ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures

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	Protein Summary
	AS Summary
	Protein Functional Features
	Gene Isoform Structures and Expression Levels
	Protein Structures
	pLDDT Score Distribution
	Ramachandran Plot of Protein Structures
	Potential Active Site Information
	Protein Structure and Feature Comparision
	Protein-Protein Interaction
	Related Drugs
	Related Diseases
	Clinically Important Variants

Protein:BCOR

Protein Summary

Gene summary

Gene name: BCOR
ASpdb.0 ID: 54880
	Gene
Gene symbol	BCOR
Gene ID	54880
Gene name	BCL6 corepressor
Synonyms	ANOP2\|MAA2\|MCOPS2
Cytomap	Xp11.4
Type of gene	protein-coding
Description	BCL-6 corepressorBCL-6 coreceptorBCL-6 interacting corepressorBCL6 interacting corepressor
Modification date	20240403
UniProtAcc	Q6W2J9

Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Gene	BCOR	GO:0003714	transcription corepressor activity	10898795
Gene	BCOR	GO:0004842	ubiquitin-protein transferase activity	16943429
Gene	BCOR	GO:0005634	nucleus	10898795\|25331958
Gene	BCOR	GO:0005654	nucleoplasm	-
Gene	BCOR	GO:0006338	chromatin remodeling	16943429
Gene	BCOR	GO:0031072	heat shock protein binding	16943429
Gene	BCOR	GO:0045892	negative regulation of DNA-templated transcription	10898795
Gene	BCOR	GO:0140261	BCOR complex	16943429

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
Q6W2J9-1	Q6W2J9-1_4hpl_A.pdb	4HPL	X-ray	2.0	A	1636	1748

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

Q6W2J9

BCOR

Q6W2J9-1

Q6W2J9-2

1755

1721

1168

1201

Deletion

none

1167

Q6W2J9

BCOR

Q6W2J9-1

Q6W2J9-3

1755

1004

1000

1004

Substitution

MEGLQ

VSPPT

1000

1004

Q6W2J9

BCOR

Q6W2J9-1

Q6W2J9-3

1755

1004

1005

1755

Deletion

none

1004

Multiple sequence alignment of our canonical and alternatively spliced BCOR

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of BCOR

UniProt-id	ENSG	ENST	ENSP
Q6W2J9-1	ENSG00000183337.18	ENST00000378444.9	ENSP00000367705.4
Q6W2J9-1	ENSG00000183337.18	ENST00000406200.4	ENSP00000384485.3
Q6W2J9-1	ENSG00000183337.18	ENST00000615339.2	ENSP00000483217.2
Q6W2J9-1	ENSG00000183337.18	ENST00000672922.2	ENSP00000499892.2
Q6W2J9-1	ENSG00000183337.18	ENST00000679513.1	ENSP00000505761.1
Q6W2J9-1	ENSG00000183337.18	ENST00000680831.1	ENSP00000505507.1
Q6W2J9-2	ENSG00000183337.18	ENST00000342274.8	ENSP00000345923.4
Q6W2J9-2	ENSG00000183337.18	ENST00000397354.7	ENSP00000380512.3
Q6W2J9-2	ENSG00000183337.18	ENST00000673391.1	ENSP00000500446.1

UniProt-id	NM ID	NP ID
Q6W2J9-1	NM_001123385.1	NP_001116857.1
Q6W2J9-1	XM_005272616.1	XP_005272673.1
Q6W2J9-1	XM_005272618.3	XP_005272675.1
Q6W2J9-1	XM_006724536.3	XP_006724599.1
Q6W2J9-1	XM_011543929.2	XP_011542231.1
Q6W2J9-1	XM_011543930.1	XP_011542232.1
Q6W2J9-1	XM_011543931.2	XP_011542233.1
Q6W2J9-2	NM_001123383.1	NP_001116855.1
Q6W2J9-2	NM_017745.5	NP_060215.4
Q6W2J9-2	XM_017029615.1	XP_016885104.1

Amino acid sequences of our canonical and alternatively spliced BCOR

accession_id	Protein sequence
Q6W2J9-1	MLSATPLYGNVHSWMNSERVRMCGASEDRKILVNDGDASKARLELREENPLNHNVVDASTAHRIDGLAALSMDRTGLIREGLRVPGNIVY SSLCGLGSEKGREAATSTLGGLGFSSERNPEMQFKPNTPETVEASAVSGKPPNGFSAIYKTPPGIQKSAVATAEALGLDRPASDKQSPLN INGASYLRLPWVNPYMEGATPAIYPFLDSPNKYSLNMYKALLPQQSYSLAQPLYSPVCTNGERFLYLPPPHYVGPHIPSSLASPMRLSTP SASPAIPPLVHCADKSLPWKMGVSPGNPVDSHAYPHIQNSKQPRVPSAKAVTSGLPGDTALLLPPSPRPSPRVHLPTQPAADTYSEFHKH YARISTSPSVALSKPYMTVSSEFPAARLSNGKYPKAPEGGEGAQPVPGHARKTAVQDRKDGSSPPLLEKQTVTKDVTDKPLDLSSKVVDV DASKADHMKKMAPTVLVHSRAGSGLVLSGSEIPKETLSPPGNGCAIYRSEIISTAPSSWVVPGPSPNEENNGKSMSLKNKALDWAIPQQR SSSCPRMGGTDAVITNVSGSVSSAGRPASASPAPNANADGTKTSRSSVETTPSVIQHVGQPPATPAKHSSSTSSKGAKASNPEPSFKANE NGLPPSSIFLSPNEAFRSPPIPYPRSYLPYPAPEGIAVSPLSLHGKGPVYPHPVLLPNGSLFPGHLAPKPGLPYGLPTGRPEFVTYQDAL GLGMVHPMLIPHTPIEITKEEKPERRSRSHERARYEDPTLRNRFSEILETSSTKLHPDVPTDKNLKPNPNWNQGKTVVKSDKLVYVDLLR EEPDAKTDTNVSKPSFAAESVGQSAEPPKPSVEPALQQHRDFIALREELGRISDFHETYTFKQPVFTVSKDSVLAGTNKENLGLPVSTPF LEPPLGSDGPAVTFGKTQEDPKPFCVGSAPPSVDVTPTYTKDGADEAESNDGKVLKPKPSKLAKRIANSAGYVGDRFKCVTTELYADSSQ LSREQRALQMEGLQEDSILCLPAAYCERAMMRFSELEMKEREGGHPATKDSEMCKFSPADWERLKGNQDKKPKSVTLEEAIAEQNESERC EYSVGNKHRDPFEAPEDKDLPVEKYFVERQPVSEPPADQVASDMPHSPTLRVDRKRKVSGDSSHTETTAEEVPEDPLLKAKRRRVSKDDW PEREMTNSSSNHLEDPHYSELTNLKVCIELTGLHPKKQRHLLHLRERWEQQVSAADGKPGRQSRKEVTQATQPEAIPQGTNITEEKPGRK RAEAKGNRSWSEESLKPSDNEQGLPVFSGSPPMKSLSSTSAGGKKQAQPSCAPASRPPAKQQKIKENQKTDVLCADEEEDCQAASLLQKY TDNSEKPSGKRLCKTKHLIPQESRRGLPLTGEYYVENADGKVTVRRFRKRPEPSSDYDLSPAKQEPKPFDRLQQLLPASQSTQLPCSSSP QETTQSRPMPPEARRLIVNKNAGETLLQRAARLGYEEVVLYCLENKICDVNHRDNAGYCALHEACARGWLNIVRHLLEYGADVNCSAQDG TRPLHDAVENDHLEIVRLLLSYGADPTLATYSGRTIMKMTHSELMEKFLTDYLNDLQGRNDDDASGTWDFYGSSVCEPDDESGYDVLANP PGPEDQDDDDDAYSDVFEFEFSETPLLPCYNIQVSVAQGPRNWLLLSDVLKKLKMSSRIFRCNFPNVEIVTIAEAEFYRQVSASLLFSCS
Q6W2J9-2	MLSATPLYGNVHSWMNSERVRMCGASEDRKILVNDGDASKARLELREENPLNHNVVDASTAHRIDGLAALSMDRTGLIREGLRVPGNIVY SSLCGLGSEKGREAATSTLGGLGFSSERNPEMQFKPNTPETVEASAVSGKPPNGFSAIYKTPPGIQKSAVATAEALGLDRPASDKQSPLN INGASYLRLPWVNPYMEGATPAIYPFLDSPNKYSLNMYKALLPQQSYSLAQPLYSPVCTNGERFLYLPPPHYVGPHIPSSLASPMRLSTP SASPAIPPLVHCADKSLPWKMGVSPGNPVDSHAYPHIQNSKQPRVPSAKAVTSGLPGDTALLLPPSPRPSPRVHLPTQPAADTYSEFHKH YARISTSPSVALSKPYMTVSSEFPAARLSNGKYPKAPEGGEGAQPVPGHARKTAVQDRKDGSSPPLLEKQTVTKDVTDKPLDLSSKVVDV DASKADHMKKMAPTVLVHSRAGSGLVLSGSEIPKETLSPPGNGCAIYRSEIISTAPSSWVVPGPSPNEENNGKSMSLKNKALDWAIPQQR SSSCPRMGGTDAVITNVSGSVSSAGRPASASPAPNANADGTKTSRSSVETTPSVIQHVGQPPATPAKHSSSTSSKGAKASNPEPSFKANE NGLPPSSIFLSPNEAFRSPPIPYPRSYLPYPAPEGIAVSPLSLHGKGPVYPHPVLLPNGSLFPGHLAPKPGLPYGLPTGRPEFVTYQDAL GLGMVHPMLIPHTPIEITKEEKPERRSRSHERARYEDPTLRNRFSEILETSSTKLHPDVPTDKNLKPNPNWNQGKTVVKSDKLVYVDLLR EEPDAKTDTNVSKPSFAAESVGQSAEPPKPSVEPALQQHRDFIALREELGRISDFHETYTFKQPVFTVSKDSVLAGTNKENLGLPVSTPF LEPPLGSDGPAVTFGKTQEDPKPFCVGSAPPSVDVTPTYTKDGADEAESNDGKVLKPKPSKLAKRIANSAGYVGDRFKCVTTELYADSSQ LSREQRALQMEGLQEDSILCLPAAYCERAMMRFSELEMKEREGGHPATKDSEMCKFSPADWERLKGNQDKKPKSVTLEEAIAEQNESERC EYSVGNKHRDPFEAPEDKDLPVEKYFVERQPVSEPPADQVASDMPHSPTLRVDRKRKVSGDSSHTETTAEEVPEDPLLKAKRRRVSKGLH PKKQRHLLHLRERWEQQVSAADGKPGRQSRKEVTQATQPEAIPQGTNITEEKPGRKRAEAKGNRSWSEESLKPSDNEQGLPVFSGSPPMK SLSSTSAGGKKQAQPSCAPASRPPAKQQKIKENQKTDVLCADEEEDCQAASLLQKYTDNSEKPSGKRLCKTKHLIPQESRRGLPLTGEYY VENADGKVTVRRFRKRPEPSSDYDLSPAKQEPKPFDRLQQLLPASQSTQLPCSSSPQETTQSRPMPPEARRLIVNKNAGETLLQRAARLG YEEVVLYCLENKICDVNHRDNAGYCALHEACARGWLNIVRHLLEYGADVNCSAQDGTRPLHDAVENDHLEIVRLLLSYGADPTLATYSGR TIMKMTHSELMEKFLTDYLNDLQGRNDDDASGTWDFYGSSVCEPDDESGYDVLANPPGPEDQDDDDDAYSDVFEFEFSETPLLPCYNIQV SVAQGPRNWLLLSDVLKKLKMSSRIFRCNFPNVEIVTIAEAEFYRQVSASLLFSCSKDLEAFNPESKELLDLVEFTNEIQTLLGSSVEWL
Q6W2J9-3	MLSATPLYGNVHSWMNSERVRMCGASEDRKILVNDGDASKARLELREENPLNHNVVDASTAHRIDGLAALSMDRTGLIREGLRVPGNIVY SSLCGLGSEKGREAATSTLGGLGFSSERNPEMQFKPNTPETVEASAVSGKPPNGFSAIYKTPPGIQKSAVATAEALGLDRPASDKQSPLN INGASYLRLPWVNPYMEGATPAIYPFLDSPNKYSLNMYKALLPQQSYSLAQPLYSPVCTNGERFLYLPPPHYVGPHIPSSLASPMRLSTP SASPAIPPLVHCADKSLPWKMGVSPGNPVDSHAYPHIQNSKQPRVPSAKAVTSGLPGDTALLLPPSPRPSPRVHLPTQPAADTYSEFHKH YARISTSPSVALSKPYMTVSSEFPAARLSNGKYPKAPEGGEGAQPVPGHARKTAVQDRKDGSSPPLLEKQTVTKDVTDKPLDLSSKVVDV DASKADHMKKMAPTVLVHSRAGSGLVLSGSEIPKETLSPPGNGCAIYRSEIISTAPSSWVVPGPSPNEENNGKSMSLKNKALDWAIPQQR SSSCPRMGGTDAVITNVSGSVSSAGRPASASPAPNANADGTKTSRSSVETTPSVIQHVGQPPATPAKHSSSTSSKGAKASNPEPSFKANE NGLPPSSIFLSPNEAFRSPPIPYPRSYLPYPAPEGIAVSPLSLHGKGPVYPHPVLLPNGSLFPGHLAPKPGLPYGLPTGRPEFVTYQDAL GLGMVHPMLIPHTPIEITKEEKPERRSRSHERARYEDPTLRNRFSEILETSSTKLHPDVPTDKNLKPNPNWNQGKTVVKSDKLVYVDLLR EEPDAKTDTNVSKPSFAAESVGQSAEPPKPSVEPALQQHRDFIALREELGRISDFHETYTFKQPVFTVSKDSVLAGTNKENLGLPVSTPF LEPPLGSDGPAVTFGKTQEDPKPFCVGSAPPSVDVTPTYTKDGADEAESNDGKVLKPKPSKLAKRIANSAGYVGDRFKCVTTELYADSSQ

Protein Functional Features

Main function of this protein. (from UniProt)

BCOR (go to UniProt):Q6W2J9

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
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_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q6W2J9	Repeat	1462	1495	Note=ANK 1	Type=Deletion;Start=1005;End=1755
Q6W2J9	Repeat	1496	1525	Note=ANK 2	Type=Deletion;Start=1005;End=1755
Q6W2J9	Repeat	1529	1558	Note=ANK 3	Type=Deletion;Start=1005;End=1755
Q6W2J9	Region	1071	1187	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1168;End=1201
Q6W2J9	Region	1071	1187	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1005;End=1755
Q6W2J9	Region	1220	1328	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1005;End=1755
Q6W2J9	Region	1430	1451	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1005;End=1755
Q6W2J9	Region	1634	1748	Note=Necessary and sufficient for interaction with PCGF1	Type=Deletion;Start=1005;End=1755
Q6W2J9	Compositional bias	1071	1105	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1005;End=1755
Q6W2J9	Compositional bias	1128	1180	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1168;End=1201
Q6W2J9	Compositional bias	1128	1180	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1005;End=1755
Q6W2J9	Compositional bias	1234	1249	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1005;End=1755
Q6W2J9	Compositional bias	1254	1275	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1005;End=1755
Q6W2J9	Compositional bias	1276	1306	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1005;End=1755
Q6W2J9	Compositional bias	1430	1448	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1005;End=1755

Gene Isoform Structures and Expression Levels for BCOR

Gene structures of our canonical and alternative spliced genes of BCOR
* 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 Q6W2J9-1

3D view using mol* of Q6W2J9-2

3D view using mol* of Q6W2J9-3

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 Q6W2J9-1

pLDDT distribution across the protein length of Q6W2J9-2

pLDDT distribution across the protein length of Q6W2J9-3

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 Q6W2J9-1

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
Q6W2J9-1	1.017	325	1.053	806.736	0.554	0.687	0.9	0.656	0.917	0.716	1.04	1588,1589,1590,1591,1593,1594,1595,1596,1598,1599, 1600,1601,1603,1604,1615,1617,1635,1636,1637,1638, 1639,1640,1641,1642,1643,1644,1645,1646,1647,1648, 1649,1650,1651,1662,1664,1672,1701,1704,1706,1707, 1708,1709,1712,1729,1734,1737,1738,1739,1740,1741, 1742,1743,1744,1745,1746,1749
Q6W2J9-2	1.038	143	1.097	401.653	0.631	0.673	0.811	0.611	0.755	0.808	1.022	1605,1606,1608,1612,1613,1614,1615,1617,1618,1619, 1626,1628,1630,1638,1666,1669,1670,1671,1672,1695, 1703,1705,1706,1707,1708,1709,1710,1711,1712
Q6W2J9-3	0.695	48	0.575	73.059	0.556	0.579	0.848	0.099	1.299	0.076	0.508	13,14,15,16,17,18,752,753,754,755

Protein Structure and Feature Comparision

Protein Structure Comparision Using Template Modeling Scores (TM-score).

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)

3D view using mol* of Q6W2J9-1_Q6W2J9-1_4hpl_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 Q6W2J9-1_4hpl_A_Q6W2J9-2.pdb

3D view using mol* of Q6W2J9-1_4hpl_A_Q6W2J9-3.pdb

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of Q6W2J9-1_Q6W2J9-2.pdb

3D view using mol* of Q6W2J9-1_Q6W2J9-3.pdb

Protein Feature Comparison of the protein sequendary structures among the protiens.

./stats/secondary_structure/figure/Q6W2J9-1_vs_Q6W2J9-2.png

./stats/secondary_structure/figure/Q6W2J9-1_vs_Q6W2J9-3.png

Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.

./stats/relative_asa/Q6W2J9-1_vs_Q6W2J9-2.png

./stats/relative_asa/Q6W2J9-1_vs_Q6W2J9-3.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q6W2J9	Region	1634	1748	Note=Necessary and sufficient for interaction with PCGF1	Type=Deletion;Start=1005;End=1755

Interactors from STRING.

Gene name

Interactors

Related Drugs to BCOR

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to BCOR

Previous studies relating to the alternative splicing of BCOR and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in BCOR

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance