SMED30000340

Overview
NameSMED30000340
Smed IDSMED30000340
Length (bp)1694
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ 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



 

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 SMED30000340 (SMED30000340) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30000340 (SMED30000340) in cells (dots) of each of the 12 neoblast clusters.

 

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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 SMED30000340 (SMED30000340) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30000340 (SMED30000340) 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.
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



SMED30000340

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
Smed sexual biotypeSMED30000340SMESG000040152.1 Contig40721newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000340SMESG000040152.1 Contig40721uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30000340 dd_Smed_v4_48515_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30000340 dd_Smed_v4_48515_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30000340 dd_Smed_v4_48515_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
SMED30000340 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004013:50408..54613 +7765
v31.001262:106384..108609 +5998
v31.005732:37809..39777 +5454
Homology
[Close]
BLAST of SMED30000340 vs. TrEMBL
Match: A0A087T0R5 (Uncharacterized protein (Fragment) OS=Stegodyphus mimosarum OX=407821 GN=X975_17494 PE=4 SV=1)

HSP 1 Score: 101.293 bits (251), Expect = 9.021e-37
Identity = 46/72 (63.89%), Postives = 58/72 (80.56%), Query Frame = -2 
Query:  839 NCTIPLKYRAMILRDSG-EDPDRILAIGDLELLKELQKDTIFGDGTFDKVPKMFYQLYIWHSKIGSSYPSCI 1051
            N  IP KY  ++L DSG +D +RIL +GD ELL EL+KD+I+GDGTFDKVP MFYQLY WH+K+G+SYP C+
Sbjct:  273 NFEIPEKYINLVLYDSGADDINRILVLGDKELLAELKKDSIYGDGTFDKVPSMFYQLYTWHAKVGNSYPPCV 344

HSP 2 Score: 74.3294 bits (181), Expect = 9.021e-37
Identity = 33/82 (40.24%), Postives = 51/82 (62.20%), Query Frame = -1 
Query: 1200 RGGKIMAYQGFEYKLRKSLNEIAQWRCRDQQQLRCKSWMKVTVDERPQIITEPTEHSHDSIPQKIKANIAMQEMKETIISLG 1445
            +G +++ Y GFEY   +++N +  WRCR  +  RC S++K    +   I+ EPTEH HDS PQK+ AN A  +M+E + S+ 
Sbjct:  147 KGKEVLIYSGFEYLKFRTVNGVVTWRCRRHRSTRCHSFLKT---KDGSIMKEPTEHCHDSCPQKVIANAARSQMREDMKSVA 225

HSP 3 Score: 29.6462 bits (65), Expect = 9.021e-37
Identity = 17/39 (43.59%), Postives = 23/39 (58.97%), Query Frame = -3 
Query: 1084 ANPKNVMGTVLNKLQLSREVQVRMPKNASITRTFNRIRK 1200
            A P+NV+G VL+ L  S +V    PK +S+TR     RK
Sbjct:  226 ATPRNVIGNVLSGL--SNDVLACFPKQSSLTRNLLHHRK 262

HSP 4 Score: 71.2478 bits (173), Expect = 3.595e-9
Identity = 37/97 (38.14%), Postives = 54/97 (55.67%), Query Frame = -3 
Query:  598 EDSLNQLMGYFESTYIRGPAGRDPLFPIRIWNRL*S-----------CQDLHN-------CSLPEVWDLLEGLRKDIAIHCKTLAEAENGRPYSKKK 834
            E+S N+++ YF +TYI G AGR+P FP+R+WN   +           C+  HN       CS P +W L +GL++D+A     L+ A+ GR   KKK
Sbjct:  458 EESYNEVLTYFFTTYIEGAAGREPQFPMRLWNHYEAALERSPKTTNCCEGFHNSLNSLFHCSHPSIWFLFDGLQRDLACQRLLLSNAQAGRLEIKKK 554
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BLAST of SMED30000340 vs. TrEMBL
Match: D7EIQ5 (MULE domain-containing protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005116 PE=4 SV=1)

HSP 1 Score: 97.8265 bits (242), Expect = 4.192e-19
Identity = 47/69 (68.12%), Postives = 54/69 (78.26%), Query Frame = -2 
Query:  839 IPLKYRAMILRDSG-EDPDRILAIGDLELLKELQKDTIFGDGTFDKVPKMFYQLYIWHSKIGSSYPSCI 1042
            IP KY+ +IL DSG  + DRIL +GD EL+ EL KD IFGDGTFDKVP MFYQLY WH++IGSSY  CI
Sbjct:   56 IPEKYQHLILYDSGLYEEDRILVLGDKELMLELNKDIIFGDGTFDKVPNMFYQLYTWHAQIGSSYRPCI 124
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BLAST of SMED30000340 vs. TrEMBL
Match: A0A0B7BPZ7 (MULE domain-containing protein (Fragment) OS=Arion vulgaris OX=1028688 GN=ORF204522 PE=4 SV=1)

HSP 1 Score: 93.9745 bits (232), Expect = 1.349e-18
Identity = 44/71 (61.97%), Postives = 55/71 (77.46%), Query Frame = -2 
Query:  839 TIPLKYRAMILRDSG-EDPDRILAIGDLELLKELQKDT-IFGDGTFDKVPKMFYQLYIWHSKIGSSYPSCI 1045
            +IP  Y  +IL DS  +DPDRI A GD +L++ L  +T I+GDGTFDKVP+MFYQLY WH+KIG+SYP CI
Sbjct:   19 SIPETYAHLILHDSDIDDPDRIFACGDFDLMQVLNSNTTIYGDGTFDKVPRMFYQLYTWHAKIGNSYPPCI 89
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BLAST of SMED30000340 vs. TrEMBL
Match: A0A0B7BPQ3 (Uncharacterized protein (Fragment) OS=Arion vulgaris OX=1028688 GN=ORF204515 PE=4 SV=1)

HSP 1 Score: 85.5001 bits (210), Expect = 2.169e-16
Identity = 46/110 (41.82%), Postives = 63/110 (57.27%), Query Frame = -3 
Query:  502 GRDPLFPIRIWNRL*S-----------CQDLHN-------CSLPEVWDLLEGLRKDIAIHCKTLAEAENGRP-YSKKKYRELNDKVIAAVQKYYNEEDKMKYLRKLANLQ 774
            GRDP FP+R+WN   +           C+  HN       CS P +W LL+GL +D+A H  TL +A  G+P   KKKY  L+ +V   VQ Y  E+DK+ +LR++ANLQ
Sbjct:    1 GRDPQFPLRVWNHHEASAERSPKTTNCCEGFHNSLNSIFHCSHPSIWLLLDGLERDLACHKLTLEKARVGQPEVKKKKYEALHQQVAHVVQGYAEEQDKLSFLRRMANLQ 110
[Close]
BLAST of SMED30000340 vs. TrEMBL
Match: A0A0N7ZDD8 (Uncharacterized protein OS=Scylla olivacea OX=85551 PE=4 SV=1)

HSP 1 Score: 70.0922 bits (170), Expect = 2.395e-13
Identity = 34/74 (45.95%), Postives = 50/74 (67.57%), Query Frame = -2 
Query:  839 NCTIPLKYRAMILRDSG-EDPDRILAIGDLELLKELQKDTIF--GDGTFDKVPKMFYQLYIWHSKIGSSYPSCI 1051
            N  IP +Y+ +IL DSG +D DRI+ +GD+ ++  L  ++     DGTF+  P +FYQLY  H+K+GS+YP CI
Sbjct:  142 NFDIPPEYQEIILHDSGVDDVDRIICMGDINIVTNLSGNSKLWMCDGTFETTPILFYQLYTIHAKVGSNYPPCI 215

HSP 2 Score: 35.8094 bits (81), Expect = 2.395e-13
Identity = 28/113 (24.78%), Postives = 44/113 (38.94%), Query Frame = -1 
Query: 1119 RGGKIMAYQGFEYKLRKS----LNEIAQWRCRDQQQLRCKSWMKVTVDERPQIITEPTEHSHDSIPQKIKANIAMQEMKETIISLGQIQKMSWEQY*INCNCHGKCKSACQKM 1445
            RG  ++ Y G EY  R         I+ WRCR  ++ +C   M+   D    +  EP  H+H   P        +Q++  T+ S  +    S      NC  +    + C  M
Sbjct:   10 RGKSLLLYGGHEYVERSREPWMTQGISYWRCRHYRKHKCSGSMQTEGD---SVTKEPGVHTHSGDP----VTAQVQQVVSTLHSFAEDSSDSVR----NCVANSVTSATCDVM 111
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BLAST of SMED30000340 vs. Planmine SMEST
Match: SMESG000073500.1 (SMESG000073500.1)

HSP 1 Score: 108.227 bits (269), Expect = 3.965e-24
Identity = 49/70 (70.00%), Postives = 57/70 (81.43%), Query Frame = -2 
Query:  839 TIPLKYRAMILRDSG-EDPDRILAIGDLELLKELQKDTIFGDGTFDKVPKMFYQLYIWHSKIGSSYPSCI 1045
            TIP KY AMIL D+G +DPDRIL IG+ ELL EL K+TI+GDGTFDK P MFYQLY WH ++G+SYP CI
Sbjct: 1484 TIPEKYSAMILHDTGFDDPDRILVIGNKELLLELNKETIYGDGTFDKCPSMFYQLYTWHVQVGTSYPPCI 1553

HSP 2 Score: 87.4261 bits (215), Expect = 1.371e-17
Identity = 53/150 (35.33%), Postives = 78/150 (52.00%), Query Frame = -3 
Query:  514 CSTSSIFGIQRLAALILHASS---EDSLNQLMGYFESTYIRGPAGRDPLFPIRIWNRL*S-----------CQDLHN-------CSLPEVWDLLEGLRKDIAIHCKTLAEAENGRPYSKK-KYRELNDKVIAAVQKYYNEEDKMKYLRKL 897
            C+ + +   + ++A  + A +   ED  N ++ YF  TYI G  GRD +FP+RIWN+  +           C+  HN       CS P +W L +GL++DIA H  TLA  +  RP  KK KY  L+  V  AVQ+Y +  D    L+K+
Sbjct: 1643 CALAFVPANEVMSAFDILARTFPDEDPYNAVLSYFFQTYIEGAIGRDSMFPVRIWNQWEAAAENSPKTTNCCEGFHNALNATFHCSHPSIWLLYDGLQRDIACHRLTLANYQTERPEKKKRKYESLHQGVATAVQEYDSHADDESKLKKI 1792
[Close]
BLAST of SMED30000340 vs. Planmine SMEST
Match: SMESG000059983.1 (SMESG000059983.1)

HSP 1 Score: 50.0618 bits (118), Expect = 1.548e-7
Identity = 18/33 (54.55%), Postives = 24/33 (72.73%), Query Frame = -3 
Query:  736 EDSLNQLMGYFESTYIRGPAGRDPLFPIRIWNR 834
            ED  N ++ +F  TYI G  GRDP+FP+RIWN+
Sbjct:   30 EDPYNAVLSFFFQTYIEGAIGRDPMFPVRIWNQ 62
[Close]
BLAST of SMED30000340 vs. Planmine SMEST
Match: SMESG000025087.1 (SMESG000025087.1)

HSP 1 Score: 50.8322 bits (120), Expect = 1.671e-7
Identity = 25/83 (30.12%), Postives = 45/83 (54.22%), Query Frame = -1 
Query: 1200 RGGKIMAYQGFEY-KLRKSLNEIAQWRCRDQQQLRCKSWMKVTVDERPQIITEPTEHSHDSIPQKIKANIAMQEMKETIISLG 1445
            +G  ++   GF+Y K R++   +  WRCR+ Q+  CK+ +K+  +    I ++   H H S  QK+  NI   +MK  + ++G
Sbjct:    8 KGKNVLTLNGFDYIKHRENKAGVTTWRCREHQKNHCKALLKIFAN---TIRSDIPTHFHGSCSQKVSVNITKAKMKNDMRNVG 87
The following BLAST results are available for this feature:
BLAST of SMED30000340 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 SMED30000340 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 SMED30000340 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 SMED30000340 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 SMED30000340 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 SMED30000340 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 SMED30000340 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 SMED30000340 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A087T0R59.021e-3763.89Uncharacterized protein (Fragment) OS=Stegodyphus ... [more]
D7EIQ54.192e-1968.12MULE domain-containing protein OS=Tribolium castan... [more]
A0A0B7BPZ71.349e-1861.97MULE domain-containing protein (Fragment) OS=Arion... [more]
A0A0B7BPQ32.169e-1641.82Uncharacterized protein (Fragment) OS=Arion vulgar... [more]
A0A0N7ZDD82.395e-1345.95Uncharacterized protein OS=Scylla olivacea OX=8555... [more]
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BLAST of SMED30000340 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 SMED30000340 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 SMED30000340 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 SMED30000340 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 SMED30000340 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 SMED30000340 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000073500.13.965e-2470.00SMESG000073500.1[more]
SMESG000059983.11.548e-754.55SMESG000059983.1[more]
SMESG000025087.11.671e-730.12SMESG000025087.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000340 ID=SMED30000340|Name=SMED30000340|organism=Schmidtea mediterranea sexual|type=transcript|length=1694bp
CCTTCTTTAATTGTATTTTACCTTTAATTGTATTTGACTTTTTTTATTTG
TATTTGATCTTCTATGTTTGTATTTGACCTTCTTTATTTGTATTTGACCT
ACTCTTTTTGTATTTGACTTTATCTTTATATGGCCTTATTTATTTATGTT
TCTAATCTTGTAAATTTACAAACATTTACAAAAAAAATTGAAATTTTAAC
ACAACTTTGATGTTATAATTAGCATTTGAATATATTAATAAGATCAAAAA
CTGATCATATGAATCGGTGACTAGACACCTCATCATACGATACATTTCAT
CATTTCATAAAGTACATTTATCTATTATCCTACAACAGAATTCATTGCAG
TAAAACACAAAGACATTACACACAAAACAAATTTAATGCCAAAACATTTT
TTGAAAATATTTCCAACTTTCTGACTCACCAGGTGCATGGACTCCTATAA
AAAAGGTTATTAATGACTGACTAGATTAAGTTTTGAGTTTATGGTATGCT
ACTGCAAATTAGCTAATTTTCTCAAGTACTTCATTTTATCTTCTTCATTG
TAATACTTCTGTACAGCAGCAATTACCTTATCATTTAATTCCCTATACTT
CTTTTTTGAATATGGGCGACCATTTTCAGCCTCTGCCAGTGTTTTGCAGT
GGATGGCAATGTCTTTCCTTAATCCCTCAAGGAGATCCCACACTTCTGGA
AGGCTGCAGTTATGAAGGTCCTGGCAGCTTCATAGTCGATTCCAGATCCT
AATTGGGAAGAGGGGATCTCTTCCAGCTGGGCCTCTTATATAGGTTGACT
CAAAATATCCCATCAATTGATTCAAGCTATCTTCACTAGATGCATGAAGG
ATAAGAGCTGCCAATCTTTGAATGCCAAATATAGAGCTGGTAGAACATTT
TTGGAACTTTGTCAAAGGTTCCATCTCCAAAGATTGTGTCCTTTTGAAGT
TCCTTCAAGAGCTCCAAATCCCCAATTGCCAAAATTCTGTCAGGATCTTC
TCCTGAATCACGAAGAATCATGGCTCTGTATTTTAGAGGAATTGTGCAAT
TTCTGGATCTACTGTATCATTTCCTTCTGCGTTCTTCCTGATTCTGTTGA
AAGTTCTTGTAATGGAAGCATTTTTTGGCATGCGGACTTGCACTTCCCGT
GACAATTGCAGTTTATTCAGTACTGTTCCCATGACATTTTTTGGATTTGC
CCAAGAGAAATGATTGTTTCCTTCATTTCCTGCATTGCAATATTGGCTTT
GATTTTTTGAGGGATGGAATCATGTGAGTGCTCTGTTGGTTCAGTAATAA
TTTGAGGTCTCTCATCAACAGTGACTTTCATCCAGGACTTGCATCTCAAT
TGCTGTTGGTCCCTGCAACGCCATTGAGCAATCTCATTAAGAGACTTGCG
CAGTTTGTATTCAAAACCTTGATAGGCCATGATCTTTCCACCTCTTGTGC
TTAAATAATAAGTAATAAGCGAGTATTAAATATATTTAACTTTTACTTTT
AAATTAAAAAATAATTTTCTATATTAATTACTATAACTTCTTATTATATA
AATTTAGCTTTAATATCACTTTACCTGAAAGATCTCTACAAGAGATGTTG
TCAGTTCGACAGTCAGCATAAAATGCGGGCACTGCTCCTGTGTACTGAGG
GTATATCAAAGCATAATCTGATAAGAAATTTCTTTGCAAGGCCA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR007588Znf_FLYWCH