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:GALNT10

Protein Summary

Gene summary

Gene name: GALNT10
ASpdb.0 ID: 55568
	Gene
Gene symbol	GALNT10
Gene ID	55568
Gene name	polypeptide N-acetylgalactosaminyltransferase 10
Synonyms	GALNACT10\|PPGALNACT10\|PPGANTASE10
Cytomap	5q33.2
Type of gene	protein-coding
Description	polypeptide N-acetylgalactosaminyltransferase 10GalNAc transferase 10UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 10UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)
Modification date	20240305
UniProtAcc	Q86SR1

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	GALNT10	GO:0004653	polypeptide N-acetylgalactosaminyltransferase activity	12417297\|18562306\|19460755
Gene	GALNT10	GO:0006493	protein O-linked glycosylation	12417297
Gene	GALNT10	GO:0016266	O-glycan processing	18562306\|19460755

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
Q86SR1-1	Q86SR1-1_2d7i_A.pdb	2D7I	X-ray	2.5	A	68	603

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

Q86SR1

GALNT10

Q86SR1-1

Q86SR1-2

603

541

190

251

Deletion

none

189

Q86SR1

GALNT10

Q86SR1-1

Q86SR1-3

603

366

354

366

Substitution

WMCGGRMEDIPCS

SQLSRRPVLGTAS

354

366

Q86SR1

GALNT10

Q86SR1-1

Q86SR1-3

603

366

367

603

Deletion

none

366

Q86SR1

GALNT10

Q86SR1-1

Q86SR1-4

603

276

329

Deletion

none

Q86SR1

GALNT10

Q86SR1-1

Q86SR1-4

603

276

330

352

Substitution

WELGGYDPGLEIWGGEQYEISFK

MLAWRDGELEAETSSSLFLLAMQ

Q86SR1

GALNT10

Q86SR1-1

Q86SR1-4

603

276

389

Substitution

VRT

Multiple sequence alignment of our canonical and alternatively spliced GALNT10

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of GALNT10

UniProt-id	ENSG	ENST	ENSP
Q86SR1-1	ENSG00000164574.16	ENST00000297107.11	ENSP00000297107.6
Q86SR1-2	ENSG00000164574.16	ENST00000377661.2	ENSP00000366889.2
Q86SR1-3	ENSG00000164574.16	ENST00000425427.6	ENSP00000415210.2

UniProt-id	NM ID	NP ID
Q86SR1-1	NM_198321.3	NP_938080.1

Amino acid sequences of our canonical and alternatively spliced GALNT10

accession_id	Protein sequence
Q86SR1-1	MRRKEKRLLQAVALVLAALVLLPNVGLWALYRERQPDGTPGGSGAAVAPAAGQGSHSRQKKTFFLGDGQKLKDWHDKEAIRRDAQRVGNG EQGRPYPMTDAERVDQAYRENGFNIYVSDKISLNRSLPDIRHPNCNSKRYLETLPNTSIIIPFHNEGWSSLLRTVHSVLNRSPPELVAEI VLVDDFSDREHLKKPLEDYMALFPSVRILRTKKREGLIRTRMLGASVATGDVITFLDSHCEANVNWLPPLLDRIARNRKTIVCPMIDVID HDDFRYETQAGDAMRGAFDWEMYYKRIPIPPELQKADPSDPFESPVMAGGLFAVDRKWFWELGGYDPGLEIWGGEQYEISFKVWMCGGRM EDIPCSRVGHIYRKYVPYKVPAGVSLARNLKRVAEVWMDEYAEYIYQRRPEYRHLSAGDVAVQKKLRSSLNCKSFKWFMTKIAWDLPKFY PPVEPPAAAWGEIRNVGTGLCADTKHGALGSPLRLEGCVRGRGEAAWNNMQVFTFTWREDIRPGDPQHTKKFCFDAISHTSPVTLYDCHS
Q86SR1-2	MRRKEKRLLQAVALVLAALVLLPNVGLWALYRERQPDGTPGGSGAAVAPAAGQGSHSRQKKTFFLGDGQKLKDWHDKEAIRRDAQRVGNG EQGRPYPMTDAERVDQAYRENGFNIYVSDKISLNRSLPDIRHPNCNSKRYLETLPNTSIIIPFHNEGWSSLLRTVHSVLNRSPPELVAEI VLVDDFSDRDRIARNRKTIVCPMIDVIDHDDFRYETQAGDAMRGAFDWEMYYKRIPIPPELQKADPSDPFESPVMAGGLFAVDRKWFWEL GGYDPGLEIWGGEQYEISFKVWMCGGRMEDIPCSRVGHIYRKYVPYKVPAGVSLARNLKRVAEVWMDEYAEYIYQRRPEYRHLSAGDVAV QKKLRSSLNCKSFKWFMTKIAWDLPKFYPPVEPPAAAWGEIRNVGTGLCADTKHGALGSPLRLEGCVRGRGEAAWNNMQVFTFTWREDIR PGDPQHTKKFCFDAISHTSPVTLYDCHSMKGNQLWKYRKDKTLYHPVSGSCMDCSESDHRIFMNTCNPSSLTQQWLFEHTNSTVLEKFNR
Q86SR1-3	MRRKEKRLLQAVALVLAALVLLPNVGLWALYRERQPDGTPGGSGAAVAPAAGQGSHSRQKKTFFLGDGQKLKDWHDKEAIRRDAQRVGNG EQGRPYPMTDAERVDQAYRENGFNIYVSDKISLNRSLPDIRHPNCNSKRYLETLPNTSIIIPFHNEGWSSLLRTVHSVLNRSPPELVAEI VLVDDFSDREHLKKPLEDYMALFPSVRILRTKKREGLIRTRMLGASVATGDVITFLDSHCEANVNWLPPLLDRIARNRKTIVCPMIDVID HDDFRYETQAGDAMRGAFDWEMYYKRIPIPPELQKADPSDPFESPVMAGGLFAVDRKWFWELGGYDPGLEIWGGEQYEISFKVSQLSRRP
Q86SR1-4	MLAWRDGELEAETSSSLFLLAMQVWMCGGRMEDIPCSRVGHIYRKYVPYKVPAGVSLARVRTLKRVAEVWMDEYAEYIYQRRPEYRHLSA GDVAVQKKLRSSLNCKSFKWFMTKIAWDLPKFYPPVEPPAAAWGEIRNVGTGLCADTKHGALGSPLRLEGCVRGRGEAAWNNMQVFTFTW REDIRPGDPQHTKKFCFDAISHTSPVTLYDCHSMKGNQLWKYRKDKTLYHPVSGSCMDCSESDHRIFMNTCNPSSLTQQWLFEHTNSTVL

Protein Functional Features

Main function of this protein. (from UniProt)

GALNT10 (go to UniProt):Q86SR1

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
Q86SR1	Topological domain	1	11	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1;End=329
Q86SR1	Transmembrane	12	31	Note=Helical%3B Signal-anchor for type II membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1;End=329
Q86SR1	Topological domain	32	603	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=190;End=251
Q86SR1	Topological domain	32	603	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=354;End=366
Q86SR1	Topological domain	32	603	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=367;End=603
Q86SR1	Topological domain	32	603	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1;End=329
Q86SR1	Topological domain	32	603	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=330;End=352
Q86SR1	Topological domain	32	603	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=389;End=389
Q86SR1	Domain	458	590	Note=Ricin B-type lectin;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00174	Type=Deletion;Start=367;End=603
Q86SR1	Region	38	59	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=329
Q86SR1	Region	144	253	Note=Catalytic subdomain A	Type=Deletion;Start=190;End=251
Q86SR1	Region	144	253	Note=Catalytic subdomain A	Type=Deletion;Start=1;End=329
Q86SR1	Region	311	373	Note=Catalytic subdomain B	Type=Substitution;Start=354;End=366
Q86SR1	Region	311	373	Note=Catalytic subdomain B	Type=Deletion;Start=367;End=603
Q86SR1	Region	311	373	Note=Catalytic subdomain B	Type=Deletion;Start=1;End=329
Q86SR1	Region	311	373	Note=Catalytic subdomain B	Type=Substitution;Start=330;End=352
Q86SR1	Region	373	384	Note=Flexible loop	Type=Deletion;Start=367;End=603

Gene Isoform Structures and Expression Levels for GALNT10

Gene structures of our canonical and alternative spliced genes of GALNT10
* 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 Q86SR1-1

3D view using mol* of Q86SR1-2

3D view using mol* of Q86SR1-3

3D view using mol* of Q86SR1-4

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.

pLDDT distribution across the protein length of Q86SR1-1

pLDDT distribution across the protein length of Q86SR1-2

pLDDT distribution across the protein length of Q86SR1-3

pLDDT distribution across the protein length of Q86SR1-4

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 Q86SR1-1

Ramachandran plot of Q86SR1-2

Ramachandran plot of Q86SR1-4

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
Q86SR1-1	1.084	184	0.987	408.17	0.41	0.824	1.056	0.563	1.374	0.41	0.66	111,152,153,154,155,156,185,214,216,217,220,221,23 7,238,239,266,291,292,293,294,318,319,320,321,341, 342,343,344,345,346,347,370,371,372,373,376,377,37 8,386,390,409
Q86SR1-2	1.066	745	1.09	2290.897	0.49	0.777	1.008	0.765	0.969	0.789	0.9	73,74,75,76,79,80,82,83,84,92,110,111,113,123,124, 125,126,127,128,129,130,131,138,139,140,141,144,14 5,147,149,150,151,152,153,154,155,156,160,161,163, 164,166,167,168,169,170,171,172,173,174,176,177,18 0,185,186,187,189,190,191,194,200,201,202,203,204, 205,207,214,216,217,220,221,222,224,229,230,231,23 2,234,247,248,249,250,252,254,255,256,257,258,259, 260,261,262,273,277,278,279,280,281,282,283,284,28 5,300,301,302,303,304,305,306,307,308,309,310,311, 314,315,316,317,324,327,328,347
Q86SR1-3	1.14	90	1.018	126.224	0.262	0.963	1.324	0.991	1.386	0.715	0.392	263,264,265,266,267,278,279,282,283,284,285,286,29 4,296,312,314,316,317,318,319,321,322,363
Q86SR1-4	1.051	154	1.099	521.703	0.596	0.71	0.911	1.244	0.82	1.517	0.646	15,18,21,22,63,66,71,74,77,78,80,81,82,108,111,112 ,115,119,123,124,125,126,127,128,129,130,133,177,1 79,180,181,185,189,190,191,192,194,213,266

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 Q86SR1-1_Q86SR1-1_2d7i_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 Q86SR1-1_2d7i_A_Q86SR1-2.pdb

3D view using mol* of Q86SR1-1_2d7i_A_Q86SR1-3.pdb

3D view using mol* of Q86SR1-1_2d7i_A_Q86SR1-4.pdb

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

3D view using mol* of Q86SR1-1_Q86SR1-2.pdb

3D view using mol* of Q86SR1-1_Q86SR1-3.pdb

3D view using mol* of Q86SR1-1_Q86SR1-4.pdb

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

./stats/secondary_structure/figure/Q86SR1-1_vs_Q86SR1-2.png

./stats/secondary_structure/figure/Q86SR1-1_vs_Q86SR1-3.png

./stats/secondary_structure/figure/Q86SR1-1_vs_Q86SR1-4.png

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

./stats/relative_asa/Q86SR1-1_vs_Q86SR1-2.png

./stats/relative_asa/Q86SR1-1_vs_Q86SR1-3.png

./stats/relative_asa/Q86SR1-1_vs_Q86SR1-4.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id

Subsection

Start

End

Funcitonal feature

Splicing information

Interactors from STRING.

Gene name

Interactors

Related Drugs to GALNT10

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to GALNT10

Previous studies relating to the alternative splicing of GALNT10 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in GALNT10

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance