SMED30024329

Overview
NameSMED30024329
Smed IDSMED30024329
Length (bp)1685
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30024329 (SMED30024329) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024329 (SMED30024329) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30024329 (SMED30024329) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024329 (SMED30024329) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30024329

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30024329SMESG000051020.1 dd_Smed_v4_3927_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30024329SMESG000051020.1 dd_Smed_v4_3927_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30024329SMESG000051020.1 dd_Smed_v4_3927_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30024329SMESG000051020.1 dd_Smed_v4_3927_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30024329SMESG000051020.1 Contig39437newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30024329SMESG000051020.1 Contig39437uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
gutSMED30024329SMESG000051020.1 Contig24429newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30024329SMESG000051020.1 Contig24429newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30024329SMESG000051020.1 Contig24429newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
cholinergic neuronSMED30024329SMESG000051020.1 dd_Smed_v6_3927_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30024329SMESG000051020.1 dd_Smed_v4_3927_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30024329 vs. Planmine SMEST
Match: SMESG000051020.1 (SMESG000051020.1)

HSP 1 Score: 252.292 bits (643), Expect = 3.060e-72
Identity = 183/183 (100.00%), Postives = 183/183 (100.00%), Query Frame = 2 
Query:   23 APNRMKSSYSQNNNRPDNHHTANFXXXXXXXXXXXXXXXXXXXXXXXGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKLDINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNXXXXXXXXXXXXPLXXXXXXXXXXXXXXXXXPDFIG 571
            APNRMKSSYSQNNNRPDNHHTANFHQLQHPPPSQHHHQQQPSQLLPPGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKLDINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNRKTRTKTSKHKSPLDSSSEDSFEENDNIDSDPDFIG
Sbjct: 2331 APNRMKSSYSQNNNRPDNHHTANFHQLQHPPPSQHHHQQQPSQLLPPGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKLDINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNRKTRTKTSKHKSPLDSSSEDSFEENDNIDSDPDFIG 2513
[Close]
BLAST of SMED30024329 vs. Planmine SMEST
Match: SMESG000051020.1 (SMESG000051020.1)

HSP 1 Score: 252.292 bits (643), Expect = 3.240e-72
Identity = 183/183 (100.00%), Postives = 183/183 (100.00%), Query Frame = 2 
Query:   23 APNRMKSSYSQNNNRPDNHHTANFXXXXXXXXXXXXXXXXXXXXXXXGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKLDINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNXXXXXXXXXXXXPLXXXXXXXXXXXXXXXXXPDFIG 571
            APNRMKSSYSQNNNRPDNHHTANFHQLQHPPPSQHHHQQQPSQLLPPGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKLDINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNRKTRTKTSKHKSPLDSSSEDSFEENDNIDSDPDFIG
Sbjct: 2334 APNRMKSSYSQNNNRPDNHHTANFHQLQHPPPSQHHHQQQPSQLLPPGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKLDINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNRKTRTKTSKHKSPLDSSSEDSFEENDNIDSDPDFIG 2516
[Close]
BLAST of SMED30024329 vs. Planmine SMEST
Match: SMESG000051020.1 (SMESG000051020.1)

HSP 1 Score: 244.588 bits (623), Expect = 1.457e-69
Identity = 183/193 (94.82%), Postives = 183/193 (94.82%), Query Frame = 2 
Query:   23 APNRMKSSYSQNNNRPDNHHTANFXXXXXXXXXXXXXXXXXXXXXXXGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKL----------DINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNXXXXXXXXXXXXPLXXXXXXXXXXXXXXXXXPDFIG 571
            APNRMKSSYSQNNNRPDNHHTANFHQLQHPPPSQHHHQQQPSQLLPPGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKL          DINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNRKTRTKTSKHKSPLDSSSEDSFEENDNIDSDPDFIG
Sbjct: 2331 APNRMKSSYSQNNNRPDNHHTANFHQLQHPPPSQHHHQQQPSQLLPPGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKLESIQDQFYFSDINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNRKTRTKTSKHKSPLDSSSEDSFEENDNIDSDPDFIG 2523
[Close]
BLAST of SMED30024329 vs. Planmine SMEST
Match: SMESG000051020.1 (SMESG000051020.1)

HSP 1 Score: 244.202 bits (622), Expect = 1.602e-69
Identity = 183/193 (94.82%), Postives = 183/193 (94.82%), Query Frame = 2 
Query:   23 APNRMKSSYSQNNNRPDNHHTANFXXXXXXXXXXXXXXXXXXXXXXXGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKL----------DINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNXXXXXXXXXXXXPLXXXXXXXXXXXXXXXXXPDFIG 571
            APNRMKSSYSQNNNRPDNHHTANFHQLQHPPPSQHHHQQQPSQLLPPGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKL          DINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNRKTRTKTSKHKSPLDSSSEDSFEENDNIDSDPDFIG
Sbjct: 2334 APNRMKSSYSQNNNRPDNHHTANFHQLQHPPPSQHHHQQQPSQLLPPGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKLESIQDQFYFSDINSIPHLTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPLIRPNRKTRTKTSKHKSPLDSSSEDSFEENDNIDSDPDFIG 2526
[Close]
BLAST of SMED30024329 vs. Planmine SMEST
Match: SMESG000080779.1 (SMESG000080779.1)

HSP 1 Score: 149.828 bits (377), Expect = 1.330e-42
Identity = 92/124 (74.19%), Postives = 103/124 (83.06%), Query Frame = 1 
Query: 1087 EEVAKLRAEIKALNAKLSQKQEPLXXXXXXXXXXXXXXXXXXLKDEIRAGLVRCRSQLSAKQEAIVIRNVIGKDIGVKILTPGTSRPPEKKPKMNIQPNWPCKKERERQNKLKTARMEGHILKS 1458
            EEV KLR EI++L+ KL+Q+ E L QAEQ+I+ QD EI EL LKDEIRAGLVRC SQLSA+QEA VIRNVIGKD GVKI+TPGTSRPPE+KPK N   N P K ERERQNK+KTARM GHILKS
Sbjct:    3 EEVIKLRVEIESLHLKLAQRDEALKQAEQRIRTQDSEIAELILKDEIRAGLVRCGSQLSAEQEATVIRNVIGKDNGVKIITPGTSRPPEEKPKRNRHRNRPGKMERERQNKVKTARMAGHILKS 126
The following BLAST results are available for this feature:
BLAST of SMED30024329 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024329 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000051020.13.060e-72100.00SMESG000051020.1[more]
SMESG000051020.13.240e-72100.00SMESG000051020.1[more]
SMESG000051020.11.457e-6994.82SMESG000051020.1[more]
SMESG000051020.11.602e-6994.82SMESG000051020.1[more]
SMESG000080779.11.330e-4274.19SMESG000080779.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024329 ID=SMED30024329|Name=SMED30024329|organism=Schmidtea mediterranea sexual|type=transcript|length=1685bp
GGGAGGAGGAGGTGGAGGTGGAGCTCCCAATCGGATGAAATCATCATATT
CCCAGAATAATAATAGACCAGATAATCATCACACTGCGAATTTCCACCAG
TTGCAGCATCCGCCGCCATCCCAACACCATCACCAACAGCAACCGTCACA
GTTACTGCCGCCTGGCAACGGCTCCCATCCACCGTCAATTGTAGATCACG
ACGCAATCATATCAAAATCCAATTCACATCACATGGCATTCATTCAGGGA
CAAAACCTCCGGGTGGAAGTCGACAAGTTGGACATCAACTCCATACCTCA
CCTCACGTCTCGCAGGGTGGTTCATCCTAAAAAGACCGTTGTACCTCGCC
AGCCAAATATCTCATCAGATGAAGATTCAGATGAATTTCTGAAGGACAAA
AGATCAAATATCTTCCGAAAAAAATCTGGATTGCTATCAAAAACTCCTTT
AATAAGGCCAAACAGAAAAACTCGGACAAAAACATCAAAACATAAATCTC
CATTGGATAGTTCTAGCGAAGACTCATTTGAAGAAAACGACAACATTGAT
TCAGATCCGGATTTTATTGGATAAGTAAATGGAAATTTTCTCACGCTTTC
TTTTTGTACAGGAATGAATGAAAATATTATTACCGACCTTTATTCTTATA
TATTATTTTTATTATTATTATTTTATTGTTTTTACTGTTATTTTCATTGT
ATACATAATGATTTATTTTTTTATAATTTATGTTCTCTAAACAATGTATA
TTATTCTCTGGTTCTCTTAGTTAGAATGACCCTCATTTGAGAAACCAACT
TCGTAGTCGAACATGGGTAACTAAAGATATGTAATTAATTATTTAATAGA
AAGTTAAATAAATACATAATGCTGAGGCGGTGTTGTAAGTTTCATAGTGT
AAATTTTTGTAAATCAATTTTTTTATGAAGGGTGTTTAAAATTATGCAGA
ATAGATATGTGAAGCTTATAACTAACAAATTAATTTTTTTAAAAATAAAA
TGTAAGAATTAATAAAAAGATCCTAAATAATAAGATCCCGAAAAAGCACG
TGTTAATAGAATTTCAAGAGTAAGCTTGTGAGATCAGAAGAAGTTGCTAA
ATTGAGAGCCGAGATCAAAGCCCTAAATGCTAAACTATCCCAAAAACAGG
AACCTCTAATACAAGCCGAGCAGAAGATACAAATTCAGGATAAGGAAATT
ATTGAACTGAAATTGAAAGACGAGATCCGAGCTGGACTCGTACGATGCAG
AAGCCAGCTATCTGCCAAGCAAGAGGCGATAGTTATTCGAAATGTAATAG
GAAAAGACATTGGAGTGAAAATCCTCACTCCAGGAACCTCGCGCCCGCCA
GAAAAAAAACCGAAAATGAATATACAACCAAATTGGCCTTGCAAGAAGGA
GCGCGAGAGGCAGAACAAACTCAAAACGGCTCGCATGGAGGGACACATCC
TCAAGTCCAACGGGATTTGAGTACCCACAATAATAAATTAACTTTTAATG
TGATATTTGTTTTGTTGGTTATTGAATTTAAATTATTAATAATAATATTA
TTTGTGTTTAGTTTTGATTTTATGGTTAAAAAGTTAAATCAGATAGATAA
TTGAGAATGGGGACCATTAAAATCAAATTATGACGTCTTCTATGACAGAT
CATGAACGCAGCCGAATATTAGGGCATTGGCAGCC
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protein sequence of SMED30024329-orf-1

>SMED30024329-orf-1 ID=SMED30024329-orf-1|Name=SMED30024329-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=120bp
MQKPAICQARGDSYSKCNRKRHWSENPHSRNLAPARKKTENEYTTKLALQ
EGAREAEQTQNGSHGGTHPQVQRDLSTHNNKLTFNVIFVLLVIEFKLLII
ILFVFSFDFMVKKLNQIDN*
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protein sequence of SMED30024329-orf-2

>SMED30024329-orf-2 ID=SMED30024329-orf-2|Name=SMED30024329-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=191bp
GGGGGGGAPNRMKSSYSQNNNRPDNHHTANFHQLQHPPPSQHHHQQQPSQ
LLPPGNGSHPPSIVDHDAIISKSNSHHMAFIQGQNLRVEVDKLDINSIPH
LTSRRVVHPKKTVVPRQPNISSDEDSDEFLKDKRSNIFRKKSGLLSKTPL
IRPNRKTRTKTSKHKSPLDSSSEDSFEENDNIDSDPDFIG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000136whole organism
PLANA:0000463cholinergic neuron
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 171..188
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 9..51
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 138..188
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..57