SMED30020944

Overview
NameSMED30020944
Smed IDSMED30020944
Length (bp)462
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



SMED30020944

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
neoblastSMED30020944 dd_Smed_v4_15635_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30020944 dd_Smed_v4_15635_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30020944 dd_Smed_v4_15635_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
Homology
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BLAST of SMED30020944 vs. Planmine SMEST
Match: SMESG000015004.1 (SMESG000015004.1)

HSP 1 Score: 78.9518 bits (193), Expect = 1.518e-19
Identity = 40/60 (66.67%), Postives = 48/60 (80.00%), Query Frame = 1 
Query:  277 VRTNSRDYDVKIPSLIIKREPGRNPAREARQCTEFSLY*CEEQERKTHWKVTITRRRLKH 456
            +RTN RD +V+IPSL+IK EPG+NPA EARQ  EFSLY  E+QERK H KV + RRRLK+
Sbjct:    8 IRTNFRDDEVEIPSLVIKLEPGQNPACEARQRAEFSLYGYEDQERKAHCKVFMARRRLKN 67
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BLAST of SMED30020944 vs. Planmine SMEST
Match: SMESG000014849.1 (SMESG000014849.1)

HSP 1 Score: 64.6994 bits (156), Expect = 2.091e-17
Identity = 29/57 (50.88%), Postives = 39/57 (68.42%), Query Frame = 1 
Query:  280 RTNSRDYDVKIPSLIIKREPGRNPAREARQCTEFSLY*CEEQERKTHWKVTITRRRL 450
            R+  R  ++++PS+ IKREPG NPAREARQ  E++    EE ERK H K  + R+RL
Sbjct:  923 RSEYRAEEIELPSIAIKREPGHNPAREARQRAEYAAMKMEELERKYHRKAVLARQRL 979

HSP 2 Score: 40.817 bits (94), Expect = 2.091e-17
Identity = 19/44 (43.18%), Postives = 27/44 (61.36%), Query Frame = 2 
Query:  134 SMDMDYRRNNA-WSDTDRFTMKFLSQMTAKYRQALWNADYILST 262
            SM ++ R  +  WSD  R T++  S   A+YRQ LW+  Y+LST
Sbjct:  871 SMGINRRDPHGNWSDNSRVTLQIPSASAARYRQVLWDNGYLLST 914
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BLAST of SMED30020944 vs. Planmine SMEST
Match: SMESG000042475.1 (SMESG000042475.1)

HSP 1 Score: 58.5362 bits (140), Expect = 4.941e-17
Identity = 27/57 (47.37%), Postives = 38/57 (66.67%), Query Frame = 1 
Query:  280 RTNSRDYDVKIPSLIIKREPGRNPAREARQCTEFSLY*CEEQERKTHWKVTITRRRL 450
            R+  +  ++++PS+ IKREPG NPAREA Q  E++    EE ERK H K  + R+RL
Sbjct: 1371 RSEYQAEEIELPSIAIKREPGHNPAREAHQRAEYAAMKMEELERKYHRKAVLARQRL 1427

HSP 2 Score: 45.8246 bits (107), Expect = 4.941e-17
Identity = 21/52 (40.38%), Postives = 32/52 (61.54%), Query Frame = 2 
Query:  113 KNSDQFTSMDMDYRRN--NAWSDTDRFTMKFLSQMTAKYRQALWNADYILST 262
            K+ +  T  + +YRR+   +WSD  R T++  S   A+YRQ LW+  Y+LST
Sbjct: 1311 KDLNAITQKEFEYRRDTSGSWSDNSRVTLQIPSASAARYRQVLWDNGYLLST 1362
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BLAST of SMED30020944 vs. Planmine SMEST
Match: SMESG000032127.1 (SMESG000032127.1)

HSP 1 Score: 70.0922 bits (170), Expect = 2.263e-16
Identity = 35/49 (71.43%), Postives = 39/49 (79.59%), Query Frame = 2 
Query:    2 MNSMNNEGVIPTRETRPKVQTGTDHGRMNTRDVNWISKNSDQFTSMDMD 148
            MNSMNNE V+PTRET  K QTGTDH RM TR+V  ISKN+DQFTS D +
Sbjct:    1 MNSMNNESVMPTRETSTKEQTGTDHRRMKTRNVTRISKNNDQFTSGDQN 49
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BLAST of SMED30020944 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1)

HSP 1 Score: 58.5362 bits (140), Expect = 2.368e-16
Identity = 27/57 (47.37%), Postives = 38/57 (66.67%), Query Frame = 1 
Query:  280 RTNSRDYDVKIPSLIIKREPGRNPAREARQCTEFSLY*CEEQERKTHWKVTITRRRL 450
            R+  +  ++++PS+ IKREPG NPAREARQ  +++    EE ERK H K    R+RL
Sbjct: 1686 RSEYQAEEIELPSIAIKREPGHNPAREARQRAKYAAMKMEELERKYHRKAVSARQRL 1742

HSP 2 Score: 43.5134 bits (101), Expect = 2.368e-16
Identity = 19/41 (46.34%), Postives = 27/41 (65.85%), Query Frame = 2 
Query:  146 DYRRN--NAWSDTDRFTMKFLSQMTAKYRQALWNADYILST 262
            +YRR+   +WSD  R T++  S   A+YRQ LW+  Y+LST
Sbjct: 1637 NYRRDPHGSWSDNSRVTLEIPSASAARYRQVLWDNGYLLST 1677
The following BLAST results are available for this feature:
BLAST of SMED30020944 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 SMED30020944 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 SMED30020944 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 SMED30020944 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 SMED30020944 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 SMED30020944 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 SMED30020944 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 SMED30020944 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 SMED30020944 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 SMED30020944 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 SMED30020944 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 SMED30020944 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 SMED30020944 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 SMED30020944 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000015004.11.518e-1966.67SMESG000015004.1[more]
SMESG000014849.12.091e-1750.88SMESG000014849.1[more]
SMESG000042475.14.941e-1747.37SMESG000042475.1[more]
SMESG000032127.12.263e-1671.43SMESG000032127.1[more]
SMESG000057533.12.368e-1647.37SMESG000057533.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020944 ID=SMED30020944|Name=SMED30020944|organism=Schmidtea mediterranea sexual|type=transcript|length=462bp
CATGAATTCCATGAACAATGAGGGGGTTATTCCTACGAGAGAGACCCGCC
CTAAGGTGCAAACTGGCACTGACCATGGAAGGATGAATACAAGGGATGTA
AATTGGATTTCCAAAAACAGCGATCAATTCACATCAATGGATATGGACTA
CCGGAGAAACAATGCTTGGAGCGATACTGATCGGTTCACCATGAAGTTCC
TATCCCAAATGACCGCAAAATATCGCCAGGCCCTCTGGAATGCCGACTAC
ATCTTGTCCACGATGAGTGGGGTGATGTCCGGACGAATTCACGAGACTAT
GATGTCAAAATTCCTAGCCTTATCATTAAACGCGAACCTGGACGGAATCC
GGCTCGCGAGGCGCGTCAATGCACAGAATTTTCCTTATATTGATGTGAAG
AGCAAGAGAGAAAAACACATTGGAAAGTGACCATAACTCGAAGAAGACTG
AAACATTACCGC
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protein sequence of SMED30020944-orf-1

>SMED30020944-orf-1 ID=SMED30020944-orf-1|Name=SMED30020944-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp
MNSMNNEGVIPTRETRPKVQTGTDHGRMNTRDVNWISKNSDQFTSMDMDY
RRNNAWSDTDRFTMKFLSQMTAKYRQALWNADYILSTMSGVMSGRIHETM
MSKFLALSLNANLDGIRLARRVNAQNFPYIDVKSKREKHIGK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
PLANA:0003116parenchymal cell