SMED30026240

Overview
NameSMED30026240
Smed IDSMED30026240
Length (bp)379
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

 

 

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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30026240 (SMED30026240) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026240 (SMED30026240) in cells (dots) of each of the 12 neoblast clusters.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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



SMED30026240

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30026240 SmedASXL_019083SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30026240 SmedASXL_019083SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30026240 Contig51725newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
parenchymaSMED30026240 dd_Smed_v4_3860_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30026240 dd_Smed_v6_3860_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30026240 vs. TrEMBL
Match: V9XTG6 (X1.D.A5.1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 5.236e-7
Identity = 29/96 (30.21%), Postives = 52/96 (54.17%), Query Frame = 2 
Query:   41 MNKILYQTFIIICLNAFVHSEDSMGQGYTNSKGEPVVNINGKEYSAKQNNVIKIGEGEKCTKCSIE----SDPPFYECQGPVLV---DESKYVSPC 307
            MN I     + +CL ++ +SE   G+G+ +  G  +V I  +++ A +   +++   +KC KC IE     + P +EC+GP LV   ++  Y+ PC
Sbjct:    1 MNFIYSFVGLAMCLMSYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIEPAVSGEQPLFECEGPSLVRVDEKDIYLDPC 96
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BLAST of SMED30026240 vs. Planmine SMEST
Match: SMESG000013213.1 (SMESG000013213.1)

HSP 1 Score: 187.578 bits (475), Expect = 4.708e-63
Identity = 91/92 (98.91%), Postives = 91/92 (98.91%), Query Frame = 2 
Query:   41 MNKILYQTFIIICLNAFVHSEDSMGQGYTNSKGEPVVNINGKEYSAKQNNVIKIGEGEKCTKCSIESDPPFYECQGPVLVDESKYVSPCDSD 316
            MNKILYQ FIIICLNAFVHSEDSMGQGYTNSKGEPVVNINGKEYSAKQNNVIKIGEGEKCTKCSIESDPPFYECQGPVLVDESKYVSPCDSD
Sbjct:    1 MNKILYQIFIIICLNAFVHSEDSMGQGYTNSKGEPVVNINGKEYSAKQNNVIKIGEGEKCTKCSIESDPPFYECQGPVLVDESKYVSPCDSD 92
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BLAST of SMED30026240 vs. Planmine SMEST
Match: SMESG000013213.1 (SMESG000013213.1)

HSP 1 Score: 142.124 bits (357), Expect = 2.058e-45
Identity = 69/69 (100.00%), Postives = 69/69 (100.00%), Query Frame = 2 
Query:  110 MGQGYTNSKGEPVVNINGKEYSAKQNNVIKIGEGEKCTKCSIESDPPFYECQGPVLVDESKYVSPCDSD 316
            MGQGYTNSKGEPVVNINGKEYSAKQNNVIKIGEGEKCTKCSIESDPPFYECQGPVLVDESKYVSPCDSD
Sbjct:    1 MGQGYTNSKGEPVVNINGKEYSAKQNNVIKIGEGEKCTKCSIESDPPFYECQGPVLVDESKYVSPCDSD 69
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BLAST of SMED30026240 vs. Planmine SMEST
Match: SMESG000013036.1 (SMESG000013036.1)

HSP 1 Score: 54.6842 bits (130), Expect = 9.232e-11
Identity = 28/79 (35.44%), Postives = 44/79 (55.70%), Query Frame = 2 
Query:   41 MNKILYQTFIIICLNAFVHSEDSMGQGYTNSKGEPVVNINGKEYSAKQNNVIKIGEGEKCTKCSIES-DPPFYECQGPV 274
            M+ + Y     I LN ++ +++  G GY +S G+P V I  + + A     +K+    +C KCSI++ D P YEC GPV
Sbjct:    1 MSLVSYLIIFAISLN-YISADEFFGYGYKDSNGKPFVKIADRIFEADTAREVKVNINSQCYKCSIKTGDRPMYECSGPV 78
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BLAST of SMED30026240 vs. Planmine SMEST
Match: SMESG000046988.1 (SMESG000046988.1)

HSP 1 Score: 53.1434 bits (126), Expect = 3.734e-10
Identity = 26/76 (34.21%), Postives = 43/76 (56.58%), Query Frame = 2 
Query:  107 SMGQGYTNSKGEPVVNINGKEYSAKQNNVIKIGEGEKCTKCSIE-----SDPPFYECQGPVLVDES----KYVSPC 307
            S+G+G  +S+G P+V I G+++ A     +++G+  KC KCSI+      D  ++ C+ P+L        KYVS C
Sbjct:   23 SIGKGSFDSEGRPIVVIRGQQFPAHVARTVRVGKASKCVKCSIKPPKSLGDVAYFRCEEPILSQTKEGVIKYVSSC 98
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BLAST of SMED30026240 vs. Planmine SMEST
Match: SMESG000061917.1 (SMESG000061917.1)

HSP 1 Score: 53.1434 bits (126), Expect = 3.791e-10
Identity = 31/86 (36.05%), Postives = 49/86 (56.98%), Query Frame = 2 
Query:   71 IICLNAFVHSEDSMGQGYTNSKGEPVVNINGKEYSAKQNNVIKIGEGEKCTKCSIES----DPPFYECQGPVLVDES---KYVSPC 307
            II L+A   +   +G+GY NS+G P V I  + + A++++  KI + E+C  C+I++      P Y CQGP     +   KY+SPC
Sbjct:    8 IIVLSAMADASLFLGRGYRNSEGVPYVKIFDQVFKAEESSTQKIYQNERCYLCNIKAPGSGRLPRYTCQGPSPSSTNGKIKYISPC 93
The following BLAST results are available for this feature:
BLAST of SMED30026240 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 SMED30026240 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 SMED30026240 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 SMED30026240 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 SMED30026240 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 SMED30026240 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 SMED30026240 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 SMED30026240 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XTG65.236e-730.21X1.D.A5.1 OS=Schmidtea mediterranea OX=79327 PE=2 ... [more]
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BLAST of SMED30026240 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 SMED30026240 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 SMED30026240 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 SMED30026240 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 SMED30026240 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 SMED30026240 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000013213.14.708e-6398.91SMESG000013213.1[more]
SMESG000013213.12.058e-45100.00SMESG000013213.1[more]
SMESG000013036.19.232e-1135.44SMESG000013036.1[more]
SMESG000046988.13.734e-1034.21SMESG000046988.1[more]
SMESG000061917.13.791e-1036.05SMESG000061917.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026240 ID=SMED30026240|Name=SMED30026240|organism=Schmidtea mediterranea sexual|type=transcript|length=379bp
ATTTAAACAAAAACTCAATCCAAAAAACATTTTAAACAAAATGAATAAAA
TTTTATATCAGACTTTTATTATCATTTGTTTGAATGCTTTTGTACATTCA
GAAGACTCAATGGGACAAGGCTACACAAATTCCAAGGGCGAGCCAGTGGT
GAATATCAATGGGAAAGAGTATTCAGCAAAACAAAATAACGTTATTAAAA
TCGGAGAAGGTGAGAAATGTACAAAATGTTCAATTGAATCTGATCCTCCA
TTTTATGAATGCCAGGGACCGGTTCTAGTTGATGAGTCGAAATATGTTTC
TCCTTGTGATTCCGATTAAATTACTTTTAAAATAAATAGTTTGATCGTTA
ATAAAGCTTTGGATTTTCGTCAAAAAAAA
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protein sequence of SMED30026240-orf-1

>SMED30026240-orf-1 ID=SMED30026240-orf-1|Name=SMED30026240-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=106bp
FKQKLNPKNILNKMNKILYQTFIIICLNAFVHSEDSMGQGYTNSKGEPVV
NINGKEYSAKQNNVIKIGEGEKCTKCSIESDPPFYECQGPVLVDESKYVS
PCDSD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..20
score: 0.766