SMED30003292

Overview
NameSMED30003292
Smed IDSMED30003292
Length (bp)897
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 SMED30003292 (SMED30003292) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003292 (SMED30003292) 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



SMED30003292

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30003292h1SMcG0004645 SmedASXL_011566SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30003292h1SMcG0004645 SmedASXL_013655SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
cilated neuronSMED30003292h1SMcG0004645 dd_Smed_v4_23595_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30003292h1SMcG0004645 dd_Smed_v4_19593_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30003292h1SMcG0004645 dd_Smed_v4_19593_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30003292h1SMcG0004645 dd_Smed_v4_19593_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30003292h1SMcG0004645 dd_Smed_v4_19593_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30003292h1SMcG0004645 dd_Smed_v4_19593_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
esophagusSMED30003292h1SMcG0004645 dd_19593dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
neuronSMED30003292h1SMcG0004645 dd_19593dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
pharynx tipSMED30003292h1SMcG0004645 dd_19593dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30003292 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.022972:983..9503 +1967
Homology
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BLAST of SMED30003292 vs. Planmine SMEST
Match: SMESG000066258.1 (SMESG000066258.1)

HSP 1 Score: 377.867 bits (969), Expect = 4.310e-128
Identity = 216/217 (99.54%), Postives = 217/217 (100.00%), Query Frame = 1 
Query:  208 VRIDKHEASYHHVIDGTKWRYNMSVPINIFQFKNSYEKFQTVIALDIFNFCLTSNSTKQCSEIVTYSINQNDVLLLPESPIILENGSLSIEMFVNYSIMNEIGKQEKFVPPFILSQIWNSPSPNLQSLVENIKRIYPEDLDFNFMTTDKSTESTLISSHFWSLTTKPPDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKRISIFDKLCLMSILLTG 858
            VRIDKHEASYHHVIDGTKWRYNMSVPINIFQFKNSYEKFQTVIALDIFNFCLTS+STKQCSEIVTYSINQNDVLLLPESPIILENGSLSIEMFVNYSIMNEIGKQEKFVPPFILSQIWNSPSPNLQSLVENIKRIYPEDLDFNFMTTDKSTESTLISSHFWSLTTKPPDSSGMNTTTSTSTGMDTITSTSTGMNTTSTSKRISIFDKLCLMSILLTG
Sbjct:  288 VRIDKHEASYHHVIDGTKWRYNMSVPINIFQFKNSYEKFQTVIALDIFNFCLTSSSTKQCSEIVTYSINQNDVLLLPESPIILENGSLSIEMFVNYSIMNEIGKQEKFVPPFILSQIWNSPSPNLQSLVENIKRIYPEDLDFNFMTTDKSTESTLISSHFWSLTTKPPDSSGMNTTTSTSTGMDTITSTSTGMNTTSTSKRISIFDKLCLMSILLTG 504
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BLAST of SMED30003292 vs. Planmine SMEST
Match: SMESG000031543.1 (SMESG000031543.1)

HSP 1 Score: 122.094 bits (305), Expect = 2.478e-32
Identity = 58/140 (41.43%), Postives = 89/140 (63.57%), Query Frame = 1 
Query:  205 KVRIDKHE--ASYHHVIDGTKWRYNMSVPINIFQFKNSYEKFQTVIALDIFNFCLTSNSTKQCSEIVTYSINQNDVLLLPESPIILENGSLSIEMFVNYSIMNEIGKQEKFVPPFILSQIWNSPSPNLQSLVENIKRIYP 618
            +  I+K +  ASY+HVIDG  WR+ M++P+N+ +FKNSY +FQ  I  DI N+C    S + C +I    +N N+VL +   P++LENGSL++ +F N S+  +   +E  V   +L  + N+PS  L+ L++N KRIYP
Sbjct:  152 QCEINKRQFSASYYHVIDGLPWRHGMNIPVNLLEFKNSYSEFQRFIHSDILNYCKHKQSNEDCQKIKNIPLNSNNVLPIQGFPLLLENGSLALRIFFNLSVSLQASYKESLVSSALLGYVLNNPSKELEKLIDNSKRIYP 291
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BLAST of SMED30003292 vs. Planmine SMEST
Match: SMESG000031543.1 (SMESG000031543.1)

HSP 1 Score: 122.094 bits (305), Expect = 1.742e-31
Identity = 58/140 (41.43%), Postives = 89/140 (63.57%), Query Frame = 1 
Query:  205 KVRIDKHE--ASYHHVIDGTKWRYNMSVPINIFQFKNSYEKFQTVIALDIFNFCLTSNSTKQCSEIVTYSINQNDVLLLPESPIILENGSLSIEMFVNYSIMNEIGKQEKFVPPFILSQIWNSPSPNLQSLVENIKRIYP 618
            +  I+K +  ASY+HVIDG  WR+ M++P+N+ +FKNSY +FQ  I  DI N+C    S + C +I    +N N+VL +   P++LENGSL++ +F N S+  +   +E  V   +L  + N+PS  L+ L++N KRIYP
Sbjct:  285 QCEINKRQFSASYYHVIDGLPWRHGMNIPVNLLEFKNSYSEFQRFIHSDILNYCKHKQSNEDCQKIKNIPLNSNNVLPIQGFPLLLENGSLALRIFFNLSVSLQASYKESLVSSALLGYVLNNPSKELEKLIDNSKRIYP 424
[Close]
BLAST of SMED30003292 vs. Planmine SMEST
Match: SMESG000066259.1 (SMESG000066259.1)

HSP 1 Score: 108.227 bits (269), Expect = 3.648e-26
Identity = 54/137 (39.42%), Postives = 95/137 (69.34%), Query Frame = 1 
Query:  205 KVRIDKHEASYHHVIDGTKWRYNMSVPINIFQFKNSYEKFQTVIALDIFNFCLTS-NSTKQCSEIVTYSINQNDVLLLPESPIILENGSLSIEMFVNYSIMNEIGKQEKFVPPFILSQIWNSPSPNLQSLVENIKRI 612
            ++R D+ ++S+++V+DGT WRYNM +P+N  +FK S+ KFQ  IA  I  FC+ + NS  +C +I    I  ++VLL+P  P +LENGSL+I +F+ ++ + +  KQE+FV   +L +I  + S ++++L+EN++++
Sbjct:  288 EIRKDQFDSSFYYVVDGTDWRYNMMIPVNAIEFKKSFYKFQNAIARLINEFCVKNLNSYPECKKIEENQIIYDNVLLIPGFPHLLENGSLAIRIFIIFNDVTDNVKQERFVSTSLLREILTN-SDDIKNLIENVRKV 423
The following BLAST results are available for this feature:
BLAST of SMED30003292 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 SMED30003292 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 SMED30003292 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 SMED30003292 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 SMED30003292 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 SMED30003292 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 SMED30003292 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 SMED30003292 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 SMED30003292 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 SMED30003292 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 SMED30003292 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 SMED30003292 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 SMED30003292 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 SMED30003292 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000066258.14.310e-12899.54SMESG000066258.1[more]
SMESG000031543.12.478e-3241.43SMESG000031543.1[more]
SMESG000031543.11.742e-3141.43SMESG000031543.1[more]
SMESG000066259.13.648e-2639.42SMESG000066259.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003292 ID=SMED30003292|Name=SMED30003292|organism=Schmidtea mediterranea sexual|type=transcript|length=897bp
TAAAATAATAGACTTTTTAGACCAACCTCAAAGTAACCAAGTAAGATTCG
TAGTTTATGAGAATACCCAACGCTGTAATTCACTTTAACTCTGTCAGTGA
CCCAGATCTTATGAACCATCGATATAATGTATGATTTCCTTGATTTTTGA
ATGAATTTTGATATATGATTAATATTTATATATATATATTTTTTCCTTAA
TATAAAAGTCAGAATCGACAAACATGAAGCGTCTTACCATCACGTTATTG
ATGGAACCAAGTGGAGATACAATATGTCAGTGCCAATAAATATTTTTCAA
TTTAAGAATTCTTATGAAAAATTCCAAACAGTTATTGCACTCGACATTTT
CAATTTTTGCTTAACATCGAATTCAACTAAACAATGTTCTGAAATTGTCA
CATATTCTATCAATCAAAATGATGTGCTACTTCTACCAGAATCACCAATA
ATACTTGAAAATGGATCTCTTTCTATTGAGATGTTTGTCAATTATAGTAT
CATGAATGAAATTGGAAAACAAGAAAAATTTGTACCTCCTTTCATTTTGA
GTCAAATATGGAATTCGCCATCACCAAATTTGCAGTCACTAGTTGAGAAT
ATAAAAAGAATATATCCAGAAGATTTAGACTTTAATTTTATGACTACTGA
TAAGTCTACAGAATCTACTTTAATCAGTTCACATTTTTGGAGTTTGACAA
CCAAACCTCCAGATTCTAGTGGAATGAATACAACAACATCTACTTCCACC
GGAATGGATACAATAACATCTACTTCCACTGGAATGAATACAACATCTAC
TTCGAAAAGAATTTCTATATTTGATAAATTATGCTTAATGTCGATTTTAT
TGACAGGTTTGTGTTCGTGAAATACAGTGAAAATACCTAACAGAAGA
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protein sequence of SMED30003292-orf-1

>SMED30003292-orf-1 ID=SMED30003292-orf-1|Name=SMED30003292-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=199bp
MSVPINIFQFKNSYEKFQTVIALDIFNFCLTSNSTKQCSEIVTYSINQND
VLLLPESPIILENGSLSIEMFVNYSIMNEIGKQEKFVPPFILSQIWNSPS
PNLQSLVENIKRIYPEDLDFNFMTTDKSTESTLISSHFWSLTTKPPDSSG
MNTTTSTSTGMDTITSTSTGMNTTSTSKRISIFDKLCLMSILLTGLCS*
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protein sequence of SMED30003292-orf-2

>SMED30003292-orf-2 ID=SMED30003292-orf-2|Name=SMED30003292-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=115bp
LLLGIFTVFHEHKPVNKIDIKHNLSNIEILFEVDVVFIPVEVDVIVSIPV
EVDVVVFIPLESGGLVVKLQKCELIKVDSVDLSVVIKLKSKSSGYILFIF
STSDCKFGDGEFHI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000062esophagus
PLANA:0000099neuron
PLANA:0000420parapharyngeal region
PLANA:0002074pharynx tip