SMED30011717

Overview
NameSMED30011717
Smed IDSMED30011717
Length (bp)635
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 SMED30011717 (SMED30011717) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011717 (SMED30011717) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30011717

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30011717h1SMcG0016624 SmedASXL_008823SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30011717h1SMcG0016624 SmedASXL_008822SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30011717h1SMcG0016624 SmedASXL_025119SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30011717h1SMcG0016624 dd_Smed_v4_16420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011717h1SMcG0016624 dd_Smed_v4_16420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30011717h1SMcG0016624 dd_Smed_v4_16420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30011717h1SMcG0016624 dd_Smed_v4_18559_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011717h1SMcG0016624 dd_Smed_v4_18559_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30011717h1SMcG0016624 dd_Smed_v4_18559_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
non-ciliated neuronSMED30011717h1SMcG0016624 dd_Smed_v4_18559_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30011717h1SMcG0016624 dd_Smed_v6_16420_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30011717h1SMcG0016624 dd_Smed_v6_18559_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30011717h1SMcG0016624 OX_Smed_1.0.12980ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Category 4 cellSMED30011717h1SMcG0016624 dd_Smed_v4_16420_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011717 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004337:8236..9374 +2986
Homology
[Close]
BLAST of SMED30011717 vs. Planmine SMEST
Match: SMESG000078112.1 (SMESG000078112.1)

HSP 1 Score: 243.047 bits (619), Expect = 3.432e-75
Identity = 116/116 (100.00%), Postives = 116/116 (100.00%), Query Frame = 1 
Query:   25 QSQITDEEKTILKQQMTPPPMGRRHSFAFSSIPDSPVDLITASVCEGPFQHPASNKLESRRSQPAHRDSVVGRLTRQNSVLNLNPSEKSPVTRQSSFTVLSDAVLNFFCPNAQPKQ 372
            QSQITDEEKTILKQQMTPPPMGRRHSFAFSSIPDSPVDLITASVCEGPFQHPASNKLESRRSQPAHRDSVVGRLTRQNSVLNLNPSEKSPVTRQSSFTVLSDAVLNFFCPNAQPKQ
Sbjct:  770 QSQITDEEKTILKQQMTPPPMGRRHSFAFSSIPDSPVDLITASVCEGPFQHPASNKLESRRSQPAHRDSVVGRLTRQNSVLNLNPSEKSPVTRQSSFTVLSDAVLNFFCPNAQPKQ 885
[Close]
BLAST of SMED30011717 vs. Planmine SMEST
Match: SMESG000078112.1 (SMESG000078112.1)

HSP 1 Score: 229.95 bits (585), Expect = 1.622e-70
Identity = 112/116 (96.55%), Postives = 112/116 (96.55%), Query Frame = 1 
Query:   25 QSQITDEEKTILKQQMTPPPMGRRHSFAFSSIPDSPVDLITASVCEGPFQHPASNKLESRRSQPAHRDSVVGRLTRQNSVLNLNPSEKSPVTRQSSFTVLSDAVLNFFCPNAQPKQ 372
            QSQITDEEKTILKQQMTPPPMGRRHSFAFSSIPDSPVDLITASVCEGPFQHPASNKLESRRSQPAHRDSVVGRLTRQNS    NPSEKSPVTRQSSFTVLSDAVLNFFCPNAQPKQ
Sbjct:  725 QSQITDEEKTILKQQMTPPPMGRRHSFAFSSIPDSPVDLITASVCEGPFQHPASNKLESRRSQPAHRDSVVGRLTRQNS----NPSEKSPVTRQSSFTVLSDAVLNFFCPNAQPKQ 836
[Close]
BLAST of SMED30011717 vs. Planmine SMEST
Match: SMESG000078112.1 (SMESG000078112.1)

HSP 1 Score: 229.95 bits (585), Expect = 2.926e-70
Identity = 112/116 (96.55%), Postives = 112/116 (96.55%), Query Frame = 1 
Query:   25 QSQITDEEKTILKQQMTPPPMGRRHSFAFSSIPDSPVDLITASVCEGPFQHPASNKLESRRSQPAHRDSVVGRLTRQNSVLNLNPSEKSPVTRQSSFTVLSDAVLNFFCPNAQPKQ 372
            QSQITDEEKTILKQQMTPPPMGRRHSFAFSSIPDSPVDLITASVCEGPFQHPASNKLESRRSQPAHRDSVVGRLTRQNS    NPSEKSPVTRQSSFTVLSDAVLNFFCPNAQPKQ
Sbjct:  770 QSQITDEEKTILKQQMTPPPMGRRHSFAFSSIPDSPVDLITASVCEGPFQHPASNKLESRRSQPAHRDSVVGRLTRQNS----NPSEKSPVTRQSSFTVLSDAVLNFFCPNAQPKQ 881
[Close]
BLAST of SMED30011717 vs. Planmine SMEST
Match: SMESG000015319.1 (SMESG000015319.1)

HSP 1 Score: 54.299 bits (129), Expect = 1.248e-8
Identity = 37/90 (41.11%), Postives = 51/90 (56.67%), Query Frame = 1 
Query:   88 GRRHSFAFSSIPDSPVDLITASVCEGPFQHPASNKLESRRSQPAHRDSVVGRLTRQNSVLNLNPSEK---SPVTRQSSFTVLSDAVLNFF 348
            GRRHSF  S+I  S  ++ITASVCEGPF   ++N+  S  S      + +  L    S+     SE+    P++R+SSF  LSD V+N F
Sbjct:  300 GRRHSFGSSTILQSSENMITASVCEGPF-FGSNNQQTSFYSGSRRPSNAMVPLLPNQSLSRRESSERLTVIPISRRSSFNALSDTVMNLF 388
[Close]
BLAST of SMED30011717 vs. Planmine SMEST
Match: SMESG000028722.1 (SMESG000028722.1)

HSP 1 Score: 49.2914 bits (116), Expect = 8.300e-7
Identity = 42/112 (37.50%), Postives = 56/112 (50.00%), Query Frame = 1 
Query:   70 MTPPPMGRRHSFAFS-SIPDSPVDLITASVCEGPFQHPASNKLESRR-SQPAHRDSVVGRLTRQNSVL----------------NLNPSEKS-PVTRQSSFTVLSDAVLNFF 348
            + P   GRRHS+  + S  +S  ++IT SVCEGPF  P S+K  SRR S  + + S+    T  N+ L                NL+      PV R+SSF  LSD V+N F
Sbjct:  717 LVPQSSGRRHSYGSTGSKSNSNSNMITESVCEGPFISPPSSKPTSRRPSAVSQQISI----TSNNNYLQQSNNNNKLQMNNSAQNLSDGLTVIPVVRRSSFNSLSDTVMNLF 824
The following BLAST results are available for this feature:
BLAST of SMED30011717 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30011717 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000078112.13.432e-75100.00SMESG000078112.1[more]
SMESG000078112.11.622e-7096.55SMESG000078112.1[more]
SMESG000078112.12.926e-7096.55SMESG000078112.1[more]
SMESG000015319.11.248e-841.11SMESG000015319.1[more]
SMESG000028722.18.300e-737.50SMESG000028722.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011717 ID=SMED30011717|Name=SMED30011717|organism=Schmidtea mediterranea sexual|type=transcript|length=635bp
CCTGTAATGGGCGTAAACCCTCGACAATCTCAAATAACAGATGAAGAAAA
AACAATATTAAAGCAACAAATGACTCCCCCACCAATGGGAAGAAGGCACA
GCTTTGCTTTTTCTTCGATTCCTGACTCTCCCGTAGACCTTATTACTGCT
AGTGTTTGTGAAGGACCATTTCAACATCCAGCATCTAACAAACTTGAAAG
TCGACGATCTCAACCAGCTCATCGAGATTCTGTTGTTGGGCGTCTAACGA
GACAAAATTCAGTACTTAACCTAAATCCATCGGAGAAATCGCCAGTTACA
AGACAATCAAGTTTCACTGTTCTCAGTGATGCCGTCTTAAATTTTTTTTG
TCCCAATGCACAACCAAAACAATGAACCGATATATTTTGATTTTTAATTT
TGACTGCAGATGCCAGTAAAACCGATAACAAAAAATGAAAGCTTATTTTT
TAATTGCATATTTTTGATTGAAAATTATCTTGTCAATATATTGTGTTAGC
GTAAATAAAATATATCATTTAATGAAAAGAAAAACAACAACAATATCAAT
GAAAATTTGCTATGTAAAAGTGGAATGGTTTTTTAAACGTTATTTTTAGG
TTGTTGAATGATGTTATTGCTTTTGAGATTAAAAT
back to top

protein sequence of SMED30011717-orf-1

>SMED30011717-orf-1 ID=SMED30011717-orf-1|Name=SMED30011717-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
PVMGVNPRQSQITDEEKTILKQQMTPPPMGRRHSFAFSSIPDSPVDLITA
SVCEGPFQHPASNKLESRRSQPAHRDSVVGRLTRQNSVLNLNPSEKSPVT
RQSSFTVLSDAVLNFFCPNAQPKQ*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000099neuron
PLANA:0000418head