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:ING4

Protein Summary

Gene summary

Gene name: ING4
ASpdb.0 ID: 51147
	Gene
Gene symbol	ING4
Gene ID	51147
Gene name	inhibitor of growth family member 4
Synonyms	my036\|p29ING4
Cytomap	12p13.31
Type of gene	protein-coding
Description	inhibitor of growth protein 4brain my036 proteincandidate tumor suppressor p33 ING1 homolog
Modification date	20240403
UniProtAcc	Q9UNL4

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	ING4	GO:0000123	histone acetyltransferase complex	16387653
Gene	ING4	GO:0001558	regulation of cell growth	22144582
Gene	ING4	GO:0003713	transcription coactivator activity	16387653
Gene	ING4	GO:0005634	nucleus	15029197
Gene	ING4	GO:0005654	nucleoplasm	16387653
Gene	ING4	GO:0005829	cytosol	-
Gene	ING4	GO:0006355	regulation of DNA-templated transcription	22144582
Gene	ING4	GO:0006473	protein acetylation	12750254
Gene	ING4	GO:0008285	negative regulation of cell population proliferation	12750254\|15251430
Gene	ING4	GO:0035064	methylated histone binding	16728974
Gene	ING4	GO:0036408	histone H3K14 acetyltransferase activity	16387653
Gene	ING4	GO:0043995	histone H4K5 acetyltransferase activity	16387653
Gene	ING4	GO:0043996	histone H4K8 acetyltransferase activity	16387653
Gene	ING4	GO:0043997	histone H4K12 acetyltransferase activity	16387653
Gene	ING4	GO:0045111	intermediate filament cytoskeleton	-
Gene	ING4	GO:0045892	negative regulation of DNA-templated transcription	15029197
Gene	ING4	GO:0045926	negative regulation of growth	12750254
Gene	ING4	GO:0046972	histone H4K16 acetyltransferase activity	16387653
Gene	ING4	GO:0051726	regulation of cell cycle	16387653
Gene	ING4	GO:0140889	DNA replication-dependent chromatin disassembly	16387653
Gene	ING4	GO:1902164	positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator	15251430
Gene	ING4	GO:1902749	regulation of cell cycle G2/M phase transition	15251430
Gene	ING4	GO:2000278	regulation of DNA biosynthetic process	16387653

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
Q9UNL4-1	Q9UNL4-1_4afl_A.pdb	4AFL	X-ray	2.28	A	3	104

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
Q9UNL4	ING4	Q9UNL4-1	Q9UNL4-2	249	248	131	131	Substitution	K	S	131	131
Q9UNL4	ING4	Q9UNL4-1	Q9UNL4-2	249	248	132	132	Deletion	none	none	131	131
Q9UNL4	ING4	Q9UNL4-1	Q9UNL4-3	249	225	13	37	Substitution	SIENLPFELQRNFQLMRDLDQRTED	N	13	13
Q9UNL4	ING4	Q9UNL4-1	Q9UNL4-4	249	245	129	132	Deletion	none	none	128	128
Q9UNL4	ING4	Q9UNL4-1	Q9UNL4-5	249	246	128	131	Substitution	GKKK	E	128	128
Q9UNL4	ING4	Q9UNL4-1	Q9UNL4-6	249	248	131	131	Deletion	none	none	130	130
Q9UNL4	ING4	Q9UNL4-1	Q9UNL4-7	249	246	128	130	Deletion	none	none	127	127
Q9UNL4	ING4	Q9UNL4-1	Q9UNL4-8	249	179	168	249	Substitution	SPEYGMPSVTFGSVHPSDVLDMPVDPNEPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCSQERKKK	VPLSGSILPVWG	168	179

Multiple sequence alignment of our canonical and alternatively spliced ING4

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of ING4

UniProt-id	ENSG	ENST	ENSP
Q9UNL4-1	ENSG00000111653.20	ENST00000396807.8	ENSP00000380024.4
Q9UNL4-2	ENSG00000111653.20	ENST00000341550.9	ENSP00000343396.4
Q9UNL4-3	ENSG00000111653.20	ENST00000444704.5	ENSP00000397343.2
Q9UNL4-4	ENSG00000111653.20	ENST00000446105.6	ENSP00000415903.2
Q9UNL4-5	ENSG00000111653.20	ENST00000412586.6	ENSP00000412705.2
Q9UNL4-8	ENSG00000111653.20	ENST00000423703.6	ENSP00000414008.2

UniProt-id	NM ID	NP ID
Q9UNL4-1	NM_001127582.1	NP_001121054.1
Q9UNL4-2	NM_016162.3	NP_057246.2
Q9UNL4-3	NM_001127585.1	NP_001121057.1
Q9UNL4-4	NM_001127584.1	NP_001121056.1
Q9UNL4-5	NM_001127583.1	NP_001121055.1
Q9UNL4-8	NM_001127586.1	NP_001121058.1

Amino acid sequences of our canonical and alternatively spliced ING4

accession_id	Protein sequence
Q9UNL4-1	MAAGMYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTY EMVDKHIRRLDTDLARFEADLKEKQIESSDYDSSSSKGKKKGRTQKEKKAARARSKGKNSDEEAPKTAQKKLKLVRTSPEYGMPSVTFGS
Q9UNL4-2	MAAGMYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTY EMVDKHIRRLDTDLARFEADLKEKQIESSDYDSSSSKGKKSRTQKEKKAARARSKGKNSDEEAPKTAQKKLKLVRTSPEYGMPSVTFGSV
Q9UNL4-3	MAAGMYLEHYLDNLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTYEMVDKHIRRLDTDLARFEADLKEK QIESSDYDSSSSKGKKKGRTQKEKKAARARSKGKNSDEEAPKTAQKKLKLVRTSPEYGMPSVTFGSVHPSDVLDMPVDPNEPTYCLCHQV
Q9UNL4-4	MAAGMYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTY EMVDKHIRRLDTDLARFEADLKEKQIESSDYDSSSSKGRTQKEKKAARARSKGKNSDEEAPKTAQKKLKLVRTSPEYGMPSVTFGSVHPS
Q9UNL4-5	MAAGMYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTY EMVDKHIRRLDTDLARFEADLKEKQIESSDYDSSSSKEGRTQKEKKAARARSKGKNSDEEAPKTAQKKLKLVRTSPEYGMPSVTFGSVHP
Q9UNL4-6	MAAGMYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTY EMVDKHIRRLDTDLARFEADLKEKQIESSDYDSSSSKGKKGRTQKEKKAARARSKGKNSDEEAPKTAQKKLKLVRTSPEYGMPSVTFGSV
Q9UNL4-7	MAAGMYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTY EMVDKHIRRLDTDLARFEADLKEKQIESSDYDSSSSKKGRTQKEKKAARARSKGKNSDEEAPKTAQKKLKLVRTSPEYGMPSVTFGSVHP
Q9UNL4-8	MAAGMYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTY

Protein Functional Features

Main function of this protein. (from UniProt)

ING4 (go to UniProt):Q9UNL4

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
Q9UNL4	Zinc finger	196	245	Note=PHD-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00146	Type=Substitution;Start=168;End=249
Q9UNL4	Region	115	164	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=131;End=131
Q9UNL4	Region	115	164	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=132;End=132
Q9UNL4	Region	115	164	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=129;End=132
Q9UNL4	Region	115	164	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=128;End=131
Q9UNL4	Region	115	164	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=131;End=131
Q9UNL4	Region	115	164	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=128;End=130
Q9UNL4	Coiled coil	25	118	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22334692;Dbxref=PMID:22334692	Type=Substitution;Start=13;End=37
Q9UNL4	Motif	127	148	Note=Bipartite nuclear localization signal	Type=Substitution;Start=131;End=131
Q9UNL4	Motif	127	148	Note=Bipartite nuclear localization signal	Type=Deletion;Start=132;End=132
Q9UNL4	Motif	127	148	Note=Bipartite nuclear localization signal	Type=Deletion;Start=129;End=132
Q9UNL4	Motif	127	148	Note=Bipartite nuclear localization signal	Type=Substitution;Start=128;End=131
Q9UNL4	Motif	127	148	Note=Bipartite nuclear localization signal	Type=Deletion;Start=131;End=131
Q9UNL4	Motif	127	148	Note=Bipartite nuclear localization signal	Type=Deletion;Start=128;End=130
Q9UNL4	Compositional bias	115	130	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=129;End=132
Q9UNL4	Compositional bias	115	130	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=128;End=131
Q9UNL4	Compositional bias	115	130	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=128;End=130

Gene Isoform Structures and Expression Levels for ING4

Gene structures of our canonical and alternative spliced genes of ING4
* 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 Q9UNL4-1

3D view using mol* of Q9UNL4-2

3D view using mol* of Q9UNL4-3

3D view using mol* of Q9UNL4-4

3D view using mol* of Q9UNL4-5

3D view using mol* of Q9UNL4-6

3D view using mol* of Q9UNL4-7

3D view using mol* of Q9UNL4-8

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 Q9UNL4-1

pLDDT distribution across the protein length of Q9UNL4-2

pLDDT distribution across the protein length of Q9UNL4-3

pLDDT distribution across the protein length of Q9UNL4-4

pLDDT distribution across the protein length of Q9UNL4-5

pLDDT distribution across the protein length of Q9UNL4-6

pLDDT distribution across the protein length of Q9UNL4-7

pLDDT distribution across the protein length of Q9UNL4-8

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 Q9UNL4-1

Ramachandran plot of Q9UNL4-2

Ramachandran plot of Q9UNL4-3

Ramachandran plot of Q9UNL4-4

Ramachandran plot of Q9UNL4-6

Ramachandran plot of Q9UNL4-8

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
Q9UNL4-1	0.87	65	0.889	200.312	0.645	0.642	0.865	0.616	0.78	0.789	1.787	90,93,94,97,98,101,102,183,184,187,189,190,191,192 ,193,194,195,203,204,206
Q9UNL4-2	0.837	44	0.913	84.035	0.659	0.572	0.753	2.639	0.166	15.921	1.188	3,6,7,9,10,13,99,100,103,104,107
Q9UNL4-3	0.679	36	0.63	122.451	0.561	0.635	0.928	0.343	0.967	0.355	2.51	66,70,73,74,77,165,166,167,168,169,170,171
Q9UNL4-4	0.856	71	0.859	229.81	0.548	0.631	0.868	0.471	0.958	0.491	2.349	90,94,97,98,101,183,185,186,187,188,189,190,191,20 0
Q9UNL4-5	0.79	32	0.829	86.779	0.595	0.635	0.914	2.253	0.256	8.783	2.424	180,181,183,184,200,201,203
Q9UNL4-6	0.852	36	0.896	71.001	0.556	0.688	0.984	3.265	0.249	13.089	0.662	3,6,7,9,10,100,103,104,107
Q9UNL4-7	0.829	37	0.891	76.146	0.654	0.618	0.843	2.994	0.158	18.989	1.346	3,6,7,9,10,100,103,104,107
Q9UNL4-8	0.739	31	0.804	63.798	0.713	0.525	0.626	2.468	0.107	22.999	1.122	3,6,7,10,100,103,104,107

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 Q9UNL4-1_Q9UNL4-1_4afl_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 Q9UNL4-1_4afl_A_Q9UNL4-2.pdb

3D view using mol* of Q9UNL4-1_4afl_A_Q9UNL4-3.pdb

3D view using mol* of Q9UNL4-1_4afl_A_Q9UNL4-4.pdb

3D view using mol* of Q9UNL4-1_4afl_A_Q9UNL4-5.pdb

3D view using mol* of Q9UNL4-1_4afl_A_Q9UNL4-6.pdb

3D view using mol* of Q9UNL4-1_4afl_A_Q9UNL4-7.pdb

3D view using mol* of Q9UNL4-1_4afl_A_Q9UNL4-8.pdb

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

3D view using mol* of Q9UNL4-1_Q9UNL4-2.pdb

3D view using mol* of Q9UNL4-1_Q9UNL4-3.pdb

3D view using mol* of Q9UNL4-1_Q9UNL4-4.pdb

3D view using mol* of Q9UNL4-1_Q9UNL4-5.pdb

3D view using mol* of Q9UNL4-1_Q9UNL4-6.pdb

3D view using mol* of Q9UNL4-1_Q9UNL4-7.pdb

3D view using mol* of Q9UNL4-1_Q9UNL4-8.pdb

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

./stats/secondary_structure/figure/Q9UNL4-1_vs_Q9UNL4-2.png