SMED30017616

Overview
NameSMED30017616
Smed IDSMED30017616
Length (bp)310
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



SMED30017616

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
reproductive organSMED30017616h1SMcG0007393 Contig33001newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30017616h1SMcG0007393 Contig33001uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30017616 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.022129:99..362 +1222
Homology
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BLAST of SMED30017616 vs. Planmine SMEST
Match: SMESG000067763.1 (SMESG000067763.1)

HSP 1 Score: 155.992 bits (393), Expect = 8.321e-51
Identity = 76/76 (100.00%), Postives = 76/76 (100.00%), Query Frame = 2 
Query:    2 LANAFKLSDDDVELGEEMDSNENELDENSKCKDKIGRCPKKMRDRCWMCRFVRKMNCNNFCKKTGEIYCYGKDSEQ 229
            LANAFKLSDDDVELGEEMDSNENELDENSKCKDKIGRCPKKMRDRCWMCRFVRKMNCNNFCKKTGEIYCYGKDSEQ
Sbjct:   18 LANAFKLSDDDVELGEEMDSNENELDENSKCKDKIGRCPKKMRDRCWMCRFVRKMNCNNFCKKTGEIYCYGKDSEQ 93
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BLAST of SMED30017616 vs. Planmine SMEST
Match: SMESG000067769.1 (SMESG000067769.1)

HSP 1 Score: 104.76 bits (260), Expect = 8.353e-31
Identity = 52/70 (74.29%), Postives = 59/70 (84.29%), Query Frame = 2 
Query:    2 LANAFKLSDDDVELGEEMDSNENELDENSKCKDKIGRCPKKMRDRCWMCRFVRKMNCNNFCKKTGEIYCY 211
            LANAFKLSDDDVELGEEMDSN+NELD+ SKCKD+IG+CPK+ R RC  CR+VRK N    CKKTGE YC+
Sbjct:   18 LANAFKLSDDDVELGEEMDSNDNELDKKSKCKDEIGKCPKRWRRRCHECRYVRKKNIFRTCKKTGEFYCH 87
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BLAST of SMED30017616 vs. Planmine SMEST
Match: SMESG000030634.1 (SMESG000030634.1)

HSP 1 Score: 41.5874 bits (96), Expect = 6.767e-6
Identity = 30/80 (37.50%), Postives = 44/80 (55.00%), Query Frame = 2 
Query:    2 LANAFKLSDDDVE------LGEEMDSNENELDENSK--CKDKIGRCPKKMRDRCWMCRFVRKMNCNNFCKKTGEIYCYGK 217
            LA   + ++D VE      L EE + +EN L+++ K  C   I +CPK MR  C  C F RK     FC++TG++ C+ K
Sbjct:   29 LAEEVEGAEDIVEEKDIRKLDEENEISENVLEDSMKDSCNYLIKKCPKSMRSECKTCIFYRKKK-MFFCRETGKVKCFHK 107
[Close]
BLAST of SMED30017616 vs. Planmine SMEST
Match: SMESG000030634.1 (SMESG000030634.1)

HSP 1 Score: 41.5874 bits (96), Expect = 6.889e-6
Identity = 30/80 (37.50%), Postives = 44/80 (55.00%), Query Frame = 2 
Query:    2 LANAFKLSDDDVE------LGEEMDSNENELDENSK--CKDKIGRCPKKMRDRCWMCRFVRKMNCNNFCKKTGEIYCYGK 217
            LA   + ++D VE      L EE + +EN L+++ K  C   I +CPK MR  C  C F RK     FC++TG++ C+ K
Sbjct:   24 LAEEVEGAEDIVEEKDIRKLDEENEISENVLEDSMKDSCNYLIKKCPKSMRSECKTCIFYRKKK-MFFCRETGKVKCFHK 102
The following BLAST results are available for this feature:
BLAST of SMED30017616 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 SMED30017616 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 SMED30017616 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 SMED30017616 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 SMED30017616 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 SMED30017616 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 SMED30017616 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 SMED30017616 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 SMED30017616 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 SMED30017616 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 SMED30017616 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 SMED30017616 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 SMED30017616 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 SMED30017616 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000067763.18.321e-51100.00SMESG000067763.1[more]
SMESG000067769.18.353e-3174.29SMESG000067769.1[more]
SMESG000030634.16.767e-637.50SMESG000030634.1[more]
SMESG000030634.16.889e-637.50SMESG000030634.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017616 ID=SMED30017616|Name=SMED30017616|organism=Schmidtea mediterranea sexual|type=transcript|length=310bp
CCTGGCTAATGCTTTCAAATTATCTGACGACGACGTAGAGCTAGGTGAAG
AAATGGATTCAAATGAGAATGAATTGGATGAAAATTCTAAATGTAAGGAC
AAAATAGGCAGATGTCCAAAAAAAATGAGAGACCGATGTTGGATGTGTAG
ATTTGTTAGGAAAATGAATTGTAATAACTTTTGCAAAAAAACTGGTGAAA
TTTATTGCTACGGAAAGGATTCAGAACAGTTTGGGACATTTCGGAATGAT
TTTTTTAATTTTTAAAGATTCTGAATTGTTTTTCTGTTTAATTAATTAAA
AAATTCAATG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ