SMED30021648

Overview
NameSMED30021648
Smed IDSMED30021648
Length (bp)470
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



SMED30021648

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
gutSMED30021648h1SMcG0007032 dd_Smed_v4_5227_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30021648h1SMcG0007032 dd_Smed_v4_5227_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30021648h1SMcG0007032 dd_Smed_v4_5227_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
Alignments
SMED30021648 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.013028:10324..10725 +1920
v31.024316:2055..2455 -1894
Homology
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BLAST of SMED30021648 vs. Planmine SMEST
Match: SMESG000026481.1 (SMESG000026481.1)

HSP 1 Score: 105.531 bits (262), Expect = 6.744e-27
Identity = 53/97 (54.64%), Postives = 65/97 (67.01%), Query Frame = -3 
Query:    4 KMKPTKNFRRDL---------HIHILTSKKVQRNALIYRKCAGFKLVQSSVSFSYYWIDFQSRIISNTDKIKVPINYESLLEPYEYHYTTHKSSKTL 267
            K +PT+ FR+D+          I IL+S+K++ N LI+RKC GFKL  S+ SFSYYWID Q R IS TD I+VPIN ES+   YE HYT HKS KT 
Sbjct:  909 KTQPTQVFRKDVILKISTPPVQIQILSSEKLKINGLIHRKCVGFKLAHSTESFSYYWIDSQGRTISKTDTIQVPINDESVFGRYECHYTAHKSGKTF 1005
[Close]
BLAST of SMED30021648 vs. Planmine SMEST
Match: SMESG000026481.1 (SMESG000026481.1)

HSP 1 Score: 105.531 bits (262), Expect = 7.951e-27
Identity = 53/97 (54.64%), Postives = 65/97 (67.01%), Query Frame = -3 
Query:    4 KMKPTKNFRRDL---------HIHILTSKKVQRNALIYRKCAGFKLVQSSVSFSYYWIDFQSRIISNTDKIKVPINYESLLEPYEYHYTTHKSSKTL 267
            K +PT+ FR+D+          I IL+S+K++ N LI+RKC GFKL  S+ SFSYYWID Q R IS TD I+VPIN ES+   YE HYT HKS KT 
Sbjct:  391 KTQPTQVFRKDVILKISTPPVQIQILSSEKLKINGLIHRKCVGFKLAHSTESFSYYWIDSQGRTISKTDTIQVPINDESVFGRYECHYTAHKSGKTF 487
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BLAST of SMED30021648 vs. Planmine SMEST
Match: SMESG000063572.1 (SMESG000063572.1)

HSP 1 Score: 101.293 bits (251), Expect = 2.233e-25
Identity = 51/97 (52.58%), Postives = 62/97 (63.92%), Query Frame = -3 
Query:    4 KMKPTKNFRRDL---------HIHILTSKKVQRNALIYRKCAGFKLVQSSVSFSYYWIDFQSRIISNTDKIKVPINYESLLEPYEYHYTTHKSSKTL 267
            K +PT+ FR+D+          I IL S+K+  N LI+RKC GFKL +S+  FSYYWID Q R IS TD I+VPIN ES+   YE HY  HKS KT 
Sbjct:  183 KTQPTQVFRKDVILKISQPAVQIQILASEKLIINGLIHRKCVGFKLAESTERFSYYWIDSQGRTISKTDTIQVPINDESVFGQYECHYRAHKSGKTF 279
[Close]
BLAST of SMED30021648 vs. Planmine SMEST
Match: SMESG000027826.1 (SMESG000027826.1)

HSP 1 Score: 48.1358 bits (113), Expect = 7.033e-7
Identity = 27/94 (28.72%), Postives = 49/94 (52.13%), Query Frame = -3 
Query:   10 PTKNFRRDLH---------IHILTSKKVQRNALIYRKCAGFKLVQSSV--SFSYYWIDFQSRIISNTDKIKVPINYESLLEPYEYHYTTHKSSK 258
            P   F R LH         I IL  + ++    I R+C+   L Q ++   F+Y W++ Q++ I NT+ +++P+  ES++  Y   Y + ++SK
Sbjct:  114 PQIRFNRTLHLKITIPSISIDILPEESLKIGGQIKRQCSDLGLPQETIVDDFTYTWLNQQNKTIGNTNILQIPVVDESVVGRYICQYKSKETSK 207
[Close]
BLAST of SMED30021648 vs. Planmine SMEST
Match: SMESG000027815.1 (SMESG000027815.1)

HSP 1 Score: 48.1358 bits (113), Expect = 7.415e-7
Identity = 27/94 (28.72%), Postives = 49/94 (52.13%), Query Frame = -3 
Query:   10 PTKNFRRDLH---------IHILTSKKVQRNALIYRKCAGFKLVQSSV--SFSYYWIDFQSRIISNTDKIKVPINYESLLEPYEYHYTTHKSSK 258
            P   F R LH         I IL  + ++    I R+C+   L Q ++   F+Y W++ Q++ I NT+ +++P+  ES++  Y   Y + ++SK
Sbjct:  105 PQIRFNRTLHLKITIPSISIDILPEESLKIGGQIKRQCSDLGLPQETIVDDFTYTWLNQQNKTIGNTNILQIPVVDESVVGRYICQYKSKETSK 198
The following BLAST results are available for this feature:
BLAST of SMED30021648 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 SMED30021648 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 SMED30021648 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 SMED30021648 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 SMED30021648 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 SMED30021648 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 SMED30021648 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 SMED30021648 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 SMED30021648 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 SMED30021648 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 SMED30021648 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 SMED30021648 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 SMED30021648 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 SMED30021648 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000026481.16.744e-2754.64SMESG000026481.1[more]
SMESG000026481.17.951e-2754.64SMESG000026481.1[more]
SMESG000063572.12.233e-2552.58SMESG000063572.1[more]
SMESG000027826.17.033e-728.72SMESG000027826.1[more]
SMESG000027815.17.415e-728.72SMESG000027815.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021648 ID=SMED30021648|Name=SMED30021648|organism=Schmidtea mediterranea sexual|type=transcript|length=470bp
GGTTAATGTCTTACTTGATTTATGAGTTGTATAATGATATTCATAGGGCT
CCAATAGAGATTCGTAATTTATTGGAACTTTAATTTTGTCAGTATTCGAG
ATTATTCTGCTTTGGAAATCTATCCAATAATAAGAAAAGCTTACAGATGA
TTGAACCAATTTAAATCCGGCACATTTCCTGTAAATCAACGCATTTCTTT
GAACCTTCTTGGAAGTTAGAATGTGAATGTGAAGATCTCTTCTGAAGTTT
TTTGTTGGTTTCATTTTACACTGAAACGAACGTGATGAAACTAGCACACA
ATTGAATTTTGATGTGAAAAAAGAAATTATAACATCACGCATGTTTCAAC
TGAAAAGCAAATCCTATGCTGAAATGAAAATCAATAACCTTATATTATAG
GACATGCATGCTTATCCATGTGTTGATGTGATTAGTTCGAATGAATAACA
ACTTTTAATATAGAAAGTCA
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protein sequence of SMED30021648-orf-1

>SMED30021648-orf-1 ID=SMED30021648-orf-1|Name=SMED30021648-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp
MRDVIISFFTSKFNCVLVSSRSFQCKMKPTKNFRRDLHIHILTSKKVQRN
ALIYRKCAGFKLVQSSVSFSYYWIDFQSRIISNTDKIKVPINYESLLEPY
EYHYTTHKSSKTLT
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