149N8-5
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 Q149N8-1
all structure
Ramachandran plot of Q149N8-2
all structure
Ramachandran plot of Q149N8-4
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
Q149N8-11.0382831.038672.9660.5160.7540.9720.6481.0870.5961.071272,273,274,277,278,281,374,375,848,849,850,851,85
2,902,903,904,905,906,907,917,919,1601,1603,1604,1
605,1606,1607,1608,1609,1611,1612,1613,1615,1616,1
631,1643,1645,1646,1649,1650,1653,1654,1656,1657,1
658,1659,1660,1662,1665,1666
Q149N8-21.0271611.084470.5960.5620.6610.8490.9480.7751.2230.865,66,67,68,69,70,75,90,92,97,98,99,100,101,102,10
3,104,105,106,107,110,130,133,134,137,138,227,228,
229,230,231,233,234,235,244,246
Q149N8-41.0262521.05832.4610.5430.7230.9030.4910.9910.4951.158271,272,273,274,277,278,281,284,285,288,306,307,31
0,374,375,848,849,850,851,852,901,902,903,904,905,
906,907,908,911,917,919,921,1605,1608,1609,1611,16
12,1613,1615,1616,1619,1620,1623,1635,1647,1650,16
51,1654,1657,1658
Q149N8-51.021101.06417.7740.5530.6880.8740.6050.8990.6741.319314,315,318,319,368,369,370,371,386,387,390,391,39
2,395,396,397,398,400,440,441,442,443,444

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 Q149N8-1_Q149N8-1_4qn1_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 Q149N8-1_4qn1_A_Q149N8-2.pdb
3D view using mol* of Q149N8-1_4qn1_A_Q149N8-4.pdb
3D view using mol* of Q149N8-1_4qn1_A_Q149N8-5.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 Q149N8-1_Q149N8-2.pdb
3D view using mol* of Q149N8-1_Q149N8-4.pdb
3D view using mol* of Q149N8-1_Q149N8-5.pdb

check button Protein Feature Comparison of the protein sequendary structures among the protiens.
./stats/secondary_structure/figure/Q149N8-1_vs_Q149N8-2.png
all structure<
./stats/secondary_structure/figure/Q149N8-1_vs_Q149N8-4.png
all structure<
./stats/secondary_structure/figure/Q149N8-1_vs_Q149N8-5.png
all structure<

check button Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.
./stats/relative_asa/Q149N8-1_vs_Q149N8-2.png
all structure<
./stats/relative_asa/Q149N8-1_vs_Q149N8-4.png
all structure<
./stats/relative_asa/Q149N8-1_vs_Q149N8-5.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 SHPRH


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

Related Diseases to SHPRH


check button Previous studies relating to the alternative splicing of SHPRH and disease information from the MeSH term (PubMed)
GenePMIDTitleAbstractMeSH IDMeSH term


Clinically important variants in SHPRH


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