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:DNMT3B

Protein Summary

Gene summary

Gene name: DNMT3B
ASpdb.0 ID: 1789
	Gene
Gene symbol	DNMT3B
Gene ID	1789
Gene name	DNA methyltransferase 3 beta
Synonyms	FSHD4\|ICF\|ICF1\|M.HsaIIIB
Cytomap	20q11.21
Type of gene	protein-coding
Description	DNA (cytosine-5)-methyltransferase 3BDNA (cytosine-5-)-methyltransferase 3 betaDNA MTase HsaIIIBDNA cytosine-5--methyltransferase 3 betaDNA methyltransferase HsaIIIB
Modification date	20240416
UniProtAcc	Q9UBC3

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	DNMT3B	GO:0000122	negative regulation of transcription by RNA polymerase II	17303076
Gene	DNMT3B	GO:0003714	transcription corepressor activity	17303076
Gene	DNMT3B	GO:0003886	DNA (cytosine-5-)-methyltransferase activity	16543361
Gene	DNMT3B	GO:0005634	nucleus	17303076
Gene	DNMT3B	GO:0005654	nucleoplasm	-

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
Q9UBC3-1	Q9UBC3-1_6u8w_A.pdb	6U8W	X-ray	2.95	A	563	853

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
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-2	853	833	356	375	Deletion	none	none	355	355
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-3	853	770	356	375	Deletion	none	none	355	355
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-3	853	770	745	807	Deletion	none	none	724	724
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-4	853	724	356	375	Deletion	none	none	355	355
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-4	853	724	744	744	Substitution	R	S	724	724
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-4	853	724	745	853	Deletion	none	none	724	724
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-5	853	792	356	375	Deletion	none	none	355	355
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-5	853	792	768	853	Substitution	LKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE	DLWLSCALHRRVQHGPWCPPEAAGKVLERACHPTPLRPSEGLLCM	748	792
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-6	853	845	1	1	Substitution	M	MEPSPEPPSLESM	1	13
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-6	853	845	356	375	Deletion	none	none	367	367
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-7	853	694	69	144	Deletion	none	none	68	68
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-7	853	694	356	375	Deletion	none	none	279	279
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-7	853	694	744	806	Deletion	none	none	647	647
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-8	853	728	103	144	Deletion	none	none	102	102
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-8	853	728	356	375	Deletion	none	none	313	313
Q9UBC3	DNMT3B	Q9UBC3-1	Q9UBC3-8	853	728	744	806	Deletion	none	none	681	681

Multiple sequence alignment of our canonical and alternatively spliced DNMT3B

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of DNMT3B

UniProt-id	ENSG	ENST	ENSP
Q9UBC3-1	ENSG00000088305.19	ENST00000328111.6	ENSP00000328547.2
Q9UBC3-2	ENSG00000088305.19	ENST00000353855.6	ENSP00000313397.4
Q9UBC3-3	ENSG00000088305.19	ENST00000348286.6	ENSP00000337764.2
Q9UBC3-6	ENSG00000088305.19	ENST00000201963.3	ENSP00000201963.3
Q9UBC3-7	ENSG00000088305.19	ENST00000456297.6	ENSP00000412305.1
Q9UBC3-8	ENSG00000088305.19	ENST00000443239.7	ENSP00000403169.2

UniProt-id	NM ID	NP ID
Q9UBC3-1	NM_006892.3	NP_008823.1
Q9UBC3-2	NM_175848.1	NP_787044.1
Q9UBC3-3	NM_175849.1	NP_787045.1
Q9UBC3-6	NM_175850.2	NP_787046.1
Q9UBC3-7	NM_001207056.1	NP_001193985.1
Q9UBC3-8	NM_001207055.1	NP_001193984.1

Amino acid sequences of our canonical and alternatively spliced DNMT3B

accession_id	Protein sequence
Q9UBC3-1	MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGDGEDGDGSDTPVMPKL FRETRTRSESPAVRTRNNNSVSSRERHRPSPRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGT PQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFS EVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPVVNKS KVRRAGSRKLESRKYENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLF EGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRK DWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRN ITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVM IDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFG
Q9UBC3-2	MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGDGEDGDGSDTPVMPKL FRETRTRSESPAVRTRNNNSVSSRERHRPSPRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGT PQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFS EVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPENKTR RRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYD DDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEA PKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSP CNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLP GMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLL
Q9UBC3-3	MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGDGEDGDGSDTPVMPKL FRETRTRSESPAVRTRNNNSVSSRERHRPSPRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGT PQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFS EVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPENKTR RRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYD DDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEA PKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSP CNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLP
Q9UBC3-4	MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGDGEDGDGSDTPVMPKL FRETRTRSESPAVRTRNNNSVSSRERHRPSPRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGT PQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFS EVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPENKTR RRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYD DDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEA PKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSP CNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLP
Q9UBC3-5	MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGDGEDGDGSDTPVMPKL FRETRTRSESPAVRTRNNNSVSSRERHRPSPRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGT PQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFS EVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPENKTR RRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYD DDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEA PKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSP CNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLP
Q9UBC3-6	MEPSPEPPSLESMKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGDGED GDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPSPRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTI DLTDDTEDTHGTPQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGM RWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGL KPNNTQPENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTC RDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQA FFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEE WGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSA AHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDV
Q9UBC3-7	MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQSLRRRATASAGTPWPSPPSSYL TIDLTDDTEDTHGTPQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMS GMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIE GLKPNNTQPENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQ TCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRL QAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNI EEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKV
Q9UBC3-8	MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGDGEDGDGSDTPVMPKL FRETRTRSESPASLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGTPQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKE FGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVR AGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMAS DVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGT AAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYV ASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPF FWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAP

Protein Functional Features

Main function of this protein. (from UniProt)

DNMT3B (go to UniProt):Q9UBC3

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
Q9UBC3	Domain	575	853	Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01016	Type=Deletion;Start=745;End=807
Q9UBC3	Domain	575	853	Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01016	Type=Substitution;Start=744;End=744
Q9UBC3	Domain	575	853	Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01016	Type=Deletion;Start=745;End=853
Q9UBC3	Domain	575	853	Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01016	Type=Substitution;Start=768;End=853
Q9UBC3	Domain	575	853	Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01016	Type=Deletion;Start=744;End=806
Q9UBC3	Domain	575	853	Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01016	Type=Deletion;Start=744;End=806
Q9UBC3	Region	1	298	Note=Interaction with DNMT1 and DNMT3A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12145218;Dbxref=PMID:12145218	Type=Substitution;Start=1;End=1
Q9UBC3	Region	1	298	Note=Interaction with DNMT1 and DNMT3A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12145218;Dbxref=PMID:12145218	Type=Deletion;Start=69;End=144
Q9UBC3	Region	1	298	Note=Interaction with DNMT1 and DNMT3A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12145218;Dbxref=PMID:12145218	Type=Deletion;Start=103;End=144
Q9UBC3	Region	1	218	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=1;End=1
Q9UBC3	Region	1	218	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=69;End=144
Q9UBC3	Region	1	218	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=103;End=144
Q9UBC3	Region	341	423	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Region	341	423	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Region	341	423	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Region	341	423	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Region	341	423	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Region	341	423	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Region	341	423	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Compositional bias	1	18	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=1;End=1
Q9UBC3	Compositional bias	369	387	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Compositional bias	369	387	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Compositional bias	369	387	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Compositional bias	369	387	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Compositional bias	369	387	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Compositional bias	369	387	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375
Q9UBC3	Compositional bias	369	387	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=356;End=375

Gene Isoform Structures and Expression Levels for DNMT3B

Gene structures of our canonical and alternative spliced genes of DNMT3B
* 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 Q9UBC3-1

3D view using mol* of Q9UBC3-2

3D view using mol* of Q9UBC3-3

3D view using mol* of Q9UBC3-4

3D view using mol* of Q9UBC3-5

3D view using mol* of Q9UBC3-6

3D view using mol* of Q9UBC3-7

3D view using mol* of Q9UBC3-8

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 Q9UBC3-1

pLDDT distribution across the protein length of Q9UBC3-2

pLDDT distribution across the protein length of Q9UBC3-3

pLDDT distribution across the protein length of Q9UBC3-4

pLDDT distribution across the protein length of Q9UBC3-5

pLDDT distribution across the protein length of Q9UBC3-6

pLDDT distribution across the protein length of Q9UBC3-7

pLDDT distribution across the protein length of Q9UBC3-8

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 Q9UBC3-1

Ramachandran plot of Q9UBC3-2

Ramachandran plot of Q9UBC3-3

Ramachandran plot of Q9UBC3-5

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
Q9UBC3-1	1.047	341	0.991	933.303	0.419	0.769	1.053	0.486	1.259	0.386	0.668	168,170,171,172,173,579,581,582,583,584,586,587,60 1,604,605,606,607,610,627,628,629,646,647,648,649, 650,651,652,653,655,657,658,659,660,661,662,667,66 8,670,671,674,697,698,699,700,701,730,731,732,733, 773,774,775,776,777,778,779,828,831,832,833,834,83 5
Q9UBC3-2	1.066	125	1.071	268.226	0.496	0.797	1.023	0.598	1.066	0.561	0.714	527,530,531,533,535,536,537,538,539,540,541,542,54 3,544,673,695,696,697,698,699,700,716,717,718,719, 720,721,722,723,829
Q9UBC3-3	1.092	127	1.113	264.453	0.486	0.816	1.042	1	0.971	1.029	0.698	527,530,531,532,533,535,536,538,540,541,542,543,54 4,673,696,697,698,699,700,715,716,717,718,719,720, 721,722,723
Q9UBC3-4	1.034	88	1.092	405.083	0.641	0.707	0.886	1.368	0.656	2.085	1.387	559,560,561,562,563,565,566,567,570,571,581,624,62 6,627,628,629,630,631,675,676,677,678,679,701,703, 705,706,711,713,715,719
Q9UBC3-5	1.073	95	1.101	283.661	0.57	0.793	0.963	1.174	0.893	1.314	1.223	559,561,562,563,564,566,567,626,627,628,629,630,63 1,675,677,678,679,711,713,715,788,789
Q9UBC3-6	1.099	116	1.177	280.231	0.523	0.716	0.981	1.888	0.589	3.204	2.619	69,70,71,72,73,75,76,299,301,304,305,311,338,339,3 41,342,345,346,349
Q9UBC3-7	1.058	149	0.999	273.371	0.399	0.785	1.116	0.613	1.264	0.485	0.75	485,486,487,488,490,508,509,510,511,530,531,532,53 3,552,553,554,555,556,559,575,601,602,603,635,637, 669,672,673,674,675,676
Q9UBC3-8	1.104	121	1.07	237.699	0.442	0.853	1.157	0.729	1.172	0.622	0.813	405,485,488,489,491,493,494,496,497,498,499,500,50 1,502,504,631,654,655,657,673,674,675,676,677,678, 679,680,681,724

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 Q9UBC3-1_Q9UBC3-1_6u8w_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 Q9UBC3-1_6u8w_A_Q9UBC3-2.pdb

3D view using mol* of Q9UBC3-1_6u8w_A_Q9UBC3-3.pdb

3D view using mol* of Q9UBC3-1_6u8w_A_Q9UBC3-4.pdb

3D view using mol* of Q9UBC3-1_6u8w_A_Q9UBC3-5.pdb

3D view using mol* of Q9UBC3-1_6u8w_A_Q9UBC3-6.pdb

3D view using mol* of Q9UBC3-1_6u8w_A_Q9UBC3-7.pdb

3D view using mol* of Q9UBC3-1_6u8w_A_Q9UBC3-8.pdb

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

3D view using mol* of Q9UBC3-1_Q9UBC3-2.pdb

3D view using mol* of Q9UBC3-1_Q9UBC3-3.pdb

3D view using mol* of Q9UBC3-1_Q9UBC3-4.pdb

3D view using mol* of Q9UBC3-1_Q9UBC3-5.pdb

3D view using mol* of Q9UBC3-1_Q9UBC3-6.pdb

3D view using mol* of Q9UBC3-1_Q9UBC3-7.pdb

3D view using mol* of Q9UBC3-1_Q9UBC3-8.pdb

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

./stats/secondary_structure/figure/Q9UBC3-1_vs_Q9UBC3-2.png

./stats/secondary_structure/figure/Q9UBC3-1_vs_Q9UBC3-3.png

./stats/secondary_structure/figure/Q9UBC3-1_vs_Q9UBC3-4.png

./stats/secondary_structure/figure/Q9UBC3-1_vs_Q9UBC3-5.png

./stats/secondary_structure/figure/Q9UBC3-1_vs_Q9UBC3-6.png

./stats/secondary_structure/figure/Q9UBC3-1_vs_Q9UBC3-7.png

./stats/secondary_structure/figure/Q9UBC3-1_vs_Q9UBC3-8.png

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

./stats/relative_asa/Q9UBC3-1_vs_Q9UBC3-2.png

./stats/relative_asa/Q9UBC3-1_vs_Q9UBC3-3.png

./stats/relative_asa/Q9UBC3-1_vs_Q9UBC3-4.png

./stats/relative_asa/Q9UBC3-1_vs_Q9UBC3-5.png

./stats/relative_asa/Q9UBC3-1_vs_Q9UBC3-6.png

./stats/relative_asa/Q9UBC3-1_vs_Q9UBC3-7.png

./stats/relative_asa/Q9UBC3-1_vs_Q9UBC3-8.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q9UBC3	Region	1	298	Note=Interaction with DNMT1 and DNMT3A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12145218;Dbxref=PMID:12145218	Type=Substitution;Start=1;End=1
Q9UBC3	Region	1	298	Note=Interaction with DNMT1 and DNMT3A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12145218;Dbxref=PMID:12145218	Type=Deletion;Start=69;End=144
Q9UBC3	Region	1	298	Note=Interaction with DNMT1 and DNMT3A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12145218;Dbxref=PMID:12145218	Type=Deletion;Start=103;End=144

Interactors from STRING.

Gene name

Interactors

Related Drugs to DNMT3B

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
Q9UBC3	DNMT3B	DB01262	Decitabine	approved, investigational	inhibitor

Related Diseases to DNMT3B

Previous studies relating to the alternative splicing of DNMT3B and disease information from the MeSH term (PubMed)

Gene	PMID	Title	Abstract	MeSH ID	MeSH term
DNMT3B	19825994	A novel DNMT3B splice variant expressed in tumor and pluripotent cells modulates genomic DNA methylation patterns and displays altered DNA binding.	DNA methylation is an epigenetic mark essential for mammalian development, genomic stability, and imprinting. DNA methylation patterns are established and maintained by three DNA methyltransferases: DNMT1, DNMT3A, and DNMT3B. Interestingly, all three DNMTs make use of alternative splicing. DNMT3B has nearly 40 known splice variants expressed in a tissue- and disease-specific manner, but very little is known about the role of these splice variants in modulating DNMT3B function. We describe here the identification and characterization of a novel alternatively spliced form of DNMT3B lacking exon 5 within the NH(2)-terminal regulatory domain. This variant, which we term DNMT3B3Delta5 because it is closely related in structure to the ubiquitously expressed DNMT3B3 isoform, is highly expressed in pluripotent cells and brain tissue, is downregulated during differentiation, and is conserved in the mouse. Creation of pluripotent iPS cells from fibroblasts results in marked induction of DNMT3B3Delta5. DNMT3B3Delta5 expression is also altered in human disease, with tumor cell lines displaying elevated or reduced expression depending on their tissue of origin. We then compared the DNA binding and subcellular localization of DNMT3B3Delta5 versus DNMT3B3, revealing that DNMT3B3Delta5 possessed significantly enhanced DNA binding affinity and displayed an altered nuclear distribution. Finally, ectopic overexpression of DNMT3B3Delta5 resulted in repetitive element hypomethylation and enhanced cell growth in a colony formation assay. Taken together, these results show that DNMT3B3Delta5 may play an important role in stem cell maintenance or differentiation and suggest that sequences encoded by exon 5 influence the functional properties of DNMT3B.	D042822	Genomic Instability
DNMT3B	19825994	A novel DNMT3B splice variant expressed in tumor and pluripotent cells modulates genomic DNA methylation patterns and displays altered DNA binding.	DNA methylation is an epigenetic mark essential for mammalian development, genomic stability, and imprinting. DNA methylation patterns are established and maintained by three DNA methyltransferases: DNMT1, DNMT3A, and DNMT3B. Interestingly, all three DNMTs make use of alternative splicing. DNMT3B has nearly 40 known splice variants expressed in a tissue- and disease-specific manner, but very little is known about the role of these splice variants in modulating DNMT3B function. We describe here the identification and characterization of a novel alternatively spliced form of DNMT3B lacking exon 5 within the NH(2)-terminal regulatory domain. This variant, which we term DNMT3B3Delta5 because it is closely related in structure to the ubiquitously expressed DNMT3B3 isoform, is highly expressed in pluripotent cells and brain tissue, is downregulated during differentiation, and is conserved in the mouse. Creation of pluripotent iPS cells from fibroblasts results in marked induction of DNMT3B3Delta5. DNMT3B3Delta5 expression is also altered in human disease, with tumor cell lines displaying elevated or reduced expression depending on their tissue of origin. We then compared the DNA binding and subcellular localization of DNMT3B3Delta5 versus DNMT3B3, revealing that DNMT3B3Delta5 possessed significantly enhanced DNA binding affinity and displayed an altered nuclear distribution. Finally, ectopic overexpression of DNMT3B3Delta5 resulted in repetitive element hypomethylation and enhanced cell growth in a colony formation assay. Taken together, these results show that DNMT3B3Delta5 may play an important role in stem cell maintenance or differentiation and suggest that sequences encoded by exon 5 influence the functional properties of DNMT3B.	D009369	Neoplasms

Clinically important variants in DNMT3B

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance