SMED30032748

Overview
NameSMED30032748
Smed IDSMED30032748
Length (bp)812
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 SMED30032748 (SMED30032748) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30032748 (SMED30032748) 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 SMED30032748 (SMED30032748) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30032748 (SMED30032748) 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



SMED30032748

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
head regionSMED30032748 SmedASXL_018585SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30032748h1SMcG0008213 Contig14202uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30032748h1SMcG0008213 Contig14202newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30032748h1SMcG0008212 Contig14202uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30032748h1SMcG0008212 Contig14202newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30032748 vs. Ensembl Xenopus
Match: kcnip1 (Kv channel interacting protein 1 [Source:Xenbase;Acc:XB-GENE-973728])

HSP 1 Score: 49.2914 bits (116), Expect = 3.880e-6
Identity = 31/101 (30.69%), Postives = 51/101 (50.50%), Query Frame = -2 
Query:  326 IINAMENGEDYFHFGKLLGIARNSIKIIIYKYRKFGKLSQGKIGGSISKISEENGNKLLDFVEKNVYASLEEMKNFLTSENNCKIEWNWISFNPRQCFNSW 628
            I+   ++GE Y    K L I  N+++ +I K+RK+G        G  SKI E+   KL+    K + A+L+E++ +L S   C +    IS    QC+  +
Sbjct:   14 IVKRYQSGEGYKRISKALDIPWNTVETVIIKWRKYGTTVILPRTGHPSKIDEKTRRKLVGEATKRITATLKELQEYLAS-TGCVVHVTTIS----QCYTDF 109
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BLAST of SMED30032748 vs. Planmine SMEST
Match: SMESG000062787.1 (SMESG000062787.1)

HSP 1 Score: 189.119 bits (479), Expect = 1.988e-55
Identity = 95/98 (96.94%), Postives = 96/98 (97.96%), Query Frame = -2 
Query:  386 VIKNYSSYRISEIDKIRIINAMENGEDYFHFGKLLGIARNSIKIIIYKYRKFGKLSQGKIGGSISKISEENGNKLLDFVEKNVYASLEEMKNFLTSEN 679
            +IKNYSSYRISEIDKIRIINAMENGEDYFHFGKLLGIARNSIK IIYKYRKFGKLSQGKIGGSISKISEENGNKLLDFVEKNVYASLEEMKNFL SEN
Sbjct:  496 IIKNYSSYRISEIDKIRIINAMENGEDYFHFGKLLGIARNSIKTIIYKYRKFGKLSQGKIGGSISKISEENGNKLLDFVEKNVYASLEEMKNFLISEN 593

HSP 2 Score: 123.25 bits (308), Expect = 1.545e-31
Identity = 56/58 (96.55%), Postives = 56/58 (96.55%), Query Frame = -2 
Query:   47 LSSMNFQSRFDFLKDALDNELVKEDYRDLTNYFWHIRRFFPKCIKKIHNFGDYLLLLT 220
            LSSMNFQSRFDFLKDALDNELVKEDYR LTNYFWHIRRFFPKCIKKIH FGDYLLLLT
Sbjct:  595 LSSMNFQSRFDFLKDALDNELVKEDYRYLTNYFWHIRRFFPKCIKKIHIFGDYLLLLT 652
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BLAST of SMED30032748 vs. Planmine SMEST
Match: SMESG000069530.1 (SMESG000069530.1)

HSP 1 Score: 120.939 bits (302), Expect = 5.462e-54
Identity = 57/58 (98.28%), Postives = 57/58 (98.28%), Query Frame = -2 
Query:   47 LSSMNFQSRFDFLKDALDNELVKEDYRDLTNYFWHIRRFFPKCIKKIHNFGDYLLLLT 220
            LSSMNFQSRFDFLKDALDNELVKEDYRDLTNYFWHIRRFFPKCIKKIH FGDYLLLLT
Sbjct:  197 LSSMNFQSRFDFLKDALDNELVKEDYRDLTNYFWHIRRFFPKCIKKIHIFGDYLLLLT 254

HSP 2 Score: 108.997 bits (271), Expect = 5.462e-54
Identity = 52/53 (98.11%), Postives = 53/53 (100.00%), Query Frame = -3 
Query:  232 KITVKLNGTGFRLIHDNASIHGGAISLNNVIEHLPPYSPFLNPIESVFSKIKF 390
            +ITVKLNGTGFRLIHDNASIHGGAISLNNVIEHLPPYSPFLNPIESVFSKIKF
Sbjct:  133 EITVKLNGTGFRLIHDNASIHGGAISLNNVIEHLPPYSPFLNPIESVFSKIKF 185
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BLAST of SMED30032748 vs. Planmine SMEST
Match: SMESG000005064.1 (SMESG000005064.1)

HSP 1 Score: 155.992 bits (393), Expect = 5.469e-50
Identity = 80/89 (89.89%), Postives = 84/89 (94.38%), Query Frame = -2 
Query:  386 ISEIDKIRIINAMENGEDYFHFGKLLGIARNSIKIIIYKYRKFGKLSQGKIGGSISKISEENGNKLLDFVEKNVYASLEEMKNFLTSEN 652
            ISEIDKIRIINAMENGEDYF+FGKLLGI+RNSIK IIYKYRKF KLSQGKIGG+ SKISEE+GNKLLDFVEKNVYASL EMKNFL SEN
Sbjct:  113 ISEIDKIRIINAMENGEDYFYFGKLLGISRNSIKTIIYKYRKFEKLSQGKIGGNKSKISEEHGNKLLDFVEKNVYASLVEMKNFLISEN 201

HSP 2 Score: 60.4622 bits (145), Expect = 5.469e-50
Identity = 33/39 (84.62%), Postives = 34/39 (87.18%), Query Frame = -1 
Query:  696 LSDISAETIPFRDEKEITLLSEVARPSTTSETRTKKHKL 812
            LSDISAE IPFRD KEITLLS+VARPSTT ET TKKH L
Sbjct:   75 LSDISAEIIPFRD-KEITLLSKVARPSTTPETLTKKHTL 112

HSP 3 Score: 104.375 bits (259), Expect = 4.651e-30
Identity = 49/53 (92.45%), Postives = 51/53 (96.23%), Query Frame = -3 
Query:  232 KITVKLNGTGFRLIHDNASIHGGAISLNNVIEHLPPYSPFLNPIESVFSKIKF 390
            +ITVKLNGTG+RLIHDNASIHGGAISLNN IEHLPPYSPFLN IESVFSKIKF
Sbjct:  325 EITVKLNGTGYRLIHDNASIHGGAISLNNAIEHLPPYSPFLNLIESVFSKIKF 377

HSP 4 Score: 45.4394 bits (106), Expect = 4.651e-30
Identity = 20/24 (83.33%), Postives = 21/24 (87.50%), Query Frame = -2 
Query:  149 LSSMNFQSRFDFLKDALDNELVKE 220
             SSMNFQSRFDFLKDALDNEL  +
Sbjct:  389 FSSMNFQSRFDFLKDALDNELCND 412
[Close]
BLAST of SMED30032748 vs. Planmine SMEST
Match: SMESG000005064.1 (SMESG000005064.1)

HSP 1 Score: 155.992 bits (393), Expect = 5.746e-50
Identity = 80/89 (89.89%), Postives = 84/89 (94.38%), Query Frame = -2 
Query:  386 ISEIDKIRIINAMENGEDYFHFGKLLGIARNSIKIIIYKYRKFGKLSQGKIGGSISKISEENGNKLLDFVEKNVYASLEEMKNFLTSEN 652
            ISEIDKIRIINAMENGEDYF+FGKLLGI+RNSIK IIYKYRKF KLSQGKIGG+ SKISEE+GNKLLDFVEKNVYASL EMKNFL SEN
Sbjct:  130 ISEIDKIRIINAMENGEDYFYFGKLLGISRNSIKTIIYKYRKFEKLSQGKIGGNKSKISEEHGNKLLDFVEKNVYASLVEMKNFLISEN 218

HSP 2 Score: 60.4622 bits (145), Expect = 5.746e-50
Identity = 33/39 (84.62%), Postives = 34/39 (87.18%), Query Frame = -1 
Query:  696 LSDISAETIPFRDEKEITLLSEVARPSTTSETRTKKHKL 812
            LSDISAE IPFRD KEITLLS+VARPSTT ET TKKH L
Sbjct:   92 LSDISAEIIPFRD-KEITLLSKVARPSTTPETLTKKHTL 129

HSP 3 Score: 104.375 bits (259), Expect = 1.585e-41
Identity = 49/53 (92.45%), Postives = 51/53 (96.23%), Query Frame = -3 
Query:  232 KITVKLNGTGFRLIHDNASIHGGAISLNNVIEHLPPYSPFLNPIESVFSKIKF 390
            +ITVKLNGTG+RLIHDNASIHGGAISLNN IEHLPPYSPFLN IESVFSKIKF
Sbjct:  342 EITVKLNGTGYRLIHDNASIHGGAISLNNAIEHLPPYSPFLNLIESVFSKIKF 394

HSP 4 Score: 83.9593 bits (206), Expect = 1.585e-41
Identity = 38/43 (88.37%), Postives = 38/43 (88.37%), Query Frame = -2 
Query:   92 LSSMNFQSRFDFLKDALDNELVKEDYRDLTNYFWHIRRFFPKC 220
             SSMNFQSRFDFLKDALDNELVKEDY DLTNYF HIRRFF  C
Sbjct:  406 FSSMNFQSRFDFLKDALDNELVKEDYSDLTNYFGHIRRFFRNC 448
[Close]
BLAST of SMED30032748 vs. Planmine SMEST
Match: SMESG000041908.1 (SMESG000041908.1)

HSP 1 Score: 172.94 bits (437), Expect = 1.460e-48
Identity = 87/90 (96.67%), Postives = 88/90 (97.78%), Query Frame = -2 
Query:  386 RISEIDKIRIINAMENGEDYFHFGKLLGIARNSIKIIIYKYRKFGKLSQGKIGGSISKISEENGNKLLDFVEKNVYASLEEMKNFLTSEN 655
            +ISEIDKIRIINAMENGEDYFHFGKLLGIARNSIK IIYKYRKFGKLSQGKIGGSISKISEENGNKLLDFVEKNVYASLEEMKNFL SEN
Sbjct:  507 KISEIDKIRIINAMENGEDYFHFGKLLGIARNSIKTIIYKYRKFGKLSQGKIGGSISKISEENGNKLLDFVEKNVYASLEEMKNFLISEN 596

HSP 2 Score: 109.768 bits (273), Expect = 1.551e-45
Identity = 52/53 (98.11%), Postives = 53/53 (100.00%), Query Frame = -3 
Query:  232 KITVKLNGTGFRLIHDNASIHGGAISLNNVIEHLPPYSPFLNPIESVFSKIKF 390
            +ITVKLNGTGFRLIHDNASIHGGAISLNNVIEHLPPYSPFLNPIESVFSKIKF
Sbjct:  720 EITVKLNGTGFRLIHDNASIHGGAISLNNVIEHLPPYSPFLNPIESVFSKIKF 772

HSP 3 Score: 91.6633 bits (226), Expect = 1.551e-45
Identity = 42/42 (100.00%), Postives = 42/42 (100.00%), Query Frame = -2 
Query:   95 LSSMNFQSRFDFLKDALDNELVKEDYRDLTNYFWHIRRFFPK 220
            LSSMNFQSRFDFLKDALDNELVKEDYRDLTNYFWHIRRFFPK
Sbjct:  784 LSSMNFQSRFDFLKDALDNELVKEDYRDLTNYFWHIRRFFPK 825
The following BLAST results are available for this feature:
BLAST of SMED30032748 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 SMED30032748 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 SMED30032748 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 SMED30032748 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 SMED30032748 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
kcnip13.880e-630.69Kv channel interacting protein 1 [Source:Xenbase;A... [more]
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BLAST of SMED30032748 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 SMED30032748 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 SMED30032748 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 SMED30032748 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 SMED30032748 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 SMED30032748 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 SMED30032748 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 SMED30032748 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 SMED30032748 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000062787.11.988e-5596.94SMESG000062787.1[more]
SMESG000069530.15.462e-5498.28SMESG000069530.1[more]
SMESG000005064.15.469e-5089.89SMESG000005064.1[more]
SMESG000005064.15.746e-5089.89SMESG000005064.1[more]
SMESG000041908.11.460e-4896.67SMESG000041908.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032748 ID=SMED30032748|Name=SMED30032748|organism=Schmidtea mediterranea sexual|type=transcript|length=812bp
ATCATTTATTTCATATATATTGCTATAAATAATATTTAGGAAATCAAGTA
AGTAACAATAAATAGTCTCCAAAATTATGTATTTTTTTTATACATTTCGG
AAAAAATCTCCTAATATGCCAAAAGTAATTAGTTAAATCTCTGTAGTCTT
CTTTCACCAGCTCGTTATCCAGTGCGTCCTTCAGAAAATCGAATCTGGAT
TGGAAATTCATTGAACTCAATCATTGAACTCAAATTTGATTTTACTGAAC
ACACTTTCAATTGGGTTCAGAAAAGGACTATATGGTGGTAAATGTTCAAT
AACATTATTTAGAGATATTGCACCACCATGAATTGAAGCATTGTCGTGGA
TTAAACGAAATCCAGTTCCATTCAATTTTACAGTTATTTTCGGAAGTTAA
AAAGTTCTTCATTTCCTCTAATGAAGCATAAACATTTTTCTCCACAAAAT
CAAGTAGTTTGTTGCCATTTTCTTCCGAAATTTTGGATATACTGCCACCA
ATCTTGCCTTGTGACAATTTCCCAAATTTCCGGTATTTATAAATTATTAT
TTTTATGGAATTTCTAGCTATTCCTAATAATTTTCCAAAATGGAAATAGT
CTTCACCATTTTCCATGGCATTGATAATTCGTATTTTATCGATTTCCGAA
ATTCTGTAAGAAGAATAATTTTTTATAACTTAAAAATAAAATTTACAGTT
TATGCTTTTTTGTTCGAGTCTCAGATGTTGTTGAGGGCCTAGCAACTTCT
GAAAGCAATGTGATTTCTTTTTCATCGCGAAATGGAATTGTTTCTGCAGA
AATGTCTGAAAG
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protein sequence of SMED30032748-orf-1

>SMED30032748-orf-1 ID=SMED30032748-orf-1|Name=SMED30032748-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp
MENGEDYFHFGKLLGIARNSIKIIIYKYRKFGKLSQGKIGGSISKISEEN
GNKLLDFVEKNVYASLEEMKNFLTSENNCKIEWNWISFNPRQCFNSWWCN
ISK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR009057Homeobox-like_sf
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding