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:DYNC1I2

Protein Summary

Gene summary

Gene name: DYNC1I2
ASpdb.0 ID: 1781
	Gene
Gene symbol	DYNC1I2
Gene ID	1781
Gene name	dynein cytoplasmic 1 intermediate chain 2
Synonyms	DIC74\|DNCI2\|IC2\|NEDMIBA
Cytomap	2q31.1
Type of gene	protein-coding
Description	cytoplasmic dynein 1 intermediate chain 2DH IC-2dynein intermediate chain 2, cytosolicdynein, cytoplasmic, intermediate polypeptide 2testis tissue sperm-binding protein Li 66n
Modification date	20240407
UniProtAcc	Q13409

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	DYNC1I2	GO:0005813	centrosome	21399614
Gene	DYNC1I2	GO:0005874	microtubule	21525035
Gene	DYNC1I2	GO:0031982	vesicle	20682791

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
Q13409-1	Q13409-1_6f3a_g.pdb	6F3A	EM	8.2	g	208	624

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
Q13409	DYNC1I2	Q13409-1	Q13409-2	638	632	77	82	Deletion	none	none	76	76
Q13409	DYNC1I2	Q13409-1	Q13409-3	638	612	77	82	Deletion	none	none	76	76
Q13409	DYNC1I2	Q13409-1	Q13409-3	638	612	113	132	Deletion	none	none	106	106
Q13409	DYNC1I2	Q13409-1	Q13409-5	638	637	602	602	Deletion	none	none	601	601
Q13409	DYNC1I2	Q13409-1	Q13409-6	638	611	77	82	Deletion	none	none	76	76
Q13409	DYNC1I2	Q13409-1	Q13409-6	638	611	113	132	Deletion	none	none	106	106
Q13409	DYNC1I2	Q13409-1	Q13409-6	638	611	602	602	Deletion	none	none	575	575
Q13409	DYNC1I2	Q13409-1	Q13409-7	638	630	76	81	Substitution	VFSEYW	AEQPLRVVTADTCLFHYL	76	93
Q13409	DYNC1I2	Q13409-1	Q13409-7	638	630	113	132	Deletion	none	none	124	124

Multiple sequence alignment of our canonical and alternatively spliced DYNC1I2

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of DYNC1I2

UniProt-id	ENSG	ENST	ENSP
Q13409-1	ENSG00000077380.16	ENST00000397119.8	ENSP00000380308.3
Q13409-1	ENSG00000077380.16	ENST00000409773.5	ENSP00000386415.1
Q13409-1	ENSG00000292102.1	ENST00000709731.1	ENSP00000517844.1
Q13409-1	ENSG00000292102.1	ENST00000709739.1	ENSP00000517851.1
Q13409-2	ENSG00000077380.16	ENST00000409317.5	ENSP00000386591.1
Q13409-2	ENSG00000292102.1	ENST00000709738.1	ENSP00000517850.1
Q13409-3	ENSG00000077380.16	ENST00000340296.8	ENSP00000339430.4
Q13409-3	ENSG00000077380.16	ENST00000409197.5	ENSP00000386397.1
Q13409-3	ENSG00000292102.1	ENST00000709730.1	ENSP00000517843.1
Q13409-3	ENSG00000292102.1	ENST00000709736.1	ENSP00000517848.1
Q13409-5	ENSG00000077380.16	ENST00000409453.5	ENSP00000386886.1
Q13409-5	ENSG00000292102.1	ENST00000709741.1	ENSP00000517853.1
Q13409-6	ENSG00000077380.16	ENST00000508530.5	ENSP00000423339.1
Q13409-6	ENSG00000292102.1	ENST00000709735.1	ENSP00000517847.1
Q13409-7	ENSG00000077380.16	ENST00000410079.7	ENSP00000386522.3
Q13409-7	ENSG00000292102.1	ENST00000709732.1	ENSP00000517845.1

UniProt-id	NM ID	NP ID
Q13409-1	NM_001271785.1	NP_001258714.1
Q13409-1	NM_001378.2	NP_001369.1
Q13409-2	NM_001320882.1	NP_001307811.1
Q13409-2	NM_001320883.1	NP_001307812.1
Q13409-3	NM_001271788.1	NP_001258717.1
Q13409-3	NM_001271789.1	NP_001258718.1
Q13409-6	NM_001271790.1	NP_001258719.1
Q13409-6	NM_001320884.1	NP_001307813.1
Q13409-7	NM_001271786.1	NP_001258715.1
Q13409-7	NM_001271787.1	NP_001258716.1

Amino acid sequences of our canonical and alternatively spliced DYNC1I2

accession_id	Protein sequence
Q13409-1	MSDKSELKAELERKKQRLAQIREEKKRKEEERKKKETDQKKEAVAPVQEESDLEKKRREAEALLQSMGLTPESPIVFSEYWVPPPMSPSS KSVSTPSEAGSQDSGDGAVGSRTLHWDTDPSVLQLHSDSDLGRGPIKLGMAKITQVDFPPREIVTYTKETQTPVMAQPKEDEEEDDDVVA PKPPIEPEEEKTLKKDEENDSKAPPHELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSLNRQ FFDERWSKHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLW DNRSNKRTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVG SEEGSVYTACRHGSKAGISEMFEGHQGPITGIHCHAAVGAVDFSHLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALF ACVDGMGRLDLWNLNNDTEVPTASISVEGNPALNRVRWTHSGREIAVGDSEGQIVIYDVGEQIAVPRNDEWARFGRTLAEINANRADAEE
Q13409-2	MSDKSELKAELERKKQRLAQIREEKKRKEEERKKKETDQKKEAVAPVQEESDLEKKRREAEALLQSMGLTPESPIVPPPMSPSSKSVSTP SEAGSQDSGDGAVGSRTLHWDTDPSVLQLHSDSDLGRGPIKLGMAKITQVDFPPREIVTYTKETQTPVMAQPKEDEEEDDDVVAPKPPIE PEEEKTLKKDEENDSKAPPHELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSLNRQFFDERW SKHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLWDNRSNK RTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSV YTACRHGSKAGISEMFEGHQGPITGIHCHAAVGAVDFSHLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALFACVDGM GRLDLWNLNNDTEVPTASISVEGNPALNRVRWTHSGREIAVGDSEGQIVIYDVGEQIAVPRNDEWARFGRTLAEINANRADAEEEAATRI
Q13409-3	MSDKSELKAELERKKQRLAQIREEKKRKEEERKKKETDQKKEAVAPVQEESDLEKKRREAEALLQSMGLTPESPIVPPPMSPSSKSVSTP SEAGSQDSGDGAVGSRRGPIKLGMAKITQVDFPPREIVTYTKETQTPVMAQPKEDEEEDDDVVAPKPPIEPEEEKTLKKDEENDSKAPPH ELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSLNRQFFDERWSKHRVVSCLDWSSQYPELLV ASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLWDNRSNKRTPVQRTPLSAAAHTHPVYC VNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSVYTACRHGSKAGISEMFEGHQ GPITGIHCHAAVGAVDFSHLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDTEVPTASIS
Q13409-5	MSDKSELKAELERKKQRLAQIREEKKRKEEERKKKETDQKKEAVAPVQEESDLEKKRREAEALLQSMGLTPESPIVFSEYWVPPPMSPSS KSVSTPSEAGSQDSGDGAVGSRTLHWDTDPSVLQLHSDSDLGRGPIKLGMAKITQVDFPPREIVTYTKETQTPVMAQPKEDEEEDDDVVA PKPPIEPEEEKTLKKDEENDSKAPPHELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSLNRQ FFDERWSKHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLW DNRSNKRTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVG SEEGSVYTACRHGSKAGISEMFEGHQGPITGIHCHAAVGAVDFSHLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALF ACVDGMGRLDLWNLNNDTEVPTASISVEGNPALNRVRWTHSGREIAVGDSEGQIVIYDVGEIAVPRNDEWARFGRTLAEINANRADAEEE
Q13409-6	MSDKSELKAELERKKQRLAQIREEKKRKEEERKKKETDQKKEAVAPVQEESDLEKKRREAEALLQSMGLTPESPIVPPPMSPSSKSVSTP SEAGSQDSGDGAVGSRRGPIKLGMAKITQVDFPPREIVTYTKETQTPVMAQPKEDEEEDDDVVAPKPPIEPEEEKTLKKDEENDSKAPPH ELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSLNRQFFDERWSKHRVVSCLDWSSQYPELLV ASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLWDNRSNKRTPVQRTPLSAAAHTHPVYC VNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSVYTACRHGSKAGISEMFEGHQ GPITGIHCHAAVGAVDFSHLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDTEVPTASIS
Q13409-7	MSDKSELKAELERKKQRLAQIREEKKRKEEERKKKETDQKKEAVAPVQEESDLEKKRREAEALLQSMGLTPESPIAEQPLRVVTADTCLF HYLVPPPMSPSSKSVSTPSEAGSQDSGDGAVGSRRGPIKLGMAKITQVDFPPREIVTYTKETQTPVMAQPKEDEEEDDDVVAPKPPIEPE EEKTLKKDEENDSKAPPHELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSLNRQFFDERWSK HRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLWDNRSNKRT PVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSVYT ACRHGSKAGISEMFEGHQGPITGIHCHAAVGAVDFSHLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALFACVDGMGR LDLWNLNNDTEVPTASISVEGNPALNRVRWTHSGREIAVGDSEGQIVIYDVGEQIAVPRNDEWARFGRTLAEINANRADAEEEAATRIPA

Protein Functional Features

Main function of this protein. (from UniProt)

DYNC1I2 (go to UniProt):Q13409

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
Q13409	Repeat	568	607	Note=WD 7	Type=Deletion;Start=602;End=602
Q13409	Repeat	568	607	Note=WD 7	Type=Deletion;Start=602;End=602
Q13409	Region	1	135	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=77;End=82
Q13409	Region	1	135	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=77;End=82
Q13409	Region	1	135	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=113;End=132
Q13409	Region	1	135	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=77;End=82
Q13409	Region	1	135	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=113;End=132
Q13409	Region	1	135	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=76;End=81
Q13409	Region	1	135	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=113;End=132

Gene Isoform Structures and Expression Levels for DYNC1I2

Gene structures of our canonical and alternative spliced genes of DYNC1I2
* 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 Q13409-1

3D view using mol* of Q13409-2

3D view using mol* of Q13409-3

3D view using mol* of Q13409-5

3D view using mol* of Q13409-6

3D view using mol* of Q13409-7

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 Q13409-1

pLDDT distribution across the protein length of Q13409-2

pLDDT distribution across the protein length of Q13409-3

pLDDT distribution across the protein length of Q13409-5

pLDDT distribution across the protein length of Q13409-6

pLDDT distribution across the protein length of Q13409-7

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 Q13409-1

Ramachandran plot of Q13409-2

Ramachandran plot of Q13409-6

Ramachandran plot of Q13409-7

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
Q13409-1	1.088	215	1.016	559.776	0.45	0.829	1.075	0.43	1.292	0.332	0.643	283,284,285,286,287,288,289,336,337,338,339,340,34 2,385,386,387,388,390,391,435,436,437,438,439,440, 441,442,443,444,480,481,482,483,484,486,529,530,53 1,534,575,576,577,578,579,580
Q13409-2	1.094	182	0.992	542.969	0.419	0.838	1.122	0.164	1.385	0.118	0.763	278,279,280,281,282,283,284,331,332,333,334,335,33 6,337,380,381,382,383,384,385,429,430,431,432,433, 434,435,436,437,438,474,475,476,477,478,480,523,52 4,525,528,569,571,572,574
Q13409-3	1.092	193	0.967	535.766	0.404	0.835	1.134	0.119	1.454	0.082	0.55	258,259,260,261,262,263,264,311,312,313,314,315,31 6,359,360,361,362,363,364,365,409,410,411,412,413, 414,415,416,417,418,454,455,456,457,460,503,504,50 5,508,549,551,552,553,554
Q13409-5	1.097	172	0.969	548.114	0.457	0.843	1.106	0.167	1.462	0.114	0.609	284,285,286,287,288,289,337,338,339,340,341,342,38 6,387,388,389,390,391,435,436,437,438,439,440,441, 442,443,444,480,481,482,483,486,529,530,531,534,57 5,577,578,580
Q13409-6	1.099	191	0.975	543.998	0.43	0.845	1.165	0.262	1.449	0.181	0.604	258,259,260,261,262,263,264,311,312,313,314,315,31 6,317,318,319,359,360,361,362,363,364,365,409,410, 411,412,413,414,415,416,417,418,454,455,456,457,45 8,460,503,504,505,508,549,551,552,554
Q13409-7	1.106	185	0.98	537.824	0.381	0.857	1.14	0.163	1.456	0.112	0.612	275,276,277,278,279,280,281,282,328,329,330,331,33 2,333,334,335,377,378,379,380,381,382,383,428,429, 430,431,432,433,434,435,436,472,473,474,475,476,47 8,521,522,523,526,567,569,570,571,572

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 Q13409-1_Q13409-1_6f3a_g.pdb

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

3D view using mol* of Q13409-1_6f3a_g_Q13409-2.pdb

3D view using mol* of Q13409-1_6f3a_g_Q13409-3.pdb

3D view using mol* of Q13409-1_6f3a_g_Q13409-5.pdb

3D view using mol* of Q13409-1_6f3a_g_Q13409-6.pdb

3D view using mol* of Q13409-1_6f3a_g_Q13409-7.pdb

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

3D view using mol* of Q13409-1_Q13409-2.pdb

3D view using mol* of Q13409-1_Q13409-3.pdb

3D view using mol* of Q13409-1_Q13409-5.pdb

3D view using mol* of Q13409-1_Q13409-6.pdb

3D view using mol* of Q13409-1_Q13409-7.pdb

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

./stats/secondary_structure/figure/Q13409-1_vs_Q13409-2.png