SMED30004918

Overview
NameSMED30004918
Smed IDSMED30004918
Length (bp)818
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




SMED30004918

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
posterior sideSMED30004918h1SMcG0016205 dd_Smed_v4_7714_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30004918h1SMcG0016205 dd_Smed_v4_7714_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30004918 vs. Planmine SMEST
Match: SMESG000020705.1 (SMESG000020705.1)

HSP 1 Score: 60.4622 bits (145), Expect = 3.715e-10
Identity = 33/48 (68.75%), Postives = 40/48 (83.33%), Query Frame = -3
Query:  337 KRTVKEVTCVSSKVFGHEARHEIIVSAENSKRKYEN*YIE--KGCFTS 474
            +RTVKEV  VSSKV+GHEARH +IVSAE+S+R+YEN  IE  +G FTS
Sbjct:  952 ERTVKEVNRVSSKVYGHEARHGMIVSAEDSRREYENKDIETTEGYFTS 999          
BLAST of SMED30004918 vs. Planmine SMEST
Match: SMESG000044252.1 (SMESG000044252.1)

HSP 1 Score: 54.6842 bits (130), Expect = 3.110e-8
Identity = 28/44 (63.64%), Postives = 32/44 (72.73%), Query Frame = 3
Query:    6 IKIGDLVYINKPEPKKRLSPKLQRPFKRAYVV-GRVDTKLAVLP 134
            IK+G LVY+NKPEP KRLS KLQRPFKR Y V    +T L + P
Sbjct:  858 IKVGYLVYLNKPEPTKRLSTKLQRPFKRPYTVCDTTETNLKLRP 901          
BLAST of SMED30004918 vs. Planmine SMEST
Match: SMESG000034928.1 (SMESG000034928.1)

HSP 1 Score: 53.1434 bits (126), Expect = 1.070e-7
Identity = 26/45 (57.78%), Postives = 34/45 (75.56%), Query Frame = 3
Query:    3 DIKIGDLVYINKPEPKKRLSPKLQRPFKRAYVV-GRVDTKLAVLP 134
            +I++GDLVY++KPEP K LSPKLQRPFK  Y+V    +T L + P
Sbjct: 1014 NIEVGDLVYVHKPEPAKGLSPKLQRPFKGPYIVCDTTETNLKLRP 1058          
BLAST of SMED30004918 vs. Planmine SMEST
Match: SMESG000031866.1 (SMESG000031866.1)

HSP 1 Score: 52.7582 bits (125), Expect = 1.127e-7
Identity = 31/65 (47.69%), Postives = 40/65 (61.54%), Query Frame = 3
Query:    3 DIKIGDLVYINKPEPKKRLSPKLQRPFKRAYVV-GRVDTKLAVLPCLY*K---IVFDVYCSQVNF 185
            DIK+GD VYINKPEP K L  KLQRPFK  Y+V    +T L + P    K   I+ +VY   +++
Sbjct:  160 DIKVGDFVYINKPEPTKGLLVKLQRPFKEPYLVCDSTETNLKLRPQYNKKAGTIIVNVYSVLIHY 224          
BLAST of SMED30004918 vs. Planmine SMEST
Match: SMESG000073500.1 (SMESG000073500.1)

HSP 1 Score: 51.2174 bits (121), Expect = 5.446e-7
Identity = 26/44 (59.09%), Postives = 31/44 (70.45%), Query Frame = 3
Query:    6 IKIGDLVYINKPEPKKRLSPKLQRPFKRAYVV-GRVDTKLAVLP 134
            IK+GDLVY+NKPEP K LS KLQ+PFK  Y V    +T L + P
Sbjct: 1149 IKLGDLVYLNKPEPTKGLSTKLQKPFKGPYTVCDTTETNLKLRP 1192          
The following BLAST results are available for this feature:
BLAST of SMED30004918 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 SMED30004918 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 SMED30004918 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 SMED30004918 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 SMED30004918 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 SMED30004918 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 SMED30004918 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 SMED30004918 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 SMED30004918 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 SMED30004918 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 SMED30004918 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 SMED30004918 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 SMED30004918 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 SMED30004918 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000020705.13.715e-1068.75SMESG000020705.1[more]
SMESG000044252.13.110e-863.64SMESG000044252.1[more]
SMESG000034928.11.070e-757.78SMESG000034928.1[more]
SMESG000031866.11.127e-747.69SMESG000031866.1[more]
SMESG000073500.15.446e-759.09SMESG000073500.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004918 ID=SMED30004918|Name=SMED30004918|organism=Schmidtea mediterranea sexual|type=transcript|length=818bp
ATGATATTAAAATTGGAGATTTAGTCTACATTAATAAGCCAGAGCCGAAA
AAAAGATTATCACCGAAACTGCAACGACCATTTAAAAGAGCATATGTAGT
AGGGCGAGTCGATACAAAACTTGCAGTACTACCTTGTCTCTATTAAAAAA
TTGTCTTTGACGTCTATTGTTCACAAGTAAATTTTATATCAAATTGGTTA
ATGTATAGGGTCTATACATTTATGTAAAAGAATCAGTGAAAACCACAGTG
TGTATATTTTTCAACTACTTTAAAATCACAATACAAAGATTAGCAATAAA
GGTAGGTTGAACGCTGAATACAAGAATAGCAGATCAACTTGTGAAACATC
CTTTTTCGATATATTAATTTTCATACTTTCTCTTTGAGTTTTCTGCCGAT
ACAATAATTTCATGTCTTGCTTCGTGGCCGAAAACCTTTGAGGAAACGCA
AGTAACTTCCTTTACAGTGCGTTTTCGGGTGACAAAAGTAGATGTTCCTC
TGAATAAGCTTTTCGTTTAACAAAGGCATATCTTCCATTTGTTGACCTCG
TGTTACCGACTTCTCCATTTTTGAAAAACACTATGTTGAGCTATGGTAGA
ATGTTATCTTTCGCCTAGATGGCAATTACATCCCCTGCTACAAGTTTCAT
AATATCTCGCTTAGACTGAATTGGTGATGAAGCTTCGTGTAGTTGATTTT
GATATCATAAGAAACACTTAAATACTTCTTGTGTAGGAAGCTCATTTATA
GGAAGTACACTTGGCTGAAGAAATATTCCATGTCGACCACTGGATCTAAG
TAAATTATAATAATAAAG
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