SMED30027265

Overview
NameSMED30027265
Smed IDSMED30027265
Length (bp)367
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



SMED30027265

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
vitelline glandSMED30027265h1SMcG0013572 GDAG01019077.1SmedSxl_ww_GDAG01PMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30027265 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004527:7315..7723 -1755
v31.004527:7135..7470 +425
v31.004527:7255..7640 -369
Homology
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BLAST of SMED30027265 vs. Planmine SMEST
Match: SMESG000057964.1 (SMESG000057964.1)

HSP 1 Score: 204.912 bits (520), Expect = 3.039e-68
Identity = 97/97 (100.00%), Postives = 97/97 (100.00%), Query Frame = -3 
Query:   63 MWNKKLLFIAIAIINIQRGTGESFHCEVCNRCRNSTSDIQDNYSYLQIGGCKSCRTIFEKNVIRKLCSKKTCDKNMDGKICCTGELCNAAKSANSGD 353
            MWNKKLLFIAIAIINIQRGTGESFHCEVCNRCRNSTSDIQDNYSYLQIGGCKSCRTIFEKNVIRKLCSKKTCDKNMDGKICCTGELCNAAKSANSGD
Sbjct:    1 MWNKKLLFIAIAIINIQRGTGESFHCEVCNRCRNSTSDIQDNYSYLQIGGCKSCRTIFEKNVIRKLCSKKTCDKNMDGKICCTGELCNAAKSANSGD 97
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BLAST of SMED30027265 vs. Planmine SMEST
Match: SMESG000042052.1 (SMESG000042052.1)

HSP 1 Score: 91.6633 bits (226), Expect = 2.780e-24
Identity = 51/100 (51.00%), Postives = 67/100 (67.00%), Query Frame = -3 
Query:   66 MWNKKLLFIAIAIINIQRGTGESFHCEVCNRCRNSTSDIQ--DNYSY--LQIGGCKSCRTIFEKNVIRKLCSKKTCDKNMDGKICCTGELCNAAKSANSG 353
            M  K  LFIAI ++NIQ  T ES  C++CN C NSTSD Q  D +S   +++ GCKSCRT  + N+I K CS++TCDK   G+ CCT ELCN+AK+  + 
Sbjct:    1 MQLKAFLFIAITVVNIQLRTVESISCKICNPCWNSTSDDQYSDGFSNGNMRLSGCKSCRTNIKNNIIMKSCSEETCDKKEAGEECCTEELCNSAKNRKTA 100
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BLAST of SMED30027265 vs. Planmine SMEST
Match: SMESG000042071.1 (SMESG000042071.1)

HSP 1 Score: 89.7373 bits (221), Expect = 2.797e-24
Identity = 50/97 (51.55%), Postives = 65/97 (67.01%), Query Frame = -3 
Query:   75 MWNKKLLFIAIAIINIQRGTGESFHCEVCNRCRNSTSDIQDNYSYL----QIGGCKSCRTIFEKNVIRKLCSKKTCDKNMDGKICCTGELCNAAKSA 353
            M  K  LFIAI ++NIQ  T ES  C++C+ C NSTSD Q +  +L    +I GCKSCRT  + N+I K CS++TCD    G+ CCT ELCNAAK++
Sbjct:    1 MQLKAFLFIAITVVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMRITGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNAAKNS 97
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BLAST of SMED30027265 vs. Planmine SMEST
Match: SMESG000042755.1 (SMESG000042755.1)

HSP 1 Score: 88.9669 bits (219), Expect = 5.673e-24
Identity = 49/97 (50.52%), Postives = 65/97 (67.01%), Query Frame = -3 
Query:   75 MWNKKLLFIAIAIINIQRGTGESFHCEVCNRCRNSTSDIQDNYSYL----QIGGCKSCRTIFEKNVIRKLCSKKTCDKNMDGKICCTGELCNAAKSA 353
            M  K  LFIAI ++NIQ  T ES  C++C+ C NSTSD Q +  +L    ++ GCKSCRT  + N+I K CS++TCD    G+ CCT ELCNAAK++
Sbjct:    1 MQLKAFLFIAITLVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMRLSGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNAAKNS 97
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BLAST of SMED30027265 vs. Planmine SMEST
Match: SMESG000042059.1 (SMESG000042059.1)

HSP 1 Score: 89.3521 bits (220), Expect = 1.649e-23
Identity = 51/100 (51.00%), Postives = 66/100 (66.00%), Query Frame = -3 
Query:   66 MWNKKLLFIAIAIINIQRGTGESFHCEVCNRCRNSTSDIQ--DNYSY--LQIGGCKSCRTIFEKNVIRKLCSKKTCDKNMDGKICCTGELCNAAKSANSG 353
            M  K  LFIAI ++NIQ  T ES  C +CN C +STSD Q  D +S   ++I GCKSCRT  + N+I K CS++TCDK   G+ CCT ELCN+AK+  + 
Sbjct:    1 MQLKAFLFIAITVVNIQLRTVESISCNICNPCWSSTSDDQYSDGFSNENMRITGCKSCRTNIKNNIIMKSCSEETCDKKEAGEECCTEELCNSAKNRKTA 100
The following BLAST results are available for this feature:
BLAST of SMED30027265 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 SMED30027265 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 SMED30027265 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 SMED30027265 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 SMED30027265 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 SMED30027265 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 SMED30027265 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 SMED30027265 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 SMED30027265 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 SMED30027265 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 SMED30027265 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 SMED30027265 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 SMED30027265 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 SMED30027265 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000057964.13.039e-68100.00SMESG000057964.1[more]
SMESG000042052.12.780e-2451.00SMESG000042052.1[more]
SMESG000042071.12.797e-2451.55SMESG000042071.1[more]
SMESG000042755.15.673e-2450.52SMESG000042755.1[more]
SMESG000042059.11.649e-2351.00SMESG000042059.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027265 ID=SMED30027265|Name=SMED30027265|organism=Schmidtea mediterranea sexual|type=transcript|length=367bp
TTATTTTTAGTATTTCTCCAATTTTGTGCATTATTTTTATTATTTCTCCA
ATTTGGTGCATTATCTCCACTATTTGCCGATTTCGCAGCATTGCATAGTT
CACCGGTGCAACAAATTTTTCCGTCCATGTTTTTATCACAGGTTTTTTTA
CTACATAATTTTCTTATAACATTTTTTTCAAAAATTGTTCGACAAGACTT
GCAACCTCCAATTTGTAGATAACTGTAATTATCCTGGATGTCTGAGGTAG
AGTTCCGACATCGATTGCAGACCTCGCAATGAAACGATTCACCCGTTCCT
CTTTGGATATTGATTATCGCAATAGCAATGAAAAGCAGTTTTTTATTCCA
CATTTCTAAGATCGGAA
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protein sequence of SMED30027265-orf-1

>SMED30027265-orf-1 ID=SMED30027265-orf-1|Name=SMED30027265-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=121bp
PILEMWNKKLLFIAIAIINIQRGTGESFHCEVCNRCRNSTSDIQDNYSYL
QIGGCKSCRTIFEKNVIRKLCSKKTCDKNMDGKICCTGELCNAAKSANSG
DNAPNWRNNKNNAQNWRNTKN
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000231vitelline gland
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 2..21
NoneNo IPR availableTMHMMTMhelixcoord: 36..58