SMED30011612

Overview
NameSMED30011612
Smed IDSMED30011612
Length (bp)441
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



SMED30011612

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
parenchymal cellSMED30011612 dd_Smed_v4_17222_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
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BLAST of SMED30011612 vs. Planmine SMEST
Match: SMESG000014679.1 (SMESG000014679.1)

HSP 1 Score: 249.21 bits (635), Expect = 2.247e-81
Identity = 134/142 (94.37%), Postives = 136/142 (95.77%), Query Frame = 2 
Query:    2 LISVLETVEVRLKAIHRDDELKRGYLLQRCLKKLSSTLLLNWKEMARLNESMGCLAKFREWLKIKMELLRSTKEMLFGIDENWNNDYKQTEWKDRRSKEKEMNNQVKPKRSFYAEKVVKQLQSSGKSASNKVECIKCEGEHY 427
            LISVLETVEV LKAIHRD+ELKRGYLLQRCLKKLSSTLLLNWKEMARLNESM CLAKFREWLKIKMELLRSTKEMLF IDENWNNDYKQTEWKDRRSK KEM+NQVK KRSFYAEKVVKQLQSS KSASNKVECIKCEGEHY
Sbjct:  387 LISVLETVEVHLKAIHRDNELKRGYLLQRCLKKLSSTLLLNWKEMARLNESMSCLAKFREWLKIKMELLRSTKEMLFSIDENWNNDYKQTEWKDRRSKGKEMDNQVKSKRSFYAEKVVKQLQSSVKSASNKVECIKCEGEHY 528
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BLAST of SMED30011612 vs. Planmine SMEST
Match: SMESG000034883.1 (SMESG000034883.1)

HSP 1 Score: 173.326 bits (438), Expect = 4.867e-52
Identity = 92/131 (70.23%), Postives = 108/131 (82.44%), Query Frame = 2 
Query:    2 LISVLETVEVRLKAIHRDDELKRGYLLQRCLKKLSSTLLLNWKEMARLNESMGCLAKFREWLKIKMELLRSTKEMLFGIDENWNNDYKQTEWKDRRSKEKEMNNQVKPKRSFYAEKVVKQLQSSGKSASNK 394
            LI VLETVEVRLK+I+RDDELK GY LQRCLKKLSS+LL+N KEMARLNESMGCLAKFREWL+IK+E LRSTKEMLFG+D  W    K+ EWK++RSK KEM++QVKPKRSF    + K+LQS+     N+
Sbjct:  143 LIRVLETVEVRLKSINRDDELKSGYFLQRCLKKLSSSLLVNRKEMARLNESMGCLAKFREWLQIKVEFLRSTKEMLFGMDGKWKK-VKRPEWKNQRSKWKEMDDQVKPKRSF----MRKKLQSNYSQVENQ 268
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BLAST of SMED30011612 vs. Planmine SMEST
Match: SMESG000074922.1 (SMESG000074922.1)

HSP 1 Score: 91.6633 bits (226), Expect = 8.818e-23
Identity = 47/63 (74.60%), Postives = 52/63 (82.54%), Query Frame = 2 
Query:    2 LISVLETVEVRLKAIHRDDELKRGYLLQRCLKKLSSTLLLNWKEMARLNESMGCLAKFREWLK 190
            LISVLETVE+RL  I R+DELK GYLLQRCLKK S+ LLLN K+MARLNE M   AKFREWL+
Sbjct:  260 LISVLETVEMRLLVIIREDELKSGYLLQRCLKKSSNPLLLNLKDMARLNEPMSFFAKFREWLQ 322
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BLAST of SMED30011612 vs. Planmine SMEST
Match: SMESG000000863.1 (SMESG000000863.1)

HSP 1 Score: 78.1814 bits (191), Expect = 1.649e-17
Identity = 38/62 (61.29%), Postives = 46/62 (74.19%), Query Frame = 2 
Query:  242 ENWNNDYKQTEWKDRRSKEKEMNNQVKPKRSFYAEKVVKQLQSSGKSASNKVECIKCEGEHY 427
            E+   DYK  EW D+RSK K+M++QVK KRSF+AE V K  Q+S KSASN  +CIKCE EHY
Sbjct:  176 ESGKKDYKPPEWMDQRSKWKQMDDQVKTKRSFFAENVAKPFQASRKSASNNWQCIKCEREHY 237
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BLAST of SMED30011612 vs. Planmine SMEST
Match: SMESG000067372.1 (SMESG000067372.1)

HSP 1 Score: 74.3294 bits (181), Expect = 1.508e-16
Identity = 38/68 (55.88%), Postives = 49/68 (72.06%), Query Frame = 2 
Query:  224 MLFGIDENWNNDYKQTEWKDRRSKEKEMNNQVKPKRSFYAEKVVKQLQSSGKSASNKVECIKCEGEHY 427
            MLFG+DE    DYK+ E   +RSK KEM+++VKPKRSFYA+KV K LQ+S K+ SNK +CI    E +
Sbjct:    1 MLFGMDEELKKDYKRPEMNGQRSKWKEMDDKVKPKRSFYADKVDKPLQASRKAVSNKWKCINSNSERH 68
The following BLAST results are available for this feature:
BLAST of SMED30011612 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 SMED30011612 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 SMED30011612 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 SMED30011612 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 SMED30011612 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 SMED30011612 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 SMED30011612 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 SMED30011612 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 SMED30011612 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 SMED30011612 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 SMED30011612 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 SMED30011612 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 SMED30011612 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 SMED30011612 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000014679.12.247e-8194.37SMESG000014679.1[more]
SMESG000034883.14.867e-5270.23SMESG000034883.1[more]
SMESG000074922.18.818e-2374.60SMESG000074922.1[more]
SMESG000000863.11.649e-1761.29SMESG000000863.1[more]
SMESG000067372.11.508e-1655.88SMESG000067372.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011612 ID=SMED30011612|Name=SMED30011612|organism=Schmidtea mediterranea sexual|type=transcript|length=441bp
CTTGATAAGCGTTTTAGAAACGGTGGAGGTACGCTTGAAGGCGATACACC
GAGACGATGAGTTGAAAAGAGGATACCTTCTTCAAAGGTGCTTGAAGAAG
TTATCAAGTACGCTTTTATTAAACTGGAAGGAAATGGCCAGACTAAATGA
ATCAATGGGTTGTTTGGCCAAGTTTCGAGAATGGTTGAAAATAAAAATGG
AATTGCTACGATCTACGAAAGAGATGTTATTTGGCATTGATGAAAATTGG
AATAACGATTATAAACAAACAGAATGGAAGGATCGGAGATCAAAAGAGAA
AGAAATGAATAATCAGGTAAAGCCGAAACGATCCTTTTATGCGGAAAAAG
TTGTAAAGCAATTACAGTCAAGCGGAAAATCAGCAAGCAACAAAGTTGAA
TGTATCAAGTGTGAAGGAGAGCATTATTAGATCAATGCAAG
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protein sequence of SMED30011612-orf-1

>SMED30011612-orf-1 ID=SMED30011612-orf-1|Name=SMED30011612-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp
LISVLETVEVRLKAIHRDDELKRGYLLQRCLKKLSSTLLLNWKEMARLNE
SMGCLAKFREWLKIKMELLRSTKEMLFGIDENWNNDYKQTEWKDRRSKEK
EMNNQVKPKRSFYAEKVVKQLQSSGKSASNKVECIKCEGEHY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 118..138