SMED30005897

Overview
NameSMED30005897
Smed IDSMED30005897
Length (bp)2051
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30005897 (SMED30005897) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005897 (SMED30005897) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30005897

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
tail regionSMED30005897h1SMcG0003699 SmedASXL_016638SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
tail regionSMED30005897h1SMcG0003699 SmedASXL_016639SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30005897h1SMcG0003699 dd_Smed_v4_10286_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30005897h1SMcG0003699 dd_Smed_v4_13466_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30005897h1SMcG0003699 dd_Smed_v6_13466_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
dorsal-ventral muscle cellSMED30005897h1SMcG0003699 dd_Smed_v4_10286_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30005897h1SMcG0003699 dd_Smed_v6_10286_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
dorsal ventral margin of the whole animalSMED30005897h1SMcG0003699 dd_Smed_v4_10286_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
Alignments
SMED30005897 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005415:27700..30419 -9873
Homology
[Close]
BLAST of SMED30005897 vs. Planmine SMEST
Match: SMESG000010960.1 (SMESG000010960.1)

HSP 1 Score: 1016.91 bits (2628), Expect = 0.000e+0
Identity = 547/556 (98.38%), Postives = 549/556 (98.74%), Query Frame = 1 
Query:   94 YSEEINEKVERTVIDRNRNKSSGRLSDSNKRENINQNFYSKSPTESVRQXXXXXXXQVYDTTYFNRNVLSSRTSNHNNLNSLIVGKSFSKVHNNSLNSKPNGLLPVLKTNKTYDISFTLSNIPSQNLNRTLIQPEIETVEYSKRNIYSNNEQPFGHYKNTNDKVLQTGSSLRKFNQRASVVQFDELMKDVNMNEKNQNYNVDMTDSKIDKNSNSTQRFDTNNKLARKEISYKDKTIAEGNGGQSGQSMYENRNKNVSEIIYSEPSMNGNVAATEYNEIKEWMIVEFPDGHQEKREFRKEINEEGDANYIDVVNKTILKTDKASWKSGNEYMKNNREVKRVKYEWRKDPSTNSWVKYDATTNEILKQGDWKSGSEWVRNSKGKLEERPYKYIRNQTGQWIKVDTSSGQIIDYSNCSALQGYDWISXXXXXXXXXXXXXXXXXXVENNKGKWDKIDEEXXXXXXXXXXXXXXEGIDYHMDKEGKVYKVRYIWETKESGLMEKVNKRNKKPINYSWKEGREIIMRGDAVTTTNFAWVNLGKNTWIKIDRDTGVPITGKV 1761
            YSEEI EKVERTVIDRNRNKSSGRLS SNKRENINQN YSKSPTESVRQSSSSKKKQVYDTTYFNRNVLSSRTSNHN+LNSLIVGKSFSKVHNN LNSK NGLLPVLKTNK YDISFTLSNIPSQNLNRTL QPEIETVEYSKRNIYSNNEQPFGHYKNTNDKVLQTGSSLRKFNQRASVVQFDELMKDVNMNEKNQNYNVDMTDSKIDKNSNSTQRFDTNNKLARKEISYKDKTIAEGNGGQSGQSMYENRNKNVSEIIYSEPSMNGNVAATEYNEIKEWMIVEFPDGHQEKREFRKEINEEGDANYIDVVNKTILKTDKASWKSGNEYMKNNREVKRVKYEWRKDPSTNSWVKYDATTNEILKQGDWKSGSEWVRNSKGKLEERPYKYIRNQTGQWIKVDTSSGQIIDYSNCSALQGYDWISNKNKKLKDRRWKKRDYKYVENNKGKWDKIDEETKKKIGKSTKSGWKEGIDYHMDKEGKVYKVRYIWETKE+GLMEKVNKRNKKPINYSWKEGREIIMRGDAVTTTNFAWVNLGKNTWIKIDRDTGVPITGKV
Sbjct:  120 YSEEIIEKVERTVIDRNRNKSSGRLSVSNKRENINQNSYSKSPTESVRQSSSSKKKQVYDTTYFNRNVLSSRTSNHNDLNSLIVGKSFSKVHNNFLNSKQNGLLPVLKTNKAYDISFTLSNIPSQNLNRTLTQPEIETVEYSKRNIYSNNEQPFGHYKNTNDKVLQTGSSLRKFNQRASVVQFDELMKDVNMNEKNQNYNVDMTDSKIDKNSNSTQRFDTNNKLARKEISYKDKTIAEGNGGQSGQSMYENRNKNVSEIIYSEPSMNGNVAATEYNEIKEWMIVEFPDGHQEKREFRKEINEEGDANYIDVVNKTILKTDKASWKSGNEYMKNNREVKRVKYEWRKDPSTNSWVKYDATTNEILKQGDWKSGSEWVRNSKGKLEERPYKYIRNQTGQWIKVDTSSGQIIDYSNCSALQGYDWISNKNKKLKDRRWKKRDYKYVENNKGKWDKIDEETKKKIGKSTKSGWKEGIDYHMDKEGKVYKVRYIWETKENGLMEKVNKRNKKPINYSWKEGREIIMRGDAVTTTNFAWVNLGKNTWIKIDRDTGVPITGKV 675
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BLAST of SMED30005897 vs. Planmine SMEST
Match: SMESG000046569.1 (SMESG000046569.1)

HSP 1 Score: 848.581 bits (2191), Expect = 0.000e+0
Identity = 449/456 (98.46%), Postives = 450/456 (98.68%), Query Frame = 1 
Query:   94 YSEEINEKVERTVIDRNRNKSSGRLSDSNKRENINQNFYSKSPTESVRQXXXXXXXQVYDTTYFNRNVLSSRTSNHNNLNSLIVGKSFSKVHNNSLNSKPNGLLPVLKTNKTYDISFTLSNIPSQNLNRTLIQPEIETVEYSKRNIYSNNEQPFGHYKNTNDKVLQTGSSLRKFNQRASVVQFDELMKDVNMNEKNQNYNVDMTDSKIDKNSNSTQRFDTNNKLARKEISYKDKTIAEGNGGQSGQSMYENRNKNVSEIIYSEPSMNGNVAATEYNEIKEWMIVEFPDGHQEKREFRKEINEEGDANYIDVVNKTILKTDKASWKSGNEYMKNNREVKRVKYEWRKDPSTNSWVKYDATTNEILKQGDWKSGSEWVRNSKGKLEERPYKYIRNQTGQWIKVDTSSGQIIDYSNCSALQGYDWISXXXXXXXXXXXXXXXXXXVENNKGKWDKIDEE 1461
            YSEEINEKVERTVIDRNRNKSSGRLS SNKRENINQN YSKSPTESVRQSSSSKKKQVYDTTYFNRNV SSRTSNHN+LNSLIVGKSFSKVHNNSLNSK NGLLPVLKTNKTYDISFTLSNIPSQNLNRTL QPEIETVEYSKRNIYSNNEQPFGHYKNTNDKVLQTGSSLRKFNQRASVVQFDELMKDVNMNEKNQNYNVDMTDSKIDKNSNSTQRFDTNNKLARKEISYKDKTIAEGNGGQSGQSMYENRNKNVSEIIYSEPSMNGNVAATEYNEIKEWMIVEFPDGHQEKREFRKEINEEGDANYIDVVNKTILKTDKASWKSGNEYMKN REVKRVKYEWRKDPSTNSWVKYDATTNEILKQGDWKSGSEWVRNSKGKLEERPYKYIRNQTGQWIKVDTSSGQIIDYSNCSALQGYDWISNKNKKLKDRRWKKRDYKYVENNKGKWDKIDEE
Sbjct:  124 YSEEINEKVERTVIDRNRNKSSGRLSVSNKRENINQNSYSKSPTESVRQSSSSKKKQVYDTTYFNRNVHSSRTSNHNDLNSLIVGKSFSKVHNNSLNSKQNGLLPVLKTNKTYDISFTLSNIPSQNLNRTLTQPEIETVEYSKRNIYSNNEQPFGHYKNTNDKVLQTGSSLRKFNQRASVVQFDELMKDVNMNEKNQNYNVDMTDSKIDKNSNSTQRFDTNNKLARKEISYKDKTIAEGNGGQSGQSMYENRNKNVSEIIYSEPSMNGNVAATEYNEIKEWMIVEFPDGHQEKREFRKEINEEGDANYIDVVNKTILKTDKASWKSGNEYMKNKREVKRVKYEWRKDPSTNSWVKYDATTNEILKQGDWKSGSEWVRNSKGKLEERPYKYIRNQTGQWIKVDTSSGQIIDYSNCSALQGYDWISNKNKKLKDRRWKKRDYKYVENNKGKWDKIDEE 579

HSP 2 Score: 76.2554 bits (186), Expect = 3.446e-14
Identity = 48/83 (57.83%), Postives = 56/83 (67.47%), Query Frame = 2 
Query: 1340 HCKVMTGYQ-IRIKN*KIED--GKSVTISMLKIIKVSGIK*MKKQKRKLVSRQKAVGKKELIIIWIKKVRFIRFVIFGKLKKA 1579
            +C  + GY  I  KN K++D   K      ++  K    K  ++ KRKLVSRQKAVGKKELIIIWIKKVRFIRFVIFGKLKK 
Sbjct:  536 NCSALQGYDWISNKNKKLKDRRWKKRDYKYVENNKGKWDKIDEETKRKLVSRQKAVGKKELIIIWIKKVRFIRFVIFGKLKKT 618
The following BLAST results are available for this feature:
BLAST of SMED30005897 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 SMED30005897 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 SMED30005897 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 SMED30005897 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 SMED30005897 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 SMED30005897 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 SMED30005897 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 SMED30005897 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 SMED30005897 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 SMED30005897 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 SMED30005897 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 SMED30005897 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 SMED30005897 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 SMED30005897 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000010960.10.000e+098.38SMESG000010960.1[more]
SMESG000046569.13.446e-1498.46SMESG000046569.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005897 ID=SMED30005897|Name=SMED30005897|organism=Schmidtea mediterranea sexual|type=transcript|length=2051bp
AATAATAATAATAATAATAGTAACGACGAAAATCAAAAAAATGATAATTT
CAACCGATTAAACAACAATAGGAATAACAATTTTAACAGCAATTATTCTG
AAGAGATAAATGAAAAAGTAGAAAGAACCGTTATTGATCGAAATCGTAAT
AAAAGTTCCGGAAGATTAAGTGATTCCAATAAAAGAGAAAATATTAATCA
AAATTTTTATTCAAAATCACCAACAGAATCTGTTAGACAATCGAGTAGTT
CTAAAAAGAAGCAAGTCTATGACACGACTTACTTTAATAGAAACGTCCTT
TCTAGCAGAACCTCTAATCATAATAATTTGAATTCCTTGATTGTGGGAAA
ATCATTTTCAAAAGTTCACAATAATTCTTTGAATAGTAAACCAAATGGTT
TACTTCCTGTTCTAAAAACTAATAAAACTTATGATATTTCTTTTACTTTG
AGTAACATTCCTTCACAGAATTTGAATAGGACGTTAATACAACCAGAGAT
AGAAACAGTAGAGTATTCCAAAAGAAATATTTATTCAAACAACGAGCAAC
CGTTTGGACACTATAAAAATACCAACGATAAAGTATTACAAACCGGAAGT
TCTTTGAGAAAATTCAACCAAAGAGCTTCTGTGGTTCAATTTGATGAGTT
AATGAAAGATGTGAATATGAATGAAAAGAATCAAAATTACAATGTTGACA
TGACAGATTCAAAAATTGATAAAAATTCAAACTCAACACAAAGATTTGAC
ACAAATAATAAGTTGGCAAGAAAAGAAATTAGCTACAAGGATAAAACCAT
AGCAGAAGGAAATGGAGGACAGTCCGGTCAATCAATGTACGAAAATAGAA
ATAAGAATGTTTCTGAAATTATTTACAGTGAACCATCAATGAATGGAAAT
GTTGCAGCTACAGAATATAATGAAATTAAAGAATGGATGATTGTTGAGTT
TCCCGATGGCCATCAAGAAAAAAGAGAGTTTAGAAAAGAAATAAATGAAG
AGGGAGATGCTAATTACATTGATGTCGTTAATAAAACCATTCTCAAAACT
GATAAAGCTTCTTGGAAATCTGGTAATGAATATATGAAAAATAACAGAGA
AGTTAAAAGAGTAAAGTATGAGTGGCGTAAAGATCCAAGTACTAATTCTT
GGGTTAAATATGATGCTACCACAAACGAAATACTTAAACAGGGTGATTGG
AAATCTGGTTCAGAATGGGTGAGAAATTCCAAAGGAAAATTAGAAGAAAG
GCCTTATAAATATATCCGTAATCAGACTGGCCAGTGGATAAAAGTTGATA
CGTCGTCGGGTCAAATTATAGACTATTCAAATTGTTCTGCATTGCAAGGT
TATGACTGGATATCAAATAAGAATAAAAAACTGAAAGATCGAAGATGGAA
AAAGCGTGACTATAAGTATGTTGAAAATAATAAAGGTAAGTGGGATAAAA
TAGATGAAGAAACAAAAAAGAAAATTGGTAAGTCGACAAAAAGCGGTTGG
AAAGAAGGAATTGATTATCATATGGATAAAGAAGGTAAGGTTTATAAGGT
TCGTTATATTTGGGAAACTAAAGAAAGCGGATTAATGGAAAAAGTTAACA
AGCGAAATAAAAAGCCAATTAATTATTCTTGGAAGGAAGGCAGAGAAATA
ATAATGAGAGGGGATGCAGTCACTACGACCAATTTCGCTTGGGTAAACCT
TGGAAAAAATACATGGATAAAGATAGATAGGGATACTGGTGTTCCAATCA
CTGGAAAAGTCAAAAGCAGAGAAATATCTTCCCATAACTTGCCAACATCA
ATGTCTAACCGAAAATCATTAGTTACAAAAACCACAAAACGAATTGACAA
TGACAAAATAGTGGAAGAGAAATTAAAAATTGAACAAACTGGGGGAGGAG
TGATTAAAAATACAACAAAAACAACTCAATATGTGAAATAAAAGGAGAAA
TTAGATTAACTATACCTTGCGTTGTAATGAGGAAACCTATAACTTCAATT
TTAAGAATTTTTGATTATTTTGTCACTTAAATATTGCAAGCTATTGGAAA
C
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protein sequence of SMED30005897-orf-1

>SMED30005897-orf-1 ID=SMED30005897-orf-1|Name=SMED30005897-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=647bp
NNNNNNSNDENQKNDNFNRLNNNRNNNFNSNYSEEINEKVERTVIDRNRN
KSSGRLSDSNKRENINQNFYSKSPTESVRQSSSSKKKQVYDTTYFNRNVL
SSRTSNHNNLNSLIVGKSFSKVHNNSLNSKPNGLLPVLKTNKTYDISFTL
SNIPSQNLNRTLIQPEIETVEYSKRNIYSNNEQPFGHYKNTNDKVLQTGS
SLRKFNQRASVVQFDELMKDVNMNEKNQNYNVDMTDSKIDKNSNSTQRFD
TNNKLARKEISYKDKTIAEGNGGQSGQSMYENRNKNVSEIIYSEPSMNGN
VAATEYNEIKEWMIVEFPDGHQEKREFRKEINEEGDANYIDVVNKTILKT
DKASWKSGNEYMKNNREVKRVKYEWRKDPSTNSWVKYDATTNEILKQGDW
KSGSEWVRNSKGKLEERPYKYIRNQTGQWIKVDTSSGQIIDYSNCSALQG
YDWISNKNKKLKDRRWKKRDYKYVENNKGKWDKIDEETKKKIGKSTKSGW
KEGIDYHMDKEGKVYKVRYIWETKESGLMEKVNKRNKKPINYSWKEGREI
IMRGDAVTTTNFAWVNLGKNTWIKIDRDTGVPITGKVKSREISSHNLPTS
MSNRKSLVTKTTKRIDNDKIVEEKLKIEQTGGGVIKNTTKTTQYVK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000043dorsal ventral margin of the whole animal
PLANA:0000421tail
PLANA:0002028dorsal-ventral muscle cell
PLANA:0002032epidermal 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: 51..89
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..27