SMED30031252

Overview
NameSMED30031252
Smed IDSMED30031252
Length (bp)1962
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 SMED30031252 (SMED30031252) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031252 (SMED30031252) 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 SMED30031252 (SMED30031252) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031252 (SMED30031252) 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



SMED30031252

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30031252SMESG000017120.1 dd_Smed_v4_6865_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30031252SMESG000017120.1 dd_Smed_v4_6865_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30031252SMESG000017120.1 dd_Smed_v4_6865_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30031252SMESG000017120.1 dd_Smed_v4_6865_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30031252SMESG000017120.1 dd_Smed_v4_6865_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30031252SMESG000017120.1 SMED_10667_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30031252SMESG000017120.1 SMED_10667_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30031252 vs. Planmine SMEST
Match: SMESG000017120.1 (SMESG000017120.1)

HSP 1 Score: 955.281 bits (2468), Expect = 0.000e+0
Identity = 521/521 (100.00%), Postives = 521/521 (100.00%), Query Frame = 3 
Query:  231 MNNHNNQFGLTNSAGYSHNGNYFENSHGSMINPSPIRSDMNLIRPIPKKVDLSKMIYQQFVDPYPRQNQSSILELSETMSQNIFSEMCQNAMSSNNAQNTIGNRFNEFSRRLQNPHFPFNNSRLSYNQLLMAXXXXXXSEFFKNHIYPNSINLPPSPVLGTNMDPYLYSNINYQVPIRHNQVSSMMYMSRKDSEEKSPNKELYNEMKSNNKVQYFPKTSLSDDLIENHFSMSLNSHMKFDFKSNESLLITSKQERISRKPLKQQYKPEIDKSCKAIKRAKKSKATPDNFDRSQDMSHTLCATPSDSSISPNSMVSCRSTITPQAVYQNNFNTATLLVNSQNSNNHLSVINIKTSDPXXXXXXXXXXXXXLINDGNSRSLSLHESQFQGLPLKKRIKWQIENDDTDVEVLEDNEIKKTNDGKSDEIRQTTQSTDSEKSGQTVQNDSPLGISEYPLKTFQKTFLPMEKHXXXXXXXXXNEESTDXXXXXXXXXXXXXXXXXXNGKYSFSLKDQNGLLFVDNNI 1793
            MNNHNNQFGLTNSAGYSHNGNYFENSHGSMINPSPIRSDMNLIRPIPKKVDLSKMIYQQFVDPYPRQNQSSILELSETMSQNIFSEMCQNAMSSNNAQNTIGNRFNEFSRRLQNPHFPFNNSRLSYNQLLMANNNRNNSEFFKNHIYPNSINLPPSPVLGTNMDPYLYSNINYQVPIRHNQVSSMMYMSRKDSEEKSPNKELYNEMKSNNKVQYFPKTSLSDDLIENHFSMSLNSHMKFDFKSNESLLITSKQERISRKPLKQQYKPEIDKSCKAIKRAKKSKATPDNFDRSQDMSHTLCATPSDSSISPNSMVSCRSTITPQAVYQNNFNTATLLVNSQNSNNHLSVINIKTSDPSSSFQKTSQFSTSLINDGNSRSLSLHESQFQGLPLKKRIKWQIENDDTDVEVLEDNEIKKTNDGKSDEIRQTTQSTDSEKSGQTVQNDSPLGISEYPLKTFQKTFLPMEKHSSSSDSDSDNEESTDAAVTSAAAAATATSAAVTNGKYSFSLKDQNGLLFVDNNI
Sbjct:    1 MNNHNNQFGLTNSAGYSHNGNYFENSHGSMINPSPIRSDMNLIRPIPKKVDLSKMIYQQFVDPYPRQNQSSILELSETMSQNIFSEMCQNAMSSNNAQNTIGNRFNEFSRRLQNPHFPFNNSRLSYNQLLMANNNRNNSEFFKNHIYPNSINLPPSPVLGTNMDPYLYSNINYQVPIRHNQVSSMMYMSRKDSEEKSPNKELYNEMKSNNKVQYFPKTSLSDDLIENHFSMSLNSHMKFDFKSNESLLITSKQERISRKPLKQQYKPEIDKSCKAIKRAKKSKATPDNFDRSQDMSHTLCATPSDSSISPNSMVSCRSTITPQAVYQNNFNTATLLVNSQNSNNHLSVINIKTSDPSSSFQKTSQFSTSLINDGNSRSLSLHESQFQGLPLKKRIKWQIENDDTDVEVLEDNEIKKTNDGKSDEIRQTTQSTDSEKSGQTVQNDSPLGISEYPLKTFQKTFLPMEKHSSSSDSDSDNEESTDAAVTSAAAAATATSAAVTNGKYSFSLKDQNGLLFVDNNI 521
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BLAST of SMED30031252 vs. Planmine SMEST
Match: SMESG000017120.1 (SMESG000017120.1)

HSP 1 Score: 874.004 bits (2257), Expect = 0.000e+0
Identity = 482/482 (100.00%), Postives = 482/482 (100.00%), Query Frame = 3 
Query:  348 MNLIRPIPKKVDLSKMIYQQFVDPYPRQNQSSILELSETMSQNIFSEMCQNAMSSNNAQNTIGNRFNEFSRRLQNPHFPFNNSRLSYNQLLMAXXXXXXSEFFKNHIYPNSINLPPSPVLGTNMDPYLYSNINYQVPIRHNQVSSMMYMSRKDSEEKSPNKELYNEMKSNNKVQYFPKTSLSDDLIENHFSMSLNSHMKFDFKSNESLLITSKQERISRKPLKQQYKPEIDKSCKAIKRAKKSKATPDNFDRSQDMSHTLCATPSDSSISPNSMVSCRSTITPQAVYQNNFNTATLLVNSQNSNNHLSVINIKTSDPXXXXXXXXXXXXXLINDGNSRSLSLHESQFQGLPLKKRIKWQIENDDTDVEVLEDNEIKKTNDGKSDEIRQTTQSTDSEKSGQTVQNDSPLGISEYPLKTFQKTFLPMEKHXXXXXXXXXNEESTDXXXXXXXXXXXXXXXXXXNGKYSFSLKDQNGLLFVDNNI 1793
            MNLIRPIPKKVDLSKMIYQQFVDPYPRQNQSSILELSETMSQNIFSEMCQNAMSSNNAQNTIGNRFNEFSRRLQNPHFPFNNSRLSYNQLLMANNNRNNSEFFKNHIYPNSINLPPSPVLGTNMDPYLYSNINYQVPIRHNQVSSMMYMSRKDSEEKSPNKELYNEMKSNNKVQYFPKTSLSDDLIENHFSMSLNSHMKFDFKSNESLLITSKQERISRKPLKQQYKPEIDKSCKAIKRAKKSKATPDNFDRSQDMSHTLCATPSDSSISPNSMVSCRSTITPQAVYQNNFNTATLLVNSQNSNNHLSVINIKTSDPSSSFQKTSQFSTSLINDGNSRSLSLHESQFQGLPLKKRIKWQIENDDTDVEVLEDNEIKKTNDGKSDEIRQTTQSTDSEKSGQTVQNDSPLGISEYPLKTFQKTFLPMEKHSSSSDSDSDNEESTDAAVTSAAAAATATSAAVTNGKYSFSLKDQNGLLFVDNNI
Sbjct:    1 MNLIRPIPKKVDLSKMIYQQFVDPYPRQNQSSILELSETMSQNIFSEMCQNAMSSNNAQNTIGNRFNEFSRRLQNPHFPFNNSRLSYNQLLMANNNRNNSEFFKNHIYPNSINLPPSPVLGTNMDPYLYSNINYQVPIRHNQVSSMMYMSRKDSEEKSPNKELYNEMKSNNKVQYFPKTSLSDDLIENHFSMSLNSHMKFDFKSNESLLITSKQERISRKPLKQQYKPEIDKSCKAIKRAKKSKATPDNFDRSQDMSHTLCATPSDSSISPNSMVSCRSTITPQAVYQNNFNTATLLVNSQNSNNHLSVINIKTSDPSSSFQKTSQFSTSLINDGNSRSLSLHESQFQGLPLKKRIKWQIENDDTDVEVLEDNEIKKTNDGKSDEIRQTTQSTDSEKSGQTVQNDSPLGISEYPLKTFQKTFLPMEKHSSSSDSDSDNEESTDAAVTSAAAAATATSAAVTNGKYSFSLKDQNGLLFVDNNI 482
The following BLAST results are available for this feature:
BLAST of SMED30031252 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 SMED30031252 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 SMED30031252 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 SMED30031252 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 SMED30031252 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 SMED30031252 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 SMED30031252 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 SMED30031252 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 SMED30031252 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 SMED30031252 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 SMED30031252 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 SMED30031252 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 SMED30031252 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 SMED30031252 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000017120.10.000e+0100.00SMESG000017120.1[more]
SMESG000017120.10.000e+0100.00SMESG000017120.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031252 ID=SMED30031252|Name=SMED30031252|organism=Schmidtea mediterranea sexual|type=transcript|length=1962bp
CATTAGACAAAATTGTGGTTCAATATGATTGGTCAATGAAATAACAAATC
AAATCAAAGTATATTACAGAAGTCAAATTGACAAAACTGCTGTACGAGGG
TTAAATTAACAAGTATAATTTAAAGCCATTTTTATTAACAATTTGTAGAA
CAACAAATAAATATATCTATTACTCTAATTTATTTTGATGTTATATGGAA
TTTGTGAAACTTTTCTACACAATCTAAAAAATGAACAATCACAATAATCA
ATTTGGTTTAACTAACTCAGCTGGATATAGTCACAATGGTAATTATTTCG
AGAATTCCCACGGCTCAATGATTAATCCATCTCCCATCAGATCTGACATG
AATCTTATTCGTCCAATTCCAAAGAAAGTCGATTTATCAAAAATGATATA
TCAACAATTCGTAGATCCATACCCTAGACAAAATCAATCCAGCATACTAG
AATTATCTGAAACAATGTCTCAAAATATATTTTCAGAAATGTGCCAGAAC
GCTATGTCAAGCAACAATGCTCAGAATACTATTGGAAATAGATTTAATGA
GTTCTCTCGTCGATTGCAGAATCCTCATTTTCCATTCAACAATTCAAGAC
TTTCCTATAATCAGTTGCTTATGGCTAATAATAATAGAAATAATTCTGAA
TTTTTTAAGAACCATATTTATCCAAATTCGATTAACTTACCACCATCACC
AGTATTAGGAACAAACATGGATCCTTACTTATATAGCAATATTAACTACC
AGGTTCCCATAAGACATAACCAAGTATCTAGCATGATGTATATGTCAAGG
AAAGATTCAGAGGAAAAATCACCGAATAAAGAGTTATATAATGAAATGAA
ATCAAACAATAAAGTACAATACTTTCCAAAAACATCTCTATCAGACGATT
TAATAGAGAATCATTTCTCAATGTCTTTAAATTCTCATATGAAGTTCGAT
TTTAAAAGTAATGAAAGTCTTCTTATTACTTCAAAACAAGAAAGAATATC
AAGGAAACCTCTTAAACAACAATACAAACCTGAAATCGACAAATCTTGCA
AAGCAATTAAAAGAGCCAAAAAATCTAAAGCCACACCTGATAACTTTGAT
AGATCACAAGACATGTCACATACGCTATGTGCTACTCCAAGTGACAGTTC
AATCAGTCCAAACAGTATGGTTTCTTGTAGGTCTACAATAACTCCACAAG
CAGTTTACCAGAACAATTTCAACACTGCAACACTTTTAGTTAACAGTCAA
AATTCTAACAATCACTTATCAGTTATCAATATAAAAACTTCTGACCCATC
TTCAAGCTTTCAAAAAACTTCTCAATTTAGTACTTCGTTGATAAACGACG
GAAACAGTCGTAGCTTATCTCTTCATGAATCTCAATTCCAAGGATTACCG
TTGAAGAAACGTATTAAATGGCAAATTGAAAACGATGATACTGATGTAGA
AGTATTAGAAGATAATGAAATAAAAAAGACAAATGACGGAAAGTCAGATG
AAATACGACAAACCACTCAGTCAACTGATTCTGAAAAAAGTGGCCAAACT
GTCCAAAACGACTCGCCCCTTGGAATTTCAGAATATCCTTTGAAGACATT
CCAAAAAACATTTCTACCGATGGAAAAACACTCGAGCTCATCCGACAGTG
ACAGTGACAATGAAGAAAGCACAGATGCCGCCGTCACCTCCGCCGCCGCC
GCCGCCACCGCCACCTCTGCTGCTGTAACTAATGGCAAATATTCATTCTC
TCTGAAAGATCAGAATGGCTTACTATTTGTTGATAACAACATTTGAAAAC
ATGTGATGGACCTTAATCTGAATGTAAATATTTATTGTTGACAGATGATT
AATATTTCGTTTTATTCATTCAAATTTCCATTTTGGATATGTTGTTTAAT
TATGCTTGATGTAAATTTCATTTATTTTGTTGACTAAATTTTATAATAAT
ACACTTCTGGAC
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protein sequence of SMED30031252-orf-1

>SMED30031252-orf-1 ID=SMED30031252-orf-1|Name=SMED30031252-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=522bp
MNNHNNQFGLTNSAGYSHNGNYFENSHGSMINPSPIRSDMNLIRPIPKKV
DLSKMIYQQFVDPYPRQNQSSILELSETMSQNIFSEMCQNAMSSNNAQNT
IGNRFNEFSRRLQNPHFPFNNSRLSYNQLLMANNNRNNSEFFKNHIYPNS
INLPPSPVLGTNMDPYLYSNINYQVPIRHNQVSSMMYMSRKDSEEKSPNK
ELYNEMKSNNKVQYFPKTSLSDDLIENHFSMSLNSHMKFDFKSNESLLIT
SKQERISRKPLKQQYKPEIDKSCKAIKRAKKSKATPDNFDRSQDMSHTLC
ATPSDSSISPNSMVSCRSTITPQAVYQNNFNTATLLVNSQNSNNHLSVIN
IKTSDPSSSFQKTSQFSTSLINDGNSRSLSLHESQFQGLPLKKRIKWQIE
NDDTDVEVLEDNEIKKTNDGKSDEIRQTTQSTDSEKSGQTVQNDSPLGIS
EYPLKTFQKTFLPMEKHSSSSDSDSDNEESTDAAVTSAAAAATATSAAVT
NGKYSFSLKDQNGLLFVDNNI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000101muscle cell
PLANA:0000429neoblast
PLANA:0003001lateral region of the whole animal
PLANA:0003116parenchymal 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: 431..449
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 464..502
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 410..430
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 410..449
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 480..502