SMED30020771

Overview
NameSMED30020771
Smed IDSMED30020771
Length (bp)1260
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 SMED30020771 (SMED30020771) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020771 (SMED30020771) 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 SMED30020771 (SMED30020771) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020771 (SMED30020771) 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



SMED30020771

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30020771h1SMcG0020989 SmedASXL_011021SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30020771h1SMcG0020989 SmedASXL_011021SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30020771h1SMcG0020989 SmedASXL_011020SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30020771h1SMcG0020989 SmedASXL_011020SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30020771h1SMcG0006154 Contig4948newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020771h1SMcG0006154 Contig4948uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30020771h1SMcG0020989 dd_Smed_v4_11194_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020771h1SMcG0020989 dd_Smed_v4_11194_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020771h1SMcG0020989 dd_Smed_v4_11194_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30020771h1SMcG0020989 dd_Smed_v4_11194_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020771h1SMcG0020989 Contig4948newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020771h1SMcG0020989 Contig4948uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020771 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001207:51482..53077 +6047
Homology
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BLAST of SMED30020771 vs. Planmine SMEST
Match: SMESG000016758.1 (SMESG000016758.1)

HSP 1 Score: 541.576 bits (1394), Expect = 0.000e+0
Identity = 318/351 (90.60%), Postives = 324/351 (92.31%), Query Frame = 3 
Query:    9 MHKMDNLNISDYYVSLEFLSAFPDNNIDKWIESGNSQKIKTKLSKLYKYGGSFSANHYQCTSTEPVQIPFLYKKNKNYFIEFTDTRLVHFFPKLSNILPNGPEVIPESFGDKLDKILNEIVKPKEASEPDIKIAEPDIKIAKPNNKRKLPKDKCEITPXXXXXXXXXXXXQENVDLDSLQPEIPQLILNSSSKTKAKQKSVKFNESIQIGDNNNTTIMKSDETEMKQKCQIVAGEIPRTNNESYEXXXXXXXXXXXXXXXATEMGIQNESNDVNVIDRFRSDEIAPVPDQLAVQLXXXXXXXXXXXXXXXXXA-ELGIQNESNDIDRFRLDEIAPV--PDRLAIALDENRV 1052
            MHKMDNLNISDYYVSLEFLSAFPDNNIDKWIESGNSQKIKTKLSKLYKYGGSFSANHYQCTSTEPVQIPFLYKKNKNYFIEFTDTRLVHFFPKLSN LPNGPEVIPESFGDKLDKILNEIVKPKEASEPDIK+AEPDIKIAKPNNKRKLPKDKCEITPLNKKLKTNINTKQENVDLDSLQPEIPQLILNSSS TKAKQKSVKFNES+ IGDNNNTTIMKSDETEMKQKCQIVAGEIPR NNESYEKTDSSPKKKRSKSHSATEMGIQNESND   IDRFR DEIA VPDQLA+ LNGGNN KK KK      A E GIQNESNDIDRFRLDEIAPV   D+L  A +EN +
Sbjct:    1 MHKMDNLNISDYYVSLEFLSAFPDNNIDKWIESGNSQKIKTKLSKLYKYGGSFSANHYQCTSTEPVQIPFLYKKNKNYFIEFTDTRLVHFFPKLSNTLPNGPEVIPESFGDKLDKILNEIVKPKEASEPDIKMAEPDIKIAKPNNKRKLPKDKCEITPLNKKLKTNINTKQENVDLDSLQPEIPQLILNSSSNTKAKQKSVKFNESVPIGDNNNTTIMKSDETEMKQKCQIVAGEIPRINNESYEKTDSSPKKKRSKSHSATEMGIQNESND---IDRFRLDEIAKVPDQLAIALNGGNNLKKNKKKSKIHSATEFGIQNESNDIDRFRLDEIAPVTAADQLTEAPNENNM 348

HSP 2 Score: 155.606 bits (392), Expect = 3.371e-42
Identity = 106/110 (96.36%), Postives = 107/110 (97.27%), Query Frame = 3 
Query:  792 TEMGIQNESNDVNVIDRFRSDEIAPVPDQLAVQLXXXXXXXXXXXXXXXXXAELGIQNESNDIDRFRLDEIAPVPDRLAIALDENRVXXXXXXXCSLITPNELEIETKLQ 1121
            TEMGIQNESNDVNVIDRFR DEIAPVPDQLAV+LNGGNNGKKKKKSKSHSGAELGIQNESNDIDRFRLDEIAPVPDRLAIALDENRVKKKKSKK SLITPNELEI TKLQ
Sbjct:  361 TEMGIQNESNDVNVIDRFRPDEIAPVPDQLAVELNGGNNGKKKKKSKSHSGAELGIQNESNDIDRFRLDEIAPVPDRLAIALDENRVKKKKSKKFSLITPNELEIATKLQ 470
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BLAST of SMED30020771 vs. Planmine SMEST
Match: SMESG000016758.1 (SMESG000016758.1)

HSP 1 Score: 533.487 bits (1373), Expect = 0.000e+0
Identity = 315/348 (90.52%), Postives = 321/348 (92.24%), Query Frame = 3 
Query:   18 MDNLNISDYYVSLEFLSAFPDNNIDKWIESGNSQKIKTKLSKLYKYGGSFSANHYQCTSTEPVQIPFLYKKNKNYFIEFTDTRLVHFFPKLSNILPNGPEVIPESFGDKLDKILNEIVKPKEASEPDIKIAEPDIKIAKPNNKRKLPKDKCEITPXXXXXXXXXXXXQENVDLDSLQPEIPQLILNSSSKTKAKQKSVKFNESIQIGDNNNTTIMKSDETEMKQKCQIVAGEIPRTNNESYEXXXXXXXXXXXXXXXATEMGIQNESNDVNVIDRFRSDEIAPVPDQLAVQLXXXXXXXXXXXXXXXXXA-ELGIQNESNDIDRFRLDEIAPV--PDRLAIALDENRV 1052
            MDNLNISDYYVSLEFLSAFPDNNIDKWIESGNSQKIKTKLSKLYKYGGSFSANHYQCTSTEPVQIPFLYKKNKNYFIEFTDTRLVHFFPKLSN LPNGPEVIPESFGDKLDKILNEIVKPKEASEPDIK+AEPDIKIAKPNNKRKLPKDKCEITPLNKKLKTNINTKQENVDLDSLQPEIPQLILNSSS TKAKQKSVKFNES+ IGDNNNTTIMKSDETEMKQKCQIVAGEIPR NNESYEKTDSSPKKKRSKSHSATEMGIQNESND   IDRFR DEIA VPDQLA+ LNGGNN KK KK      A E GIQNESNDIDRFRLDEIAPV   D+L  A +EN +
Sbjct:    1 MDNLNISDYYVSLEFLSAFPDNNIDKWIESGNSQKIKTKLSKLYKYGGSFSANHYQCTSTEPVQIPFLYKKNKNYFIEFTDTRLVHFFPKLSNTLPNGPEVIPESFGDKLDKILNEIVKPKEASEPDIKMAEPDIKIAKPNNKRKLPKDKCEITPLNKKLKTNINTKQENVDLDSLQPEIPQLILNSSSNTKAKQKSVKFNESVPIGDNNNTTIMKSDETEMKQKCQIVAGEIPRINNESYEKTDSSPKKKRSKSHSATEMGIQNESND---IDRFRLDEIAKVPDQLAIALNGGNNLKKNKKKSKIHSATEFGIQNESNDIDRFRLDEIAPVTAADQLTEAPNENNM 345

HSP 2 Score: 155.221 bits (391), Expect = 4.274e-42
Identity = 106/110 (96.36%), Postives = 107/110 (97.27%), Query Frame = 3 
Query:  792 TEMGIQNESNDVNVIDRFRSDEIAPVPDQLAVQLXXXXXXXXXXXXXXXXXAELGIQNESNDIDRFRLDEIAPVPDRLAIALDENRVXXXXXXXCSLITPNELEIETKLQ 1121
            TEMGIQNESNDVNVIDRFR DEIAPVPDQLAV+LNGGNNGKKKKKSKSHSGAELGIQNESNDIDRFRLDEIAPVPDRLAIALDENRVKKKKSKK SLITPNELEI TKLQ
Sbjct:  358 TEMGIQNESNDVNVIDRFRPDEIAPVPDQLAVELNGGNNGKKKKKSKSHSGAELGIQNESNDIDRFRLDEIAPVPDRLAIALDENRVKKKKSKKFSLITPNELEIATKLQ 467
[Close]
BLAST of SMED30020771 vs. Planmine SMEST
Match: SMESG000081326.1 (SMESG000081326.1)

HSP 1 Score: 129.413 bits (324), Expect = 1.936e-33
Identity = 62/122 (50.82%), Postives = 83/122 (68.03%), Query Frame = 3 
Query:    9 MHKMDNLNISDYYVSLEFLSAFPDNNIDKWIESGNSQKIKTKLSKLYKYGGSFSANHYQCTSTEPVQIPFLYKKNKNYFIEFTDTRLVHFFPKLSNILPNGPEVIPESFGDKLDKILNEIVK 374
            M  +DN++ISDYYVS+E+L  FPD+NI+KWIESGNS+KI+ KL+ L + GG+FS+NHY   S++    P LYKKN  +FIE+ +TR +HFFPK S+       V  E     +D I NE  K
Sbjct:    1 MINLDNIDISDYYVSIEYLDKFPDSNINKWIESGNSKKIRKKLNNLVQNGGTFSSNHYNVLSSDLTHTPMLYKKNDKWFIEYIETRDIHFFPKFSSSSIKSTNVSNEILSINIDSIPNETNK 122
The following BLAST results are available for this feature:
BLAST of SMED30020771 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 SMED30020771 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 SMED30020771 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 SMED30020771 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 SMED30020771 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 SMED30020771 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 SMED30020771 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 SMED30020771 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 SMED30020771 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 SMED30020771 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 SMED30020771 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 SMED30020771 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 SMED30020771 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 SMED30020771 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000016758.13.371e-4290.60SMESG000016758.1[more]
SMESG000016758.14.274e-4290.52SMESG000016758.1[more]
SMESG000081326.11.936e-3350.82SMESG000081326.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020771 ID=SMED30020771|Name=SMED30020771|organism=Schmidtea mediterranea sexual|type=transcript|length=1260bp
TATAAATGATGCATAAAATGGACAATTTAAATATATCAGATTACTATGTC
TCTTTAGAATTTTTATCCGCATTTCCTGATAATAATATTGATAAATGGAT
AGAAAGTGGAAACTCACAAAAAATTAAGACTAAATTGTCCAAACTATACA
AGTATGGTGGTTCATTTTCAGCCAATCACTATCAATGTACTAGTACTGAA
CCAGTACAAATTCCATTTTTATATAAAAAGAATAAAAATTATTTTATTGA
ATTCACAGATACTAGACTTGTTCATTTTTTCCCAAAATTAAGTAATATAC
TTCCAAATGGACCAGAAGTAATACCAGAATCGTTTGGTGATAAATTGGAT
AAGATATTAAATGAAATTGTTAAACCTAAAGAAGCTAGTGAACCTGATAT
TAAAATAGCTGAACCTGATATTAAAATAGCTAAACCTAATAACAAAAGGA
AGTTACCCAAAGATAAATGTGAGATAACACCATTAAATAAAAAACTTAAA
ACCAATATAAATACGAAACAAGAAAATGTTGATCTTGATAGTCTACAACC
AGAAATCCCTCAACTCATTTTAAATTCATCATCAAAGACGAAAGCAAAAC
AGAAAAGTGTGAAATTCAATGAAAGCATCCAAATCGGTGATAATAATAAC
ACAACAATAATGAAATCAGATGAGACAGAAATGAAACAAAAATGTCAAAT
TGTTGCAGGGGAAATTCCGCGAACCAACAACGAATCCTATGAGAAAACCG
ATTCCAGTCCGAAAAAGAAAAGATCGAAAAGTCACAGTGCTACAGAAATG
GGAATTCAGAACGAATCAAATGACGTAAATGTAATCGATCGGTTCCGATC
GGACGAAATCGCTCCAGTTCCCGATCAATTGGCAGTGCAACTGAACGGGG
GGAATAATGGTAAAAAGAAGAAGAAATCTAAAAGTCACAGCGGAGCAGAA
TTGGGAATTCAGAATGAATCAAATGATATCGATCGGTTCCGATTGGACGA
AATCGCCCCAGTTCCAGATCGATTGGCGATCGCCCTGGACGAGAATCGTG
TGAAAAAAAAGAAATCCAAAAAGTGCTCCTTGATAACCCCGAATGAACTG
GAAATCGAAACGAAATTACAAGAGCCGATTAAATCAAAGGAAATTCCGAC
GAAAGAAAAGAAGAAAGAAACCACTCGTCGAACCATCTGATTATCGATTA
TTTATTGCTGTGTATTTGTGAATATATTGATACGCCTTTATTTGTTCATA
TTGATTCTGG
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protein sequence of SMED30020771-orf-1

>SMED30020771-orf-1 ID=SMED30020771-orf-1|Name=SMED30020771-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=395bp
MMHKMDNLNISDYYVSLEFLSAFPDNNIDKWIESGNSQKIKTKLSKLYKY
GGSFSANHYQCTSTEPVQIPFLYKKNKNYFIEFTDTRLVHFFPKLSNILP
NGPEVIPESFGDKLDKILNEIVKPKEASEPDIKIAEPDIKIAKPNNKRKL
PKDKCEITPLNKKLKTNINTKQENVDLDSLQPEIPQLILNSSSKTKAKQK
SVKFNESIQIGDNNNTTIMKSDETEMKQKCQIVAGEIPRTNNESYEKTDS
SPKKKRSKSHSATEMGIQNESNDVNVIDRFRSDEIAPVPDQLAVQLNGGN
NGKKKKKSKSHSGAELGIQNESNDIDRFRLDEIAPVPDRLAIALDENRVK
KKKSKKCSLITPNELEIETKLQEPIKSKEIPTKEKKKETTRRTI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 293..320
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 234..273
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 242..261