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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:SEC23A-SEC23A (FusionGDB2 ID:79560)

Fusion Gene Summary for SEC23A-SEC23A

check button Fusion gene summary
Fusion gene informationFusion gene name: SEC23A-SEC23A
Fusion gene ID: 79560
HgeneTgene
Gene symbol

SEC23A

SEC23A

Gene ID

10484

10484

Gene nameSec23 homolog A, COPII coat complex componentSec23 homolog A, COPII coat complex component
SynonymsCLSD|hSec23ACLSD|hSec23A
Cytomap

14q21.1

14q21.1

Type of geneprotein-codingprotein-coding
Descriptionprotein transport protein Sec23ASEC23-related protein ASec23 homolog A, coat complex II componentprotein transport protein Sec23ASEC23-related protein ASec23 homolog A, coat complex II component
Modification date2020032720200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000537403, ENST00000307712, 
ENST00000536508, ENST00000545328, 
ENST00000553925, ENST00000548032, 
ENST00000557280, ENST00000553970, 
ENST00000537403, ENST00000307712, 
ENST00000536508, ENST00000545328, 
ENST00000553925, ENST00000548032, 
ENST00000557280, ENST00000553970, 
Fusion gene scores* DoF score10 X 12 X 6=7205 X 6 X 2=60
# samples 126
** MAII scorelog2(12/720*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/60*10)=0
Context

PubMed: SEC23A [Title/Abstract] AND SEC23A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSEC23A(39502269)-SEC23A(39501988), # samples:1
SEC23A(39502056)-SEC23A(39524489), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneSEC23A

GO:0090110

cargo loading into COPII-coated vesicle

17499046|18843296

TgeneSEC23A

GO:0090110

cargo loading into COPII-coated vesicle

17499046|18843296


check buttonFusion gene breakpoints across SEC23A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across SEC23A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/AD82153SEC23Achr14

39502269

-SEC23Achr14

39501988

+
ChiTaRS5.0N/AF00808SEC23Achr14

39502056

+SEC23Achr14

39524489

-


Top

Fusion Gene ORF analysis for SEC23A-SEC23A

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-3UTRENST00000537403ENST00000537403SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000537403ENST00000307712SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000537403ENST00000536508SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000537403ENST00000545328SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000537403ENST00000553925SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000537403ENST00000548032SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000537403ENST00000557280SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000537403ENST00000553970SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000307712ENST00000537403SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000307712ENST00000307712SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000307712ENST00000536508SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000307712ENST00000545328SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000307712ENST00000553925SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000307712ENST00000548032SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000307712ENST00000557280SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000307712ENST00000553970SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000536508ENST00000537403SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000536508ENST00000307712SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000536508ENST00000536508SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000536508ENST00000545328SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000536508ENST00000553925SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000536508ENST00000548032SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000536508ENST00000557280SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000536508ENST00000553970SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000545328ENST00000537403SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000545328ENST00000307712SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000545328ENST00000536508SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000545328ENST00000545328SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000545328ENST00000553925SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000545328ENST00000548032SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000545328ENST00000557280SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000545328ENST00000553970SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000553925ENST00000537403SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000553925ENST00000307712SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000553925ENST00000536508SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000553925ENST00000545328SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000553925ENST00000553925SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000553925ENST00000548032SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000553925ENST00000557280SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000553925ENST00000553970SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000548032ENST00000537403SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000548032ENST00000307712SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000548032ENST00000536508SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000548032ENST00000545328SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000548032ENST00000553925SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000548032ENST00000548032SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000548032ENST00000557280SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000548032ENST00000553970SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000557280ENST00000537403SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000557280ENST00000307712SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000557280ENST00000536508SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000557280ENST00000545328SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000557280ENST00000553925SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000557280ENST00000548032SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000557280ENST00000557280SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000557280ENST00000553970SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000553970ENST00000537403SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000553970ENST00000307712SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3UTRENST00000553970ENST00000536508SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000553970ENST00000545328SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000553970ENST00000553925SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000553970ENST00000548032SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000553970ENST00000557280SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-intronENST00000553970ENST00000553970SEC23Achr14

39502269

-SEC23Achr14

39501988

+
intron-3CDSENST00000537403ENST00000537403SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000537403ENST00000307712SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000537403ENST00000536508SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000537403ENST00000545328SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000537403ENST00000553925SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000537403ENST00000548032SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000537403ENST00000557280SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000537403ENST00000553970SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000307712ENST00000537403SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000307712ENST00000307712SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000307712ENST00000536508SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000307712ENST00000545328SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000307712ENST00000553925SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000307712ENST00000548032SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000307712ENST00000557280SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000307712ENST00000553970SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000536508ENST00000537403SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000536508ENST00000307712SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000536508ENST00000536508SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000536508ENST00000545328SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000536508ENST00000553925SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000536508ENST00000548032SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000536508ENST00000557280SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000536508ENST00000553970SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000545328ENST00000537403SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000545328ENST00000307712SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000545328ENST00000536508SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000545328ENST00000545328SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000545328ENST00000553925SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000545328ENST00000548032SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000545328ENST00000557280SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000545328ENST00000553970SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000553925ENST00000537403SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000553925ENST00000307712SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000553925ENST00000536508SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000553925ENST00000545328SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000553925ENST00000553925SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000553925ENST00000548032SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000553925ENST00000557280SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000553925ENST00000553970SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000548032ENST00000537403SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000548032ENST00000307712SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000548032ENST00000536508SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000548032ENST00000545328SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000548032ENST00000553925SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000548032ENST00000548032SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000548032ENST00000557280SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000548032ENST00000553970SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000557280ENST00000537403SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000557280ENST00000307712SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000557280ENST00000536508SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000557280ENST00000545328SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000557280ENST00000553925SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000557280ENST00000548032SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000557280ENST00000557280SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000557280ENST00000553970SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000553970ENST00000537403SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000553970ENST00000307712SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000553970ENST00000536508SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-3CDSENST00000553970ENST00000545328SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000553970ENST00000553925SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000553970ENST00000548032SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000553970ENST00000557280SEC23Achr14

39502056

+SEC23Achr14

39524489

-
intron-intronENST00000553970ENST00000553970SEC23Achr14

39502056

+SEC23Achr14

39524489

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

Top

Fusion Genomic Features for SEC23A-SEC23A


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

Top

Fusion Protein Features for SEC23A-SEC23A


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

check buttonRetention analysis result of each fusion partner 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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


Top

Fusion Gene Sequence for SEC23A-SEC23A


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

Top

Fusion Gene PPI Analysis for SEC23A-SEC23A


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for SEC23A-SEC23A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for SEC23A-SEC23A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSEC23AC0029408Degenerative polyarthritis1CTD_human
HgeneSEC23AC0086743Osteoarthrosis Deformans1CTD_human
HgeneSEC23AC1843042Craniolenticulosutural Dysplasia1CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneSEC23AC0029408Degenerative polyarthritis1CTD_human
TgeneSEC23AC0086743Osteoarthrosis Deformans1CTD_human
TgeneSEC23AC1843042Craniolenticulosutural Dysplasia1CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT