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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:SMG6

Protein Summary

check button Gene summary
Gene name: SMG6
ASpdb.0 ID: 23293
Gene
Gene symbol

SMG6

Gene ID

23293

Gene nameSMG6 nonsense mediated mRNA decay factor
SynonymsC17orf31|EST1A|SMG-6|hEST1A|hSMG5/7a
Cytomap

17p13.3

Type of geneprotein-coding
Descriptiontelomerase-binding protein EST1AEST1 telomerase component homolog Aever shorter telomeres 1Anonsense mediated mRNA decay factor SMG6smg-6 homolog, nonsense mediated mRNA decay factortelomerase subunit EST1A
Modification date20240305
UniProtAcc

Q86US8


check button Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
GeneSMG6

GO:0004521

RNA endonuclease activity

19060897

GeneSMG6

GO:0005634

nucleus

14636577

GeneSMG6

GO:0005730

nucleolus

12676087

GeneSMG6

GO:0005737

cytoplasm

14636577

GeneSMG6

GO:0005829

cytosol

19060897

GeneSMG6

GO:0035145

exon-exon junction complex

20930030

GeneSMG6

GO:0042162

telomeric DNA binding

12699629|17916692

GeneSMG6

GO:1904354

negative regulation of telomere capping

12676087



AS Summary

check button Information of the canonical protein with experimentally identified structure from PDB (2023).
UniProt AccFile namePDB IDMethodResolutionChainStartEnd
Q86US8-1Q86US8-1_4um2_A.pdb4UM2X-ray2.1A5801159

check button ASpdb's canonical and alternatively spliced isoform information.
accession_idgene_namecanonical_idalternative_idcanonical_lengthalternative_lengthcanonical_startcanonical_endtypeoriginalSEQvariationSEQalternative_startalternative_end
Q86US8SMG6Q86US8-1Q86US8-2141933011089Deletionnonenone00
Q86US8SMG6Q86US8-1Q86US8-2141933010901119SubstitutionILEEDRLLSGFVPLLAAPQDPCYVEKTSDKMRFRLCHQRGCCPHERENTCTCKMIISSLQ130
Q86US8SMG6Q86US8-1Q86US8-314195111908Deletionnonenone00

check buttonMultiple sequence alignment of our canonical and alternatively spliced SMG6

check button Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of SMG6
UniProt-idENSGENSTENSP
Q86US8-1ENSG00000070366.14ENST00000263073.11ENSP00000263073.5
Q86US8-3ENSG00000070366.14ENST00000354901.8ENSP00000346977.4
Q86US8-3ENSG00000070366.14ENST00000536871.6ENSP00000440283.2

UniProt-idNM IDNP ID
Q86US8-1NM_017575.4NP_060045.4
Q86US8-2NM_001282326.1NP_001269255.1
Q86US8-3NM_001256827.1NP_001243756.1
Q86US8-3NM_001256828.1NP_001243757.1
Q86US8-3XM_005256571.4XP_005256628.1
Q86US8-3XM_011523775.2XP_011522077.1
Q86US8-3XM_017024399.1XP_016879888.1

check buttonAmino acid sequences of our canonical and alternatively spliced SMG6
accession_idProtein sequence
Q86US8-1MAEGLERVRISASELRGILATLAPQAGSRENMKELKEARPRKDNRRPDLEIYKPGLSRLRNKPKIKEPPGSEEFKDEIVNDRDCSAVENG
TQPVKDVCKELNNQEQNGPIDPENNRGQESFPRTAGQEDRSLKIIKRTKKPDLQIYQPGRRLQTVSKESASRVEEEEVLNQVEQLRVEED
ECRGNVAKEEVANKPDRAEIEKSPGGGRVGAAKGEKGKRMGKGEGVRETHDDPARGRPGSAKRYSRSDKRRNRYRTRSTSSAGSNNSAEG
AGLTDNGCRRRRQDRTKERPRLKKQVSVSSTDSLDEDRIDEPDGLGPRRSSERKRHLERNWSGRGEGEQKNSAKEYRGTLRVTFDAEAMN
KESPMVRSARDDMDRGKPDKGLSSGGKGSEKQESKNPKQELRGRGRGILILPAHTTLSVNSAGSPESAPLGPRLLFGSGSKGSRSWGRGG
TTRRLWDPNNPDQKPALKTQTPQLHFLDTDDEVSPTSWGDSRQAQASYYKFQNSDNPYYYPRTPGPASQYPYTGYNPLQYPVGPTNGVYP
GPYYPGYPTPSGQYVCSPLPTSTMSPEEVEQHMRNLQQQELHRLLRVADNQELQLSNLLSRDRISPEGLEKMAQLRAELLQLYERCILLD
IEFSDNQNVDQILWKNAFYQVIEKFRQLVKDPNVENPEQIRNRLLELLDEGSDFFDSLLQKLQVTYKFKLEDYMDGLAIRSKPLRKTVKY
ALISAQRCMICQGDIARYREQASDTANYGKARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLF
EETKRKAEQMEKKQHEEFDLSPDQWRKGKKSTFRHVGDDTTRLEIWIHPSHPRSSQGTESGKDSEQENGLGSLSPSDLNKRFILSFLHAH
GKLFTRIGMETFPAVAEKVLKEFQVLLQHSPSPIGSTRMLQLMTINMFAVHNSQLKDCFSEECRSVIQEQAAALGLAMFSLLVRRCTCLL
KESAKAQLSSPEDQDDQDDIKVSSFVPDLKELLPSVKVWSDWMLGYPDTWNPPPTSLDLPSHVAVDVWSTLADFCNILTAVNQSEVPLYK
DPDDDLTLLILEEDRLLSGFVPLLAAPQDPCYVEKTSDKVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQ
EGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRELRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLA
SLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLG
Q86US8-2MRFRLCHQRGCCPHERENTCTCKMIISSLQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEE
EDVVIEDFEEDSEAEGSGGEDDIRELRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESR
KYILVVPLIVINELDGLAKGQETDHRAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSC
Q86US8-3METFPAVAEKVLKEFQVLLQHSPSPIGSTRMLQLMTINMFAVHNSQLKDCFSEECRSVIQEQAAALGLAMFSLLVRRCTCLLKESAKAQL
SSPEDQDDQDDIKVSSFVPDLKELLPSVKVWSDWMLGYPDTWNPPPTSLDLPSHVAVDVWSTLADFCNILTAVNQSEVPLYKDPDDDLTL
LILEEDRLLSGFVPLLAAPQDPCYVEKTSDKVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDE
EEDVVIEDFEEDSEAEGSGGEDDIRELRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLES
RKYILVVPLIVINELDGLAKGQETDHRAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILS

Protein Functional Features

check buttonMain function of this protein. (from UniProt)
SMG6 (go to UniProt):Q86US8

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
Q86US8Region2579Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Region2579Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Region3959Note=EJC-binding motif 1%3B mediates interaction with the EJCType=Deletion;Start=1;End=1089
Q86US8Region3959Note=EJC-binding motif 1%3B mediates interaction with the EJCType=Deletion;Start=1;End=908
Q86US8Region99165Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Region99165Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Region114503Note=Interaction with telomeric DNAType=Deletion;Start=1;End=1089
Q86US8Region114503Note=Interaction with telomeric DNAType=Deletion;Start=1;End=908
Q86US8Region133153Note=EJC-binding motif 2%3B mediates interaction with the EJCType=Deletion;Start=1;End=1089
Q86US8Region133153Note=EJC-binding motif 2%3B mediates interaction with the EJCType=Deletion;Start=1;End=908
Q86US8Region177405Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Region177405Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Region419472Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Region419472Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Region854883Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Region854883Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Coiled coil163193Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=1;End=1089
Q86US8Coiled coil163193Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=1;End=908
Q86US8Coiled coil567625Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=1;End=1089
Q86US8Coiled coil567625Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=1;End=908
Q86US8Compositional bias3079Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Compositional bias3079Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Compositional bias99125Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Compositional bias99125Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Compositional bias129144Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Compositional bias129144Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Compositional bias177203Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Compositional bias177203Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Compositional bias212245Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Compositional bias212245Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Compositional bias257272Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Compositional bias257272Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Compositional bias275345Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Compositional bias275345Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Compositional bias364402Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Compositional bias364402Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908
Q86US8Compositional bias861883Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=1089
Q86US8Compositional bias861883Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=908


Gene Isoform Structures and Expression Levels for SMG6

check buttonGene structures of our canonical and alternative spliced genes of SMG6
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
gene isoform structure of SMG6

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 Q86US8-1
3D view using mol* of Q86US8-2
3D view using mol* of Q86US8-3


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 Q86US8-1
all structure
pLDDT distribution across the protein length of Q86US8-2
all structure
pLDDT distribution across the protein length of Q86US8-3
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 Q86US8-1
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
Q86US8-11.0866211.1211539.3840.4370.7811.0161.1590.8811.3161.1745,7,8,9,10,12,15,16,18,19,22,501,503,504,505,506,5
07,508,509,510,511,703,705,706,707,709,710,711,712
,713,714,719,722,723,761,762,763,764,796,797,1027,
1028,1031,1034,1037,1040,1065,1068,1069,1073,1074,
1076,1077,1078,1079,1080,1081,1088,1089,1090,1094,
1097,1098,1099,1100,1103,1104,1105,1106,1107,1108,
1109,1110,1111,1126,1129,1130,1132,1133,1135,1136,
1137,1138,1139,1140,1141,1153
Q86US8-20.92720.973315.2170.7120.6170.8570.8510.5991.4210.7713,6,7,11,13,14,16,17,18,19,20,37,40,41,44,45,48
Q86US8-31.0281921.047435.610.5080.7340.9130.5661.0230.5531.24165,68,69,135,136,137,139,140,141,146,147,148,149,1
50,249,250,251,252,253,254,255,256,257,307,310,311
,313,314,317

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 Q86US8-1_Q86US8-1_4um2_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 Q86US8-1_4um2_A_Q86US8-2.pdb
3D view using mol* of Q86US8-1_4um2_A_Q86US8-3.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 Q86US8-1_Q86US8-2.pdb
3D view using mol* of Q86US8-1_Q86US8-3.pdb

check button Protein Feature Comparison of the protein sequendary structures among the protiens.
./stats/secondary_structure/figure/Q86US8-1_vs_Q86US8-2.png
all structure<
./stats/secondary_structure/figure/Q86US8-1_vs_Q86US8-3.png
all structure<

check button Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.
./stats/relative_asa/Q86US8-1_vs_Q86US8-2.png
all structure<
./stats/relative_asa/Q86US8-1_vs_Q86US8-3.png
all structure<


Protein-Protein Interaction


check button Interactors from UniProt.
Accession_idSubsectionStartEndFuncitonal featureSplicing information
Q86US8Region3959Note=EJC-binding motif 1%3B mediates interaction with the EJCType=Deletion;Start=1;End=1089
Q86US8Region3959Note=EJC-binding motif 1%3B mediates interaction with the EJCType=Deletion;Start=1;End=908
Q86US8Region114503Note=Interaction with telomeric DNAType=Deletion;Start=1;End=1089
Q86US8Region114503Note=Interaction with telomeric DNAType=Deletion;Start=1;End=908
Q86US8Region133153Note=EJC-binding motif 2%3B mediates interaction with the EJCType=Deletion;Start=1;End=1089
Q86US8Region133153Note=EJC-binding motif 2%3B mediates interaction with the EJCType=Deletion;Start=1;End=908


check button Interactors from STRING.
Gene nameInteractors


Related Drugs to SMG6


check button Drugs targeting this gene/protein.
(DrugBank)
UniProt accessionGene nameDrugBank IDDrug nameDrug groupActions
Q86US8SMG6DB05036Grn163linvestigational

Related Diseases to SMG6


check button Previous studies relating to the alternative splicing of SMG6 and disease information from the MeSH term (PubMed)
GenePMIDTitleAbstractMeSH IDMeSH term


Clinically important variants in SMG6


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