SMED30018026

Overview
NameSMED30018026
Smed IDSMED30018026
Length (bp)382
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30018026

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
muscle cellSMED30018026 dd_Smed_v4_20524_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
Homology
[Close]
BLAST of SMED30018026 vs. Ensembl Xenopus
Match: npffr2 (neuropeptide FF receptor 2 [Source:Xenbase;Acc:XB-GENE-994428])

HSP 1 Score: 57.7658 bits (138), Expect = 2.369e-10
Identity = 25/47 (53.19%), Postives = 35/47 (74.47%), Query Frame = -3 
Query:  159 TIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 299
            TI  YN  K GVD+ DQMAR Y+V+  +RR P+ +++N+LDL A+NA
Sbjct:  257 TITDYNHMKCGVDVLDQMARMYSVRAATRRWPVAVYYNMLDLAAVNA 303
[Close]
BLAST of SMED30018026 vs. TrEMBL
Match: H9IWL2 (HTH La-type RNA-binding domain-containing protein OS=Bombyx mori OX=7091 PE=4 SV=1)

HSP 1 Score: 83.9593 bits (206), Expect = 2.829e-16
Identity = 37/48 (77.08%), Postives = 42/48 (87.50%), Query Frame = -3 
Query:  159 ETIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 302
            ET++FYNKTKFGVD+TDQMARKY VK G RR PLQ+FFNILDL  IN+
Sbjct:  777 ETVLFYNKTKFGVDVTDQMARKYTVKSGCRRWPLQVFFNILDLAGINS 824
[Close]
BLAST of SMED30018026 vs. TrEMBL
Match: E2C2W5 (PiggyBac transposable element-derived protein 4 (Fragment) OS=Harpegnathos saltator OX=610380 GN=EAI_00100 PE=4 SV=1)

HSP 1 Score: 78.1814 bits (191), Expect = 1.474e-15
Identity = 34/48 (70.83%), Postives = 41/48 (85.42%), Query Frame = -3 
Query:  159 ETIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 302
            ET+ +YN TK+GVD+ DQMARKY+VK  SRR PLQ+F+NILDL AINA
Sbjct:  115 ETVTYYNSTKYGVDVLDQMARKYSVKASSRRWPLQVFYNILDLAAINA 162
[Close]
BLAST of SMED30018026 vs. TrEMBL
Match: A0A1A9V4W5 (DDE_Tnp_1_7 domain-containing protein OS=Glossina austeni OX=7395 PE=4 SV=1)

HSP 1 Score: 76.2554 bits (186), Expect = 1.953e-15
Identity = 35/48 (72.92%), Postives = 39/48 (81.25%), Query Frame = -3 
Query:  159 ETIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 302
            ETI FYN TKFG D+TDQMARKY+VK   +R PLQ+FFNILDL  INA
Sbjct:   29 ETIRFYNSTKFGADVTDQMARKYSVKSKCQRCPLQVFFNILDLAGINA 76
[Close]
BLAST of SMED30018026 vs. TrEMBL
Match: A0A0N0BG82 (DDE_Tnp_1_7 domain-containing protein OS=Melipona quadrifasciata OX=166423 GN=WN51_00315 PE=4 SV=1)

HSP 1 Score: 77.411 bits (189), Expect = 3.975e-15
Identity = 34/48 (70.83%), Postives = 41/48 (85.42%), Query Frame = -3 
Query:  159 ETIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 302
            ET+ +YN TK+GVD+ DQMARKY+VK  SRR PLQ+F+NILDL AINA
Sbjct:   48 ETVTYYNSTKYGVDVLDQMARKYSVKASSRRWPLQVFYNILDLTAINA 95
[Close]
BLAST of SMED30018026 vs. TrEMBL
Match: A0A0L7RH31 (DDE_Tnp_1_7 domain-containing protein OS=Habropoda laboriosa OX=597456 GN=WH47_08647 PE=4 SV=1)

HSP 1 Score: 76.2554 bits (186), Expect = 4.839e-15
Identity = 34/48 (70.83%), Postives = 39/48 (81.25%), Query Frame = -3 
Query:  159 ETIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 302
            ETI FYN TKFGVD+TDQMARKY+VK   RR P+ +F+NILDL  INA
Sbjct:   48 ETIKFYNSTKFGVDITDQMARKYSVKCKCRRWPMHVFYNILDLAGINA 95
[Close]
BLAST of SMED30018026 vs. Ensembl Cavefish
Match: ENSAMXT00000039501.1 (pep primary_assembly:Astyanax_mexicanus-2.0:19:21564630:21575712:1 gene:ENSAMXG00000031759.1 transcript:ENSAMXT00000039501.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 57.7658 bits (138), Expect = 1.607e-10
Identity = 27/47 (57.45%), Postives = 34/47 (72.34%), Query Frame = -3 
Query:  159 TIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 299
            +I  Y  TKF VD+ D+MA  Y VK G+RR P+ +F+NILDL AINA
Sbjct:  862 SISHYYNTKFTVDVLDRMAHLYTVKNGTRRWPVAVFYNILDLAAINA 908
[Close]
BLAST of SMED30018026 vs. Ensembl Medaka
Match: ENSORLT00000029842.1 (piggyBac transposable element-derived protein 4 [Source:NCBI gene;Acc:101157644])

HSP 1 Score: 46.2098 bits (108), Expect = 2.095e-6
Identity = 21/48 (43.75%), Postives = 32/48 (66.67%), Query Frame = -3 
Query:  159 ETIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 302
            E I+ YNKTK GVD  D++   Y+ +  ++R PL +F N++D+ A NA
Sbjct:  670 EMILDYNKTKGGVDNLDKLLATYSCRRMTKRWPLAMFHNMIDMSAYNA 717
[Close]
BLAST of SMED30018026 vs. Ensembl Medaka
Match: ENSORLT00000027888.1 (pep primary_assembly:ASM223467v1:17:9217998:9219211:-1 gene:ENSORLG00000025878.1 transcript:ENSORLT00000027888.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 44.669 bits (104), Expect = 6.007e-6
Identity = 21/48 (43.75%), Postives = 31/48 (64.58%), Query Frame = -3 
Query:  159 ETIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 302
            + I+ YN TK GVD  D++   Y+ +  + R P+ IFFNI+D+ A NA
Sbjct:  221 QMILDYNSTKGGVDNLDKVTATYSCQRKTARWPMAIFFNIVDVSAYNA 268
[Close]
BLAST of SMED30018026 vs. Ensembl Medaka
Match: ENSORLT00000037833.1 (piggyBac transposable element-derived protein 4-like [Source:NCBI gene;Acc:101160710])

HSP 1 Score: 44.669 bits (104), Expect = 6.353e-6
Identity = 21/48 (43.75%), Postives = 31/48 (64.58%), Query Frame = -3 
Query:  159 ETIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 302
            + I+ YN TK GVD  D++   Y+ +  + R P+ IFFNI+D+ A NA
Sbjct:  418 QMILDYNSTKGGVDNLDKVTATYSCQRKTARWPMAIFFNIVDVSAYNA 465
[Close]
BLAST of SMED30018026 vs. Planmine SMEST
Match: SMESG000035129.1 (SMESG000035129.1)

HSP 1 Score: 80.1073 bits (196), Expect = 1.010e-18
Identity = 37/48 (77.08%), Postives = 41/48 (85.42%), Query Frame = -3 
Query:  159 ETIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 302
            ET+ FYN TKFGVD+TDQMA KY VK GSRR PLQ+FFNILDL AIN+
Sbjct:  203 ETVSFYNNTKFGVDVTDQMALKYTVKSGSRRWPLQVFFNILDLAAINS 250
[Close]
BLAST of SMED30018026 vs. Planmine SMEST
Match: SMESG000031831.1 (SMESG000031831.1)

HSP 1 Score: 73.9442 bits (180), Expect = 2.706e-16
Identity = 35/48 (72.92%), Postives = 41/48 (85.42%), Query Frame = -3 
Query:  159 ETIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 302
            ET+ FYNKTK GV + DQMARKY+VK GSRR PL++F+NILDL AINA
Sbjct:  166 ETVAFYNKTKCGVYVLDQMARKYSVKTGSRRWPLKVFYNILDLEAINA 213
[Close]
BLAST of SMED30018026 vs. Planmine SMEST
Match: SMESG000018066.1 (SMESG000018066.1)

HSP 1 Score: 50.8322 bits (120), Expect = 2.807e-8
Identity = 23/32 (71.88%), Postives = 25/32 (78.12%), Query Frame = -3 
Query:  153 MARKYNVKWGSRR*PLQIFFNILDLGAINA*I 248
            M RKYN K  SRR PLQ+F+NILDL AINA I
Sbjct:    1 MTRKYNAKASSRRWPLQVFYNILDLAAINAWI 32
[Close]
BLAST of SMED30018026 vs. Planmine SMEST
Match: SMESG000032747.1 (SMESG000032747.1)

HSP 1 Score: 45.4394 bits (106), Expect = 2.503e-6
Identity = 21/48 (43.75%), Postives = 28/48 (58.33%), Query Frame = -3 
Query:  159 ETIIFYNKTKFGVDMTDQMARKYNVKWGSRR*PLQIFFNILDLGAINA 302
            + ++FYN TK GVD  D+    Y  K+  RR  +  F NILD+ A NA
Sbjct:   79 DVLLFYNATKGGVDAMDERVATYTTKFKCRRWHVAFFCNILDISAFNA 126
The following BLAST results are available for this feature:
BLAST of SMED30018026 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 SMED30018026 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 SMED30018026 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 SMED30018026 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 SMED30018026 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
npffr22.369e-1053.19neuropeptide FF receptor 2 [Source:Xenbase;Acc:XB-... [more]
back to top
BLAST of SMED30018026 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 SMED30018026 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 SMED30018026 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
H9IWL22.829e-1677.08HTH La-type RNA-binding domain-containing protein ... [more]
E2C2W51.474e-1570.83PiggyBac transposable element-derived protein 4 (F... [more]
A0A1A9V4W51.953e-1572.92DDE_Tnp_1_7 domain-containing protein OS=Glossina ... [more]
A0A0N0BG823.975e-1570.83DDE_Tnp_1_7 domain-containing protein OS=Melipona ... [more]
A0A0L7RH314.839e-1570.83DDE_Tnp_1_7 domain-containing protein OS=Habropoda... [more]
back to top
BLAST of SMED30018026 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSAMXT00000039501.11.607e-1057.45pep primary_assembly:Astyanax_mexicanus-2.0:19:215... [more]
back to top
BLAST of SMED30018026 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 SMED30018026 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 SMED30018026 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 SMED30018026 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 3
Match NameE-valueIdentityDescription
ENSORLT00000029842.12.095e-643.75piggyBac transposable element-derived protein 4 [S... [more]
ENSORLT00000027888.16.007e-643.75pep primary_assembly:ASM223467v1:17:9217998:921921... [more]
ENSORLT00000037833.16.353e-643.75piggyBac transposable element-derived protein 4-li... [more]
back to top
BLAST of SMED30018026 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000035129.11.010e-1877.08SMESG000035129.1[more]
SMESG000031831.12.706e-1672.92SMESG000031831.1[more]
SMESG000018066.12.807e-871.88SMESG000018066.1[more]
SMESG000032747.12.503e-643.75SMESG000032747.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018026 ID=SMED30018026|Name=SMED30018026|organism=Schmidtea mediterranea sexual|type=transcript|length=382bp
GCAAGATTTTCTTTTGTTATAACTTCCCGGACTTTTCGAGAGGACATGCA
AGTTTTCTAGTTCAGATGGATCTTTACATTCATTGGAAAGTTCTTCTGTT
TATTGAAACTAAAAACCTTCTCGATATATTTTCTACAGTTGTTTTCTTAT
CAAATTTATGCATTTATTGCTCCCAAGTCGAGAATATTGAAAAATATTTG
AAGAGGTCATCTTCGAGATCCCCACTTCACATTATATTTTCTGGCCATTT
GATCGGTCATGTCTACCCCGAATTTGGTTTTATTATAAAATATGATAGTT
TCAGGCAATTTTTTAGTCTTTTTCAATGTTGGCTGAATTATATTTCGAAC
TCAGAAATGTACTTTTTTAGCTGACTTACTTT
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell