SMED30032344

Overview
NameSMED30032344
Smed IDSMED30032344
Length (bp)1735
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 SMED30032344 (SMED30032344) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30032344 (SMED30032344) 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



SMED30032344

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
cephalic gangliaSMED30032344SMESG000055206.1 SMESG000055195.1 dd_Smed_v4_8451_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30032344SMESG000055206.1 SMESG000055195.1 dd_Smed_v4_8451_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30032344SMESG000055206.1 SMESG000055195.1 dd_Smed_v4_8451_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
SMED30032344 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005736:27503..30604 -8485
Homology
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BLAST of SMED30032344 vs. Planmine SMEST
Match: SMESG000055206.1 (SMESG000055206.1)

HSP 1 Score: 389.423 bits (999), Expect = 7.169e-131
Identity = 203/241 (84.23%), Postives = 205/241 (85.06%), Query Frame = 1 
Query:   34 KDLIRNDNQSVVYKKFLDSNESTSFKIIWKQERFERFCLAEIDMKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTFDNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSCVRFQGEITFRYDISQFKLICPSKIPSIPHKXXXXXXXXXXXXITLLCGASFLIYFKSKFRRQNPTFESPYNGNNYESVEVQNMAFRPLPIPEKEEKNLTEPVRSGLHG 756
            KDLIRNDNQSVVYKKFLDSNESTSFKIIWKQERFERFCLAEIDMKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTFDNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSC  F   ++F Y                              FITLLCGASFLIYFKSKFRRQNPTFESPYNGNNYESVEVQNMAFRPLPIPEKEEKNLTEPVRSGLHG
Sbjct:  204 KDLIRNDNQSVVYKKFLDSNESTSFKIIWKQERFERFCLAEIDMKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTFDNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSC--FYYFLSFGYSF----------------------------FITLLCGASFLIYFKSKFRRQNPTFESPYNGNNYESVEVQNMAFRPLPIPEKEEKNLTEPVRSGLHG 414
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BLAST of SMED30032344 vs. Planmine SMEST
Match: SMESG000055195.1 (SMESG000055195.1)

HSP 1 Score: 337.806 bits (865), Expect = 8.078e-110
Identity = 187/259 (72.20%), Postives = 200/259 (77.22%), Query Frame = 1 
Query:   34 KDLIRNDNQSVVYKKFLDSNESTSFKIIWKQERFERFCLAEIDMKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTFDNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSCVRFQGEITFRYDISQFKLICPSKIPSIPHKXXXXXXXXXXXXITLLCGASFLIYFKSKFRRQNPTFESPYNGNNYESVEVQNMA-FRPL--PIPEKEEKNLTEPVRSGLHG*ITIQEDSVYDFSLL 801
            KDLIRNDNQSVVYKKF DSNESTSFKIIWKQERFERFCLAEIDMKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTFDNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSCVRFQGEITFRYDISQFKLICPSKIPSIPHK Y+FLS  Y   +T L      + F S  +++     SP   NN E+  V+    + P+   I  + E    EP              SVYD+ +L
Sbjct:  245 KDLIRNDNQSVVYKKFPDSNESTSFKIIWKQERFERFCLAEIDMKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTFDNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSCVRFQGEITFRYDISQFKLICPSKIPSIPHKIYFFLSLIYDAMMTFLFAVLCTLRFCSNSKQKVVKITSPIEINNNETTYVEETGDYEPIYSQIATRNENTEAEP--------------SVYDYVIL 489
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BLAST of SMED30032344 vs. Planmine SMEST
Match: SMESG000055195.1 (SMESG000055195.1)

HSP 1 Score: 337.035 bits (863), Expect = 1.193e-109
Identity = 187/259 (72.20%), Postives = 200/259 (77.22%), Query Frame = 1 
Query:   34 KDLIRNDNQSVVYKKFLDSNESTSFKIIWKQERFERFCLAEIDMKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTFDNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSCVRFQGEITFRYDISQFKLICPSKIPSIPHKXXXXXXXXXXXXITLLCGASFLIYFKSKFRRQNPTFESPYNGNNYESVEVQNMA-FRPL--PIPEKEEKNLTEPVRSGLHG*ITIQEDSVYDFSLL 801
            KDLIRNDNQSVVYKKF DSNESTSFKIIWKQERFERFCLAEIDMKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTFDNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSCVRFQGEITFRYDISQFKLICPSKIPSIPHK Y+FLS  Y   +T L      + F S  +++     SP   NN E+  V+    + P+   I  + E    EP              SVYD+ +L
Sbjct:  238 KDLIRNDNQSVVYKKFPDSNESTSFKIIWKQERFERFCLAEIDMKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTFDNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSCVRFQGEITFRYDISQFKLICPSKIPSIPHKIYFFLSLIYDAMMTFLFAVLCTLRFCSNSKQKVVKITSPIEINNNETTYVEETGDYEPIYSQIATRNENTEAEP--------------SVYDYVIL 482
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BLAST of SMED30032344 vs. Planmine SMEST
Match: SMESG000050489.1 (SMESG000050489.1)

HSP 1 Score: 78.9518 bits (193), Expect = 2.589e-15
Identity = 43/125 (34.40%), Postives = 64/125 (51.20%), Query Frame = 1 
Query:  106 FKIIWKQERFERFCLAEIDMKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTFDNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSCVRFQGEITFRYDISQF 480
             K+IWK      +CL EI  ++ S  +FY+   NEL  C + N  S  C+ +SL  +TTDEI+V+   +    + +KI  G  ++TF +     IK +K+G+      C RF   I F Y   QF
Sbjct:  260 MKLIWKLNGPSNYCLMEIGTRNNSVILFYVNNLNELLMC-MRNSQSLKCSSRSLVTLTTDEIYVMTVGYAPPNLTVKIPFGSGVKTFVETVNNDIKWVKVGFRSQENVCERFTENIAFVYYKHQF 383
[Close]
BLAST of SMED30032344 vs. Planmine SMEST
Match: SMESG000055117.1 (SMESG000055117.1)

HSP 1 Score: 75.485 bits (184), Expect = 3.146e-14
Identity = 40/150 (26.67%), Postives = 74/150 (49.33%), Query Frame = 1 
Query:   34 KDLIRNDNQSVVYKKFLDSNESTSFKIIWKQERFERFCLAEIDMKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTFDNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSCVRFQGEITFRYDISQFK 483
            KDL  ++NQ  +Y+    + E +SFK+IW+      FCL  + + D S   FY+   N +           +  +++L       I++++   +++++ +KI+NG  + +F+D     +K I +G S     C  F G I   YD +QF+
Sbjct:  235 KDLSDHENQRNLYENLTSNVEESSFKLIWRFNYTNNFCLLNVILSDNSTIRFYMDNENTVRMRLTGRNSKTISLQRTL---RAGSINIIIIKCEDTELYVKITNGSSVTSFRDYISSTVKLIYLGVSTGMTDCTDFNGHIDLLYDATQFQ 381
The following BLAST results are available for this feature:
BLAST of SMED30032344 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 SMED30032344 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 SMED30032344 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 SMED30032344 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 SMED30032344 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 SMED30032344 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 SMED30032344 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 SMED30032344 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 SMED30032344 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 SMED30032344 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 SMED30032344 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 SMED30032344 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 SMED30032344 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 SMED30032344 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000055206.17.169e-13184.23SMESG000055206.1[more]
SMESG000055195.18.078e-11072.20SMESG000055195.1[more]
SMESG000055195.11.193e-10972.20SMESG000055195.1[more]
SMESG000050489.12.589e-1534.40SMESG000050489.1[more]
SMESG000055117.13.146e-1426.67SMESG000055117.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032344 ID=SMED30032344|Name=SMED30032344|organism=Schmidtea mediterranea sexual|type=transcript|length=1735bp
TTATTATTGTTGTTGTTGTTGTTAATATTTTAAAAAGACCTAATTCGTAA
TGACAATCAGAGCGTGGTCTATAAGAAATTTCTTGATTCAAATGAGTCAA
CTTCATTTAAAATTATTTGGAAACAAGAAAGGTTCGAAAGGTTTTGCTTG
GCAGAAATTGATATGAAAGATGGCTCTTATTTTATATTTTATATCACTGA
AAACAACGAGCTGTCAAAGTGCTTCATTGAAAACCGATTTTCACCGGTTT
GCACCAAAAAATCCTTATTCAATGTCACAACGGATGAGATTCACGTTTTA
ATGTTCACATTTGACAATTCACAGGTCCTCATCAAGATTTCTAATGGAAA
ATATATCCAAACATTTAAAGATGAGTTTCAAAGGAAGATAAAGCAAATAA
AAATTGGTTATTCGGAAAATACAAAAAGTTGTGTAAGATTTCAAGGAGAA
ATTACTTTTCGATACGACATTTCTCAGTTTAAATTGATATGTCCGTCAAA
GATTCCATCAATTCCCCACAAGTTTTATTATTTCTTATCGTTCGGTTATT
CTTTTTTTATTACCCTGCTCTGTGGTGCATCTTTTTTAATATATTTCAAA
TCCAAATTCCGAAGACAAAATCCCACATTTGAATCCCCTTATAACGGAAA
CAATTATGAATCTGTAGAAGTTCAGAATATGGCATTTCGGCCGTTGCCTA
TACCTGAGAAGGAAGAAAAGAATTTGACTGAGCCGGTAAGAAGTGGACTT
CATGGGTAAATAACCATTCAGGAAGATTCAGTTTATGATTTCAGTTTATT
GAAAATTTTATGCAAATTCAAAGTTTTTTGACCAACTGGTATACAAAAAA
CAATTTTACCCAAACATAGCAATGTAAAGCAAAGTCGGTGACTATTTTTT
ATGTTGCAAAATATATCTTTACCGAACCCTGCGTGGACGGGCTTCATAAA
CTTACATTAGAAATTTCATTGAATACGGGCTCGTTTATATACGAACTCTA
TTTTCATAGTTAAATTGGAAAGTTATCATTGCAAATTTTAGCAATTACTT
TAATTTCTTTGAGATAAATCACTAAATCAAACACCCTTATGACCTAAAAC
AAAATGAGCTAAATCGCTTTCCACTAAAAAAGCCATGAGCTCCGGTCGAC
TACAGGTTTTCCAGTCAATCTCACAGTAAAGTCCGAGGGTATTTTAAGTT
TTTGTTAAAAGCCATAAGTCAAAATAAACTAAATTTCCTAGTGCTAAAAG
TGTCATGTGCGGCATTGGCCAACAGGGTTTTTTAAGTAGCACCATAGTCA
GGGGTATCAGGCTTTCTTTAAAAAAGTCACAGGTCAAAGTGAACTAAATC
ACCAACCGTTAAAAACCCTATTTAAAGCAGGGACTTAATGGGATATACTT
GTCCGCACCATGGTGAAAGGCTATTTTTATCCCTTATCAAAGTTAACCTA
ATTGCCTACCATAAAAAAGCCATTAATTGCAACCTCGATAAAAATCAGAG
ATTTCAAGTCTCGATAAACAACAGTAGAGTTCACATTATAGTCAGGAGGT
AATTTCAACTCTGTTTAAAACACACTTGTAAATATTTTAAAATTTGGTCT
TAAGGTAAATAGGGCGACATGAATGTTTTGATGAAATAGGATTTAGGATT
TCGATAAAAAACATTTTTAATCATTAAATTAAAGTAAATTACTTAAATTA
AGATAAAATAAGTAAAGTAGCTAAGAAATGATAAG
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protein sequence of SMED30032344-orf-1

>SMED30032344-orf-1 ID=SMED30032344-orf-1|Name=SMED30032344-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=199bp
MKDGSYFIFYITENNELSKCFIENRFSPVCTKKSLFNVTTDEIHVLMFTF
DNSQVLIKISNGKYIQTFKDEFQRKIKQIKIGYSENTKSCVRFQGEITFR
YDISQFKLICPSKIPSIPHKFYYFLSFGYSFFITLLCGASFLIYFKSKFR
RQNPTFESPYNGNNYESVEVQNMAFRPLPIPEKEEKNLTEPVRSGLHG*
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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: 123..145