SMED30018333

Overview
NameSMED30018333
Smed IDSMED30018333
Length (bp)1415
Neoblast Clusters

Zeng et. al., 2018



 

 

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



Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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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



SMED30018333

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
head regionSMED30018333SMESG000039545.1 SmedASXL_012775SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30018333SMESG000039545.1 dd_Smed_v4_5087_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018333SMESG000039545.1 Contig37338newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018333SMESG000039545.1 Contig37338uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30018333SMESG000039545.1 dd_Smed_v4_5087_1_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30018333SMESG000039545.1 dd_Smed_v4_5087_1_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30018333SMESG000039545.1 dd_Smed_v4_5087_1_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
SMED30018333 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002122:57363..58777 -6958
Homology
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BLAST of SMED30018333 vs. Planmine SMEST
Match: SMESG000039545.1 (SMESG000039545.1)

HSP 1 Score: 804.283 bits (2076), Expect = 0.000e+0
Identity = 434/441 (98.41%), Postives = 437/441 (99.09%), Query Frame = 2 
Query:   68 METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHXXXXXXXXXXXXXXXXXXXXXXXDFNHNSNIASSENSHFRHSGVDIESQLPSRDSLFVTGEKDCNNAENNLKTTDSQSANSDLDQRLNPSSVDRQLSNGNPFNNNEYDFIKTKIDLQENESLFPNAELGNEKLFPLENEYLEGGFTNDSHNDLTPPVVDTKLLDEDLYSNGEPCSNIEEDNLEKVISQILNADVDSIEDFLTECGYFEQNLGSDNSNNDSILSMVDKQLAREDLFYNENDFIKTKTDLQQNESRFPNAELGNEIYFSGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKCINVHGKTKSFPFGNEGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELNENVEK 1390
            METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHSENNISNNNNIIINLENKSKNENDFNHN+NIASSENSHFR+SGVDIESQLPSRDSLFVTGEKDCNNAENNLKTTDSQSANSDLDQRLNPS VDRQLSNGNPFNNNEYDFIKTKIDLQENESLFPNAELGNEKLFPLENEYLEGGFTNDSHNDLTPPVVDTKLLDEDLYSNGEPCSNIEEDNLEKVISQILNADVDSIEDFLTECGYFEQNLGSDNSNNDSILSMVDKQLAREDLF NENDFIKTKTDLQ+NESRFPNAELGNEIYF GENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKCINVHGKTKSFP GNEGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELNENVEK
Sbjct:    1 METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHSENNISNNNNIIINLENKSKNENDFNHNNNIASSENSHFRYSGVDIESQLPSRDSLFVTGEKDCNNAENNLKTTDSQSANSDLDQRLNPSRVDRQLSNGNPFNNNEYDFIKTKIDLQENESLFPNAELGNEKLFPLENEYLEGGFTNDSHNDLTPPVVDTKLLDEDLYSNGEPCSNIEEDNLEKVISQILNADVDSIEDFLTECGYFEQNLGSDNSNNDSILSMVDKQLAREDLFDNENDFIKTKTDLQENESRFPNAELGNEIYFPGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKCINVHGKTKSFPSGNEGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELNENVEK 441

HSP 2 Score: 108.612 bits (270), Expect = 8.512e-25
Identity = 77/172 (44.77%), Postives = 91/172 (52.91%), Query Frame = 2 
Query:  530 FIKTKIDLQENESLFPNAELGNEKLFPLENEYLEGGFTNDSHNDLTPPVVDTKLLDEDLYSNGEPCSNIEEDNLEKVISQILNADVDSIEDFLTECGYFEQNLGSDNSNNDSILSMVDKQLAREDLFYNENDFIKTKTDLQQNESRFPNAELGNEIYFSGENEYLEGSFTND 1045
            FIKTKIDLQEN+S  PN ELG E   PLENEY EG  TNDS NDLTPPVVDTKLLDEDL SNGE                  N + D+  DF  E  Y E++   D+ N + I S    +   ED F N       KT +  NE   PN     ++  S  +EY + +  ND
Sbjct:  452 FIKTKIDLQENKS--PNKELGIEICSPLENEYFEGSLTNDSRNDLTPPVVDTKLLDEDLCSNGEQFP--------------YNEEHDTEVDFSLENEYLEESFHQDDDNKNPISSKFHSEFTNEDTFNN-----NVKTPIYTNEPTRPNPHREGKLGLSLSSEYPKVNSIND 602
The following BLAST results are available for this feature:
BLAST of SMED30018333 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 SMED30018333 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 SMED30018333 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 SMED30018333 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 SMED30018333 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 SMED30018333 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 SMED30018333 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 SMED30018333 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 SMED30018333 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 SMED30018333 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 SMED30018333 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 SMED30018333 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 SMED30018333 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 SMED30018333 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000039545.18.512e-2598.41SMESG000039545.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018333 ID=SMED30018333|Name=SMED30018333|organism=Schmidtea mediterranea sexual|type=transcript|length=1415bp
ATTTTTTTATGAAACAAATTCCAAAAACTGTAATAAATGGCTTTTTAGGG
TATAAAACGACAAAACAATGGAAACTCCAGTTCAATTGAATTCCTCATGG
ATCAGTACTTTCCAATATTCCAATGAGAATTTTGGAAACGAATATTGTCG
AGAATACCTTCAAAATGAACTTTTAAATCTTGACGACATCGTGCAAAGTC
GACATTCAGAAAATAATATTTCTAATAATAATAATATAATTATCAATTTG
GAAAATAAATCAAAAAATGAAAATGATTTTAATCACAACAGTAACATTGC
AAGTTCGGAGAATTCACATTTTCGACATTCAGGAGTAGACATTGAAAGTC
AACTGCCCAGTAGAGATTCGTTGTTTGTCACTGGGGAAAAGGATTGCAAC
AATGCTGAAAATAATCTGAAAACCACTGATTCACAAAGTGCAAATTCGGA
TCTGGATCAAAGATTGAACCCATCTAGTGTTGATAGACAGTTGTCTAATG
GAAATCCATTTAATAATAATGAATATGATTTCATTAAAACAAAAATTGAT
TTACAAGAAAATGAATCTCTATTTCCAAATGCGGAACTTGGGAACGAAAA
ATTATTTCCTTTGGAAAATGAATATCTTGAAGGAGGTTTTACTAATGACA
GTCACAATGATCTGACCCCTCCAGTAGTTGATACCAAGCTGTTGGATGAA
GACTTATACAGTAATGGAGAACCTTGTAGCAACATTGAGGAAGATAACTT
AGAAAAAGTCATATCACAAATACTAAATGCGGACGTCGACTCGATAGAAG
ACTTTTTAACTGAATGTGGATATTTTGAACAGAATTTAGGCAGTGATAAT
AGCAATAATGATTCAATTCTTTCTATGGTTGATAAACAGTTGGCTAGGGA
AGATTTATTTTATAATGAAAATGATTTCATTAAAACAAAAACTGATTTAC
AACAAAATGAATCTCGATTTCCAAATGCGGAACTTGGCAACGAAATATAT
TTTTCCGGGGAAAATGAATATCTTGAAGGAAGTTTTACTAATGACAGTCG
CAATGATCTGACCTCTCCAGCAGTTGACATTGAGCTGTTGGATGAAGATT
TATACAGTAATGGAGAATTTGGTCTCAACCATGCCGAAGCTAATTTACAA
GAAAACGGATCACAAATATTAAATACGAATCTCGATGCTAATGAATTAGT
TGAACACAAATGTATTAATGTTCATGGCAAAACGAAATCATTCCCATTTG
GAAATGAAGGAATTTTTACTAATGATATACGCAAAGATCTGACCCTTCCA
ATAGTTGATACGGAGCTGTTGGATGAAGATTTATATAGCAATGGAGAACT
TTGTCGCAACATTGAGGAACTTAATGAAAATGTTGAGAAGAATTTAGACA
ATGAAAATAATGAGA
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protein sequence of SMED30018333-orf-1

>SMED30018333-orf-1 ID=SMED30018333-orf-1|Name=SMED30018333-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=449bp
METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHSENN
ISNNNNIIINLENKSKNENDFNHNSNIASSENSHFRHSGVDIESQLPSRD
SLFVTGEKDCNNAENNLKTTDSQSANSDLDQRLNPSSVDRQLSNGNPFNN
NEYDFIKTKIDLQENESLFPNAELGNEKLFPLENEYLEGGFTNDSHNDLT
PPVVDTKLLDEDLYSNGEPCSNIEEDNLEKVISQILNADVDSIEDFLTEC
GYFEQNLGSDNSNNDSILSMVDKQLAREDLFYNENDFIKTKTDLQQNESR
FPNAELGNEIYFSGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGE
FGLNHAEANLQENGSQILNTNLDANELVEHKCINVHGKTKSFPFGNEGIF
TNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELNENVEKNLDNENNE
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000096ventral epidermis
PLANA:0000418head
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 425..449
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 113..144