SMED30029810

Overview
NameSMED30029810
Smed IDSMED30029810
Length (bp)852
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell 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




Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30029810 (SMED30029810) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029810 (SMED30029810) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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.
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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




SMED30029810

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
parenchymal cellSMED30029810SMESG000035443.1 dd_Smed_v4_19824_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30029810SMESG000035443.1 dd_Smed_v4_16064_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30029810 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011187:7644..8486 +4053
Homology
BLAST of SMED30029810 vs. Planmine SMEST
Match: SMESG000035443.1 (SMESG000035443.1)

HSP 1 Score: 419.083 bits (1076), Expect = 2.597e-149
Identity = 261/270 (96.67%), Postives = 266/270 (98.52%), Query Frame = 3
Query:   30 MTCFKXXXXXXXXXXXXXXXXXYRPCRNVQCYIDGTNTARYVTCSHGNVQRRSLLKCEYDNMDKSLTLRSPESNMKTADRFADHLFEILETSFGPIEKLTIENIQVNYIKKSDFSSLFNLTYLNIATPMIIDEDSFTSTFRSYFEISMKCNSISSSFRFNLKKKWKIILHECNYRFECSSVGSGEQYEYNIHLSNDVKYYLDLAVISKAGCEKPFFITLQHRXXXXXXXXXXXXXXXXHYXXXXXXXXXXXXXXXXXXXXGFALFTKRHL 839
            MTCFKIPLIFLLIISVIIPISSYRPCRN +CYIDGTNTARYVTCSHGNVQRRSLLKCEYDNMDKSLTLRSPE+NMKTADRFADHLFEILETSFGPIEKLTIENIQVNYIKKSDFSSLFNLTYLNIATPMIIDEDSFTSTFRS+FEISMKCNSISSSFRFNLKKKWKIILHECNYRFECSS GSGEQYEYNIHLSNDVKYYLDLAVIS AGCEKPFFITLQHRTIT+SSW SNTSNNKKHYSSFYFLFLISTFSILLFMLIGFALFTKR+L
Sbjct:    1 MTCFKIPLIFLLIISVIIPISSYRPCRNTRCYIDGTNTARYVTCSHGNVQRRSLLKCEYDNMDKSLTLRSPENNMKTADRFADHLFEILETSFGPIEKLTIENIQVNYIKKSDFSSLFNLTYLNIATPMIIDEDSFTSTFRSFFEISMKCNSISSSFRFNLKKKWKIILHECNYRFECSSAGSGEQYEYNIHLSNDVKYYLDLAVISNAGCEKPFFITLQHRTITSSSWTSNTSNNKKHYSSFYFLFLISTFSILLFMLIGFALFTKRNL 270          
BLAST of SMED30029810 vs. Planmine SMEST
Match: SMESG000035432.1 (SMESG000035432.1)

HSP 1 Score: 172.17 bits (435), Expect = 3.403e-52
Identity = 87/189 (46.03%), Postives = 123/189 (65.08%), Query Frame = 3
Query:  105 CRNVQCYIDGTNTARYVTCSHGNVQRRSLLKCEYDNMDKSLTLRSPESNMKTADRFADHLFEILETSFGPIEKLTIENIQVNYIKKSDFSSLFNLTYLNIATPMIIDEDSFTSTFRSYFEISMKCNSISSSFRFNLK-KKWKIILHECNYRFECSSVGSGEQYEYNIHLSNDVKYYLDLAVISKAGCEK 668
            C +++CY+D  +  +YV CS  +       +C+Y+  +KSL L++ +  +K+ D+FA  LFE ++   G I+ L+I  IQV YIKKSDF +LFN  YL ++ PM IDEDSF     S+FEISMKCN+ SS+ +F L+ +KW+I LH CNYR  CS V SGE+YEYNI L++D KY      I+   C +
Sbjct:   24 CGDLECYVDRISNTQYVNCSREHDPHSKTFECQYNEDEKSLKLKNKDHEVKSVDKFASGLFENIQKDLGKIKDLSINYIQVKYIKKSDFLTLFNARYLEMSIPMEIDEDSFIPFNSSFFEISMKCNNDSSNLQFKLQIEKWRIYLHYCNYRAACSLVRSGEKYEYNIQLNHDGKYTPTTVTITNENCSR 212          
BLAST of SMED30029810 vs. Planmine SMEST
Match: SMESG000035449.1 (SMESG000035449.1)

HSP 1 Score: 145.591 bits (366), Expect = 8.192e-42
Identity = 79/172 (45.93%), Postives = 102/172 (59.30%), Query Frame = 3
Query:   96 YRPCRNVQCYIDGTNTARYVTCSHGNVQRRSLLKCEYDNMDKSLTLRSPESNMKTADRFADHLFEILETSFGPIEKLTIENIQVNYIKKSDFSSLFNLTYLNIATPMIIDEDSFTSTFRSYFEISMKCNSISSSFRFNLKKK-WKIILHECNYRFECSSVGSGEQYEYNIHL 608
            +RPC N +CYID TN  RYV C+H NVQ  + L CEYD  D+ L L++    +  A+ FA++LF  L+ + G I KL +EN+ V Y K+SDF  L +L  L I TPM I EDSF     S  ++ M C   SS+  F L+ + W I L  CNY   CS   SG +YEYNI L
Sbjct:   33 FRPCSNTRCYIDETNATRYVNCTHENVQNGTSLICEYD--DEVLKLKNLNFTIGLAEEFANNLFGNLQKNLGRITKLKMENLNVKYFKRSDFLGLPDLKLLQIITPMAIKEDSFKPFNGSQLKMYMNCKLYSSNLHFKLQVQIWAIYLTNCNYSLICSYFVSGAKYEYNIQL 202          
BLAST of SMED30029810 vs. Planmine SMEST
Match: SMESG000035450.1 (SMESG000035450.1)

HSP 1 Score: 81.6481 bits (200), Expect = 1.581e-17
Identity = 55/187 (29.41%), Postives = 88/187 (47.06%), Query Frame = 3
Query:  105 CRNVQCYIDGTNTARYVTCSH----GNVQRRSLLKCEYDNMDKSLTLRSPESNMKTADRFADHLFEILETSFGPIEKLTIENIQVNYIKKSDFSSLFNLTYLNIATPMIIDEDSFTSTFRS-YFEISMKCN------SISSSFRFNLKKKWKIILHECNYRFEC------SSVGSGEQYEYNIHLSN 614
            C ++ C+I+   +AR + C +     N      LKCEYD   K+L ++   +   + D      F++   S   I +L I ++++N I +SDF  L  L  L +  P  ++EDSF     S YF++ + CN      S  S  R +  K W+I+L +C Y F C      + V  G +Y+    L N
Sbjct:   30 CEDIDCFIETDLSARVLGCDYKVLLANKTNLKFLKCEYDLKRKALFIKPLTAGDNSVDGLLTGGFKVFSESLKEITELHIPHVKINNISRSDFVGLEKLRGLTLMNPGNLEEDSFLDIINSEYFQLYIYCNNEKNHSSGISKLRIS-SKSWRIVLRDCRYSFGCNLGTCVNGVRIGNEYQVKFQLRN 215          
BLAST of SMED30029810 vs. Planmine SMEST
Match: SMESG000035431.1 (SMESG000035431.1)

HSP 1 Score: 66.2402 bits (160), Expect = 4.430e-12
Identity = 56/210 (26.67%), Postives = 97/210 (46.19%), Query Frame = 3
Query:  117 QCYIDGTNTARYVTCSHGNVQRRS----LLKCEYDNMDKSLTLRSPESNMKTADRFADHLFEILETSFGPIEKLTIENIQVNYIKKSDFSSLFNLTYLNIATPMIIDEDSFTSTFRS-YFEISMKC------------NSISSSFRFNLKKKWKIILHECNYRFECS----SVGSGEQYEYNIHL-----SNDVKYYLDLAVISKAGCEK 668
            +C++D +N +  + C +  V R       + C  D  + + +   P   M   DRF+D +F+ ++ +   I+ + + +I+VN+I++SD   L N+  L IA P   D DSF     S  F++ + C            NS S SF F+    W++I   C +R++C        SG + ++ + L     SND + YL         C+K
Sbjct:   26 ECFVDISNQS--LNCGNETVNRNQSKMRRINCALDREELTFSHNYP--GMVIVDRFSDQMFQTIKLNLSKIKAVRLSHIKVNHIRRSDLKYLSNIKSLTIANPKTFDIDSFLDIRHSDLFQLYIYCGTEIPKNYSSDYNSTSLSFLFHF-TNWRVIQINCLHRYQCEIEECVKNSGIKSKFFLKLNREKISNDTEVYLKSNNCKIKQCKK 230          
The following BLAST results are available for this feature:
BLAST of SMED30029810 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 SMED30029810 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 SMED30029810 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 SMED30029810 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 SMED30029810 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 SMED30029810 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 SMED30029810 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 SMED30029810 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 SMED30029810 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 SMED30029810 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 SMED30029810 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 SMED30029810 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 SMED30029810 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 SMED30029810 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000035443.12.597e-14996.67SMESG000035443.1[more]
SMESG000035432.13.403e-5246.03SMESG000035432.1[more]
SMESG000035449.18.192e-4245.93SMESG000035449.1[more]
SMESG000035450.11.581e-1729.41SMESG000035450.1[more]
SMESG000035431.14.430e-1226.67SMESG000035431.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029810 ID=SMED30029810|Name=SMED30029810|organism=Schmidtea mediterranea sexual|type=transcript|length=852bp
TTTTCTTTCTACTTTGGTTTCGTTTTCTTATGACTTGTTTCAAAATTCCA
TTGATATTTTTATTAATAATATCGGTAATTATCCCAATATCTTCATATCG
ACCCTGTAGAAATGTTCAGTGCTATATCGATGGGACCAATACTGCTCGAT
ATGTGACTTGCTCCCATGGAAACGTACAAAGGAGATCATTATTAAAATGT
GAATATGACAATATGGATAAAAGCTTGACATTGAGAAGTCCTGAAAGCAA
TATGAAAACAGCTGATAGATTTGCCGACCATTTATTTGAGATCCTTGAAA
CATCGTTCGGGCCGATAGAAAAACTGACAATAGAAAATATTCAAGTGAAT
TATATAAAAAAATCAGATTTTTCCAGCTTATTTAATTTGACGTACTTGAA
CATTGCAACTCCAATGATAATTGATGAAGACAGTTTCACTTCCACCTTTA
GATCTTACTTTGAAATTTCCATGAAATGCAATTCTATTTCTTCAAGTTTT
CGTTTCAATTTGAAAAAGAAATGGAAAATTATTCTCCATGAATGCAATTA
TCGCTTTGAATGCTCATCGGTTGGGTCTGGTGAGCAATATGAATACAATA
TCCATTTGTCTAATGATGTCAAATACTATCTGGACCTGGCAGTGATATCA
AAGGCTGGGTGTGAAAAACCATTCTTTATTACTCTTCAACATAGAACCAT
CACAAATTCTTCTTGGAAATCCAATACAAGTAACAATAAAAAACACTATT
CATCATTTTACTTCTTATTTTTAATAAGTACTTTTTCTATTTTACTGTTT
ATGCTAATCGGGTTTGCGTTATTTACTAAAAGACATCTTTGAATCCATAC
TA
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protein sequence of SMED30029810-orf-1

>SMED30029810-orf-1 ID=SMED30029810-orf-1|Name=SMED30029810-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=280bp
FFLLWFRFLMTCFKIPLIFLLIISVIIPISSYRPCRNVQCYIDGTNTARY
VTCSHGNVQRRSLLKCEYDNMDKSLTLRSPESNMKTADRFADHLFEILET
SFGPIEKLTIENIQVNYIKKSDFSSLFNLTYLNIATPMIIDEDSFTSTFR
SYFEISMKCNSISSSFRFNLKKKWKIILHECNYRFECSSVGSGEQYEYNI
HLSNDVKYYLDLAVISKAGCEKPFFITLQHRTITNSSWKSNTSNNKKHYS
SFYFLFLISTFSILLFMLIGFALFTKRHL*
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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 availableTMHMMTMhelixcoord: 252..274
NoneNo IPR availableTMHMMTMhelixcoord: 15..32