SMED30025552

Overview
NameSMED30025552
Smed IDSMED30025552
Length (bp)1019
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.
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



SMED30025552

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30025552SMESG000039545.1 SmedASXL_012775SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermal cellSMED30025552SMESG000039545.1 dd_Smed_v4_5087_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30025552SMESG000039545.1 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 epidermisSMED30025552SMESG000039545.1 dd_Smed_v4_5087_1_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30025552SMESG000039545.1 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
SMED30025552 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002122:57363..58777 -4966
Homology
[Close]
BLAST of SMED30025552 vs. Planmine SMEST
Match: SMESG000039545.1 (SMESG000039545.1)

HSP 1 Score: 378.252 bits (970), Expect = 2.684e-120
Identity = 252/359 (70.19%), Postives = 262/359 (72.98%), Query Frame = 2 
Query:   68 METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHXXXXXXXXXXXXXXXXXXXXXXXDFNHNSNIASSENSHFRHSGVDIESQLPSRDSLFVTGEKDCNNAENNLKTTDSQSANSDLDQRLNPSSVDRQLSNGNPFNNNEYDFIKTKIDLQENESRFPNAELGNEIYFSGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKCI---------------------------------NVHGKTKS--------FP---FGN-----------EGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELN 979
            METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHSENNISNNNNIIINLENKSKNENDFNHN+NIASSENSHFR+SGVDIESQLPSRDSLFVTGEKDCNNAENNLKTTDSQSANSDLDQRLNPS VDRQLSNGNPFNNNEYDFIKTKIDLQENES FPNAELGNE  F  ENEYLEG FTNDS NDLT P VD +LLDEDLYSNGE   N  E NL++  SQILN ++D+ E    +C                                  N   KTK+        FP    GN           EG FTND R DLT P VD ELLDEDLYSNGE   N  E N
Sbjct:    1 METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHSENNISNNNNIIINLENKSKNENDFNHNNNIASSENSHFRYSGVDIESQLPSRDSLFVTGEKDCNNAENNLKTTDSQSANSDLDQRLNPSRVDRQLSNGNPFNNNEYDFIKTKIDLQENESLFPNAELGNEKLFPLENEYLEGGFTNDSHNDLTPPVVDTKLLDEDLYSNGEPCSNIEEDNLEKVISQILNADVDSIEDFLTECGYFEQNLGSDNSNNDSILSMVDKQLAREDLFDNENDFIKTKTDLQENESRFPNAELGNEIYFPGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEAN 359

HSP 2 Score: 321.242 bits (822), Expect = 1.772e-99
Identity = 175/230 (76.09%), Postives = 184/230 (80.00%), Query Frame = 2 
Query:  371 LFVTGEKDCNNAENNLKTTDSQSANSDLD-------------QRLNP---------SSVDRQLSNGNPFNNNEYDFIKTKIDLQENESRFPNAELGNEIYFSGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKCINVHGKTKSFPFGNEGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELNENVEK 994
            L+  GE   N  E+NL+   SQ  N+D+D             Q L           S VD+QL+  + F+N E DFIKTK DLQENESRFPNAELGNEIYF GENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKCINVHGKTKSFP GNEGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELNENVEK
Sbjct:  213 LYSNGEPCSNIEEDNLEKVISQILNADVDSIEDFLTECGYFEQNLGSDNSNNDSILSMVDKQLAREDLFDN-ENDFIKTKTDLQENESRFPNAELGNEIYFPGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKCINVHGKTKSFPSGNEGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELNENVEK 441

HSP 3 Score: 87.8113 bits (216), Expect = 1.092e-18
Identity = 48/64 (75.00%), Postives = 50/64 (78.12%), Query Frame = 2 
Query:  530 FIKTKIDLQENESRFPNAELGNEIYFSGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGE 721
            FIKTKIDLQEN+S  PN ELG EI    ENEY EGS TNDSRNDLT P VD +LLDEDL SNGE
Sbjct:  452 FIKTKIDLQENKS--PNKELGIEICSPLENEYFEGSLTNDSRNDLTPPVVDTKLLDEDLCSNGE 513
The following BLAST results are available for this feature:
BLAST of SMED30025552 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 SMED30025552 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 SMED30025552 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 SMED30025552 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 SMED30025552 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 SMED30025552 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 SMED30025552 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 SMED30025552 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 SMED30025552 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 SMED30025552 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 SMED30025552 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 SMED30025552 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 SMED30025552 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 SMED30025552 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000039545.12.684e-12070.19SMESG000039545.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025552 ID=SMED30025552|Name=SMED30025552|organism=Schmidtea mediterranea sexual|type=transcript|length=1019bp
ATTTTTTTATGAAACAAATTCCAAAAACTGTAATAAATGGCTTTTTAGGG
TATAAAACGACAAAACAATGGAAACTCCAGTTCAATTGAATTCCTCATGG
ATCAGTACTTTCCAATATTCCAATGAGAATTTTGGAAACGAATATTGTCG
AGAATACCTTCAAAATGAACTTTTAAATCTTGACGACATCGTGCAAAGTC
GACATTCAGAAAATAATATTTCTAATAATAATAATATAATTATCAATTTG
GAAAATAAATCAAAAAATGAAAATGATTTTAATCACAACAGTAACATTGC
AAGTTCGGAGAATTCACATTTTCGACATTCAGGAGTAGACATTGAAAGTC
AACTGCCCAGTAGAGATTCGTTGTTTGTCACTGGGGAAAAGGATTGCAAC
AATGCTGAAAATAATCTGAAAACCACTGATTCACAAAGTGCAAATTCGGA
TCTGGATCAAAGATTGAACCCATCTAGTGTTGATAGACAGTTGTCTAATG
GAAATCCATTTAATAATAATGAATATGATTTCATTAAAACAAAAATTGAT
TTACAAGAAAATGAATCTCGATTTCCAAATGCGGAACTTGGCAACGAAAT
ATATTTTTCCGGGGAAAATGAATATCTTGAAGGAAGTTTTACTAATGACA
GTCGCAATGATCTGACCTCTCCAGCAGTTGACATTGAGCTGTTGGATGAA
GATTTATACAGTAATGGAGAATTTGGTCTCAACCATGCCGAAGCTAATTT
ACAAGAAAACGGATCACAAATATTAAATACGAATCTCGATGCTAATGAAT
TAGTTGAACACAAATGTATTAATGTTCATGGCAAAACGAAATCATTCCCA
TTTGGAAATGAAGGAATTTTTACTAATGATATACGCAAAGATCTGACCCT
TCCAATAGTTGATACGGAGCTGTTGGATGAAGATTTATATAGCAATGGAG
AACTTTGTCGCAACATTGAGGAACTTAATGAAAATGTTGAGAAGAATTTA
GACAATGAAAATAATGAGA
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protein sequence of SMED30025552-orf-1

>SMED30025552-orf-1 ID=SMED30025552-orf-1|Name=SMED30025552-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=317bp
METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHSENN
ISNNNNIIINLENKSKNENDFNHNSNIASSENSHFRHSGVDIESQLPSRD
SLFVTGEKDCNNAENNLKTTDSQSANSDLDQRLNPSSVDRQLSNGNPFNN
NEYDFIKTKIDLQENESRFPNAELGNEIYFSGENEYLEGSFTNDSRNDLT
SPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKC
INVHGKTKSFPFGNEGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNI
EELNENVEKNLDNENNE
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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: 293..317
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 113..144