SMED30023491

Overview
NameSMED30023491
Smed IDSMED30023491
Length (bp)1292
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 SMED30023491 (SMED30023491) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023491 (SMED30023491) 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 SMED30023491 (SMED30023491) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023491 (SMED30023491) 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



SMED30023491

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30023491h1SMcG0011882 SmedASXL_011283SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30023491h1SMcG0011882 Contig55263uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023491h1SMcG0011882 Contig55263newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30023491h1SMcG0011882 dd_Smed_v4_14238_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30023491h1SMcG0011882 dd_Smed_v4_14238_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30023491h1SMcG0011882 dd_Smed_v6_14238_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30023491h1SMcG0011882 dd_Smed_v4_14238_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
SMED30023491 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000471:11708..13111 -6317
Homology
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BLAST of SMED30023491 vs. TrEMBL
Match: K1PPG7 (Uncharacterized protein OS=Crassostrea gigas OX=29159 GN=CGI_10010683 PE=4 SV=1)

HSP 1 Score: 151.369 bits (381), Expect = 2.143e-38
Identity = 102/343 (29.74%), Postives = 164/343 (47.81%), Query Frame = 1 
Query:  112 TSYLGPDNPPPLSLISENYQRFLQVSKAVNNEDSLFNLGDEYYSKLVKLLQLQAAINIDDTICIIASQKSQLPKELERRLCLINPILHLTAGIFIYENSPDNERELNVGVIPVNVEDYF-----NSGKVKNSFDKIIIADGLEVIEYRQKFLENCKVALKNNSESG-LIIFHRTIDMLTLPVFLEVIHNFEKQQIEISVLVEQLLELNFLVGWNIVSAPIQIPKLKWLNQLYNYFPPIMESVATTNIYGGLRELVETSFKYSEFLVTIKDQFLLLVATISDTHIGQFYKMHLQDEEFKINVNRTSVALTDNLLRLRITDDISDKMPKILETVDKFLNNDDKFP 1122
            +S+LGP++P PLS++SE YQ   ++ K     +  ++ G  Y  K+  L+     +   D  C I   K  L + +  + CL+ P++ +  G F Y  + D E+ L+V V     E+YF     +  KVK  FDKII+ DG   + Y Q   E  +  +K   +SG L+I HR  ++ +LP+F +     E+ +     +++ L +  F V W I   PI +PK KW + L   FPP ME ++ + I  G REL E   KY   LV  +D+ L +  + S    G   K+H           R+      NL  L++   ++ ++  +L    K   +  KFP
Sbjct:    3 SSFLGPESPRPLSVVSEGYQTRFRIPKY----EEKYHFGKSYEDKMFDLIHKYLELGTTDRFCYIGDVKGSLVERIADKFCLLEPVMSVIPGHFSYVQT-DTEKLLSVRVAHTGAEEYFKQLATSKEKVKTVFDKIILKDG---VRYLQNPKECYEYVMKCVDKSGKLLIIHRPGNLNSLPIFQDAKERLEEVETPYMDIIKDLQDCKFDVQWEIECLPILLPKRKWFSMLQEKFPPQMEILSDSEIISGCRELTEGVMKYEGELVEFQDRLLFITVSHSALEDG-CPKLHRH--------GRSDTGTFPNLKDLKLKMSVTPEIKTLLRPTKK-TEDKGKFP 327
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BLAST of SMED30023491 vs. TrEMBL
Match: A0A1I8JFB5 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig009028g1 PE=4 SV=1)

HSP 1 Score: 149.828 bits (377), Expect = 1.742e-37
Identity = 83/281 (29.54%), Postives = 148/281 (52.67%), Query Frame = 1 
Query:  109 MTSYLGPDNPPPLSLISENYQRFLQVSKAVN--NEDSLFNLGDEYYSKLVKLLQLQAAINIDDTICIIASQKSQLPKELERRLCLINPILHLTAGIFIYENSPDNERELNVGVIPVNVEDYFNSGKVKNS---------FDKIIIADGLEVIEYRQKFLENCKVALKNNSESGLIIFHRTIDMLTLPVFLEVIHNFEKQQIEISVLVEQLLELNFLVGWNIVSAPIQIPKLKWLNQLYNYFPPIMESVATTNIYGGLRELVETSFKYSEFLVTIKDQFLLL 918
            M+++ GP++P P S+ISE YQR + + + +   ++ S F+ GDEY   +   +   A IN+DD +C +  +K  L K LE+RL L+  I  +T G  +YE +    R + V V+    E++F+    +           +DK+I+ D LE ++ R+ F  N    L+   +  L+I  R  DM+TLP + E     +   + +   + ++  L F V W+I++ P+ + + +WL+ LY+ +P  +E  +  ++  G+REL E S KY    +   D+ L +
Sbjct:    1 MSAFYGPESPRPFSVISERYQRDVPIQRQLPAIDDGSQFSFGDEYNKAICDSVSRLAEINVDDLVCYVGPKKGSLAKVLEQRLKLVKGIQEVTPGEIVYEAA-KTGRLIPVSVVNSEAEEHFSQLASQRDDDEDSPPIRYDKVIVRDSLEYLQDRKTFYMNAMRCLR--PQGSLLIIQRPADMITLPYYSEARDRVQDSDVPVVDTINEIQSLGFDVEWDIIALPVLLSRTQWLSLLYHRYPNHLEVTSDADVTSGVRELSEGSLKYMWDRLEFTDRLLFV 278
[Close]
BLAST of SMED30023491 vs. TrEMBL
Match: A0A1I8J6R0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig009251g1 PE=4 SV=1)

HSP 1 Score: 149.828 bits (377), Expect = 1.742e-37
Identity = 83/281 (29.54%), Postives = 147/281 (52.31%), Query Frame = 1 
Query:  109 MTSYLGPDNPPPLSLISENYQRFLQVSKAVN--NEDSLFNLGDEYYSKLVKLLQLQAAINIDDTICIIASQKSQLPKELERRLCLINPILHLTAGIFIYENSPDNERELNVGVIPVNVEDYFNSGKVKNS---------FDKIIIADGLEVIEYRQKFLENCKVALKNNSESGLIIFHRTIDMLTLPVFLEVIHNFEKQQIEISVLVEQLLELNFLVGWNIVSAPIQIPKLKWLNQLYNYFPPIMESVATTNIYGGLRELVETSFKYSEFLVTIKDQFLLL 918
            M+++ GP++P P S+ISE YQR + + + +   ++ S F+ GDEY   +   +   A IN+DD +C +  +K  L K LE+RL L+  I  +T G  +YE +    R + V V+    E++F+    +           +DK+I+ D LE ++ R+ F  N    L+   +  L+I  R  DM+TLP + E     +   + +   + ++  L F V W+I++ P+ + + +WL  LY+ +P  +E  +  ++  G+REL E S KY    +   D+ L +
Sbjct:    1 MSAFYGPESPRPFSVISERYQRDVPIQRQLPAIDDGSQFSFGDEYNKAICDSVSRLAEINVDDLVCYVGPKKGSLAKVLEQRLKLVKGIQEVTPGEIVYEAA-KTGRLIPVSVVNSEAEEHFSQLASQRDDDEDSPPIRYDKVIVRDSLEYLQDRKTFYMNAMRCLR--PQGSLLIIQRPADMITLPYYSEARDRVQDSDVPVVDTINEIQSLGFDVEWDIIALPVLLSRTQWLTLLYHRYPNHLEVTSDADVTSGVRELSEGSLKYMWDRLEFTDRLLFV 278
[Close]
BLAST of SMED30023491 vs. TrEMBL
Match: R7VAN4 (Uncharacterized protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_187136 PE=4 SV=1)

HSP 1 Score: 138.658 bits (348), Expect = 1.665e-33
Identity = 75/279 (26.88%), Postives = 133/279 (47.67%), Query Frame = 1 
Query:  112 TSYLGPDNPPPLSLISENYQRFLQVSKAVNNEDSLFNLGDEYYSKLVKLLQLQAAINIDDTICIIASQKSQLPKELERRLCLINPILHLTAGIFIYENSPDNERELNVGVIPVNVEDYFNSGKVKNS---FDKIIIADGLEVIEYRQKFLENCKVALKNNSESGLIIFHRTIDMLTLPVFLEVIHNFEKQQIEISVLVEQLLELNFLVGWNIVSAPIQIPKLKWLNQLYNYFPPIMESVATTNIYGGLRELVETSFKYSEFLVTIKDQFLLLVATISDT 939
            T +LGP+ P P +++SE + R   VS    ++   F+ G+ Y +++ +L+     +N DD +C I   +      L+ + CL+ P+  +  G   +E  P + R L + V  V  EDYF     K +   FDKI++ D +   +  +   +N K  L    +  ++I HR  +M+TLP+F +               +  L   +  V W +   P+++ + +W   + ++FPP +E+V+   +  GLREL E   KYSE  +   D+ L +     D 
Sbjct:    3 TYHLGPETPAPFAVLSEGHMR-KNVSVPFLSDQLRFSFGESYEARMCELIHKYLELNTDDRLCYIGDPRGTFVPMLQEKFCLVKPVTTVVPGHIHFEEGPTH-RMLAIRVASVGAEDYFRREATKETPAVFDKILMHDAMNYFDEHRNTFQNIKKCLAPGGK--VLIIHRPGEMMTLPIFKDAQQRICDNDQPYDAFIRDLTATHLEVTWEVECLPVKMDRDRWYAMIQDHFPPQLENVSAFEVNLGLRELSEGVMKYSEGTIEFADRLLFVTGAECDA 277
[Close]
BLAST of SMED30023491 vs. TrEMBL
Match: A0A2G8JL72 (Uncharacterized protein OS=Stichopus japonicus OX=307972 GN=BSL78_26686 PE=4 SV=1)

HSP 1 Score: 133.65 bits (335), Expect = 1.249e-31
Identity = 85/276 (30.80%), Postives = 141/276 (51.09%), Query Frame = 1 
Query:  127 PDNPPPLSLISENYQRFLQVSKAVNNEDSLFNLGDEYYSKLVKLLQLQAAINIDDTICIIASQKSQLPKELERRLCLINPILHLTAGIFIYENSPDNERELNVGVIPVNVEDYFNS-----GKVKNS-FDKIIIADGLEVIEYRQKFLENCKVALKNNSESG-LIIFHRTIDMLTLPVFLEVIHNFEKQQIE--ISVLVEQLLELNFLVGWNIVSAPIQIPKLKWLNQLYNYFPPIMESVATTNIYGGLRELVETSFKYSEFLVTIKDQFLLLVAT 927
            PD+PPP S+++E +Q  L + K    E   ++ GD Y   + KL+     ++  +    + S K  L ++++ + CL+ P++++  G+  YE +P  ++ L   +  V  E+YF       GK K + FDKI++ D +E      +   +    L+  +  G L+I HR   M TLP+F E    F     E   + +++ L  ++  V W+I + PI +PK+KWL  L   FPP ME+++   I  G+REL E   KY    V   D+ LL+ AT
Sbjct:   22 PDSPPPFSVVTEKWQNQLDIPKYRLEES--YSFGDAYEDAMFKLIHKHLELDTHERFAYVGSNKGSLAEKIKEKFCLLQPMVNIFPGLIHYEETP-GQKLLPFRISHVGAEEYFRQLAESLGKDKPAPFDKILLKDSVEHFTNPSQTFSHI---LRTLAPLGRLLIIHRPGPMSTLPMFTEANKKFVTDDSEEPYAKIIKHLQAVHVDVKWDIETLPIGMPKVKWLAMLREQFPPQMEAISRAQITTGIRELTEGMLKYQGEEVEFFDRLLLVTAT 291
The following BLAST results are available for this feature:
BLAST of SMED30023491 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 SMED30023491 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 SMED30023491 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 SMED30023491 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 SMED30023491 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 SMED30023491 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 SMED30023491 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 SMED30023491 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
K1PPG72.143e-3829.74Uncharacterized protein OS=Crassostrea gigas OX=29... [more]
A0A1I8JFB51.742e-3729.54Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8J6R01.742e-3729.54Uncharacterized protein OS=Macrostomum lignano OX=... [more]
R7VAN41.665e-3326.88Uncharacterized protein OS=Capitella teleta OX=283... [more]
A0A2G8JL721.249e-3130.80Uncharacterized protein OS=Stichopus japonicus OX=... [more]
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BLAST of SMED30023491 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 SMED30023491 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 SMED30023491 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 SMED30023491 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 SMED30023491 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 SMED30023491 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023491 ID=SMED30023491|Name=SMED30023491|organism=Schmidtea mediterranea sexual|type=transcript|length=1292bp
CACACTTCAAATGAAATTTGTTGTTTCTTACCGTATTTACTGATCGTCTG
TAAATCGAGTATAAAACAAATGTATCTCCATGCCAACGTAATAGATTTTA
AATGAAAAATGACTAGTTACTTGGGACCTGATAACCCGCCACCGTTGTCA
TTGATTTCAGAAAATTATCAAAGATTTTTGCAAGTTTCAAAAGCAGTAAA
TAATGAAGACAGTTTATTCAATCTTGGTGATGAATATTATTCGAAATTAG
TGAAATTATTACAACTTCAAGCCGCGATTAATATTGATGACACAATTTGC
ATTATAGCTTCACAAAAATCTCAACTACCGAAAGAATTGGAGAGAAGACT
GTGTTTGATAAATCCAATTTTACATTTGACGGCGGGAATATTTATCTACG
AGAACTCTCCAGATAACGAACGGGAACTAAATGTTGGAGTCATACCGGTA
AATGTTGAAGATTATTTCAACAGTGGAAAAGTGAAAAATTCTTTCGATAA
AATTATCATTGCTGATGGCTTGGAAGTTATTGAATACAGACAAAAATTCC
TAGAAAATTGTAAAGTTGCTTTGAAAAATAACTCAGAGAGTGGATTAATT
ATATTTCATAGAACAATAGATATGTTGACTTTGCCTGTTTTTCTAGAAGT
TATTCACAACTTTGAAAAACAACAAATCGAAATTTCAGTTTTAGTTGAAC
AATTATTGGAACTCAATTTCCTTGTCGGTTGGAATATTGTTTCGGCTCCT
ATTCAAATACCCAAGCTAAAATGGTTAAATCAACTCTACAATTATTTCCC
GCCTATCATGGAATCAGTTGCTACAACAAATATTTATGGTGGACTCAGAG
AATTAGTCGAAACTTCATTCAAGTATTCCGAGTTCTTGGTCACAATTAAG
GACCAATTTCTTTTACTTGTAGCAACAATATCTGATACTCACATTGGACA
GTTTTATAAAATGCATTTACAAGATGAAGAATTTAAAATTAATGTCAATC
GCACCTCAGTGGCTTTGACAGATAACTTATTGCGATTGAGGATAACTGAT
GATATTAGTGACAAAATGCCAAAAATATTGGAAACTGTTGATAAATTTTT
AAATAATGATGATAAATTTCCAGAAGAATGGTGGGGAACTATCCCTTCGG
CAACAATGGGAAAGTTAGATAAAAGCAGAATCAATCGCTCATTGTAATAA
AAACCAAGTTTATATTTTTTAAAAGATATTTAATAACTCCAAAATATATT
CTAACAATAATTTATCTAAAACTGAATAAAGAGACTTTATAG
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protein sequence of SMED30023491-orf-1

>SMED30023491-orf-1 ID=SMED30023491-orf-1|Name=SMED30023491-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=363bp
MTSYLGPDNPPPLSLISENYQRFLQVSKAVNNEDSLFNLGDEYYSKLVKL
LQLQAAINIDDTICIIASQKSQLPKELERRLCLINPILHLTAGIFIYENS
PDNERELNVGVIPVNVEDYFNSGKVKNSFDKIIIADGLEVIEYRQKFLEN
CKVALKNNSESGLIIFHRTIDMLTLPVFLEVIHNFEKQQIEISVLVEQLL
ELNFLVGWNIVSAPIQIPKLKWLNQLYNYFPPIMESVATTNIYGGLRELV
ETSFKYSEFLVTIKDQFLLLVATISDTHIGQFYKMHLQDEEFKINVNRTS
VALTDNLLRLRITDDISDKMPKILETVDKFLNNDDKFPEEWWGTIPSATM
GKLDKSRINRSL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000418head
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR029063SAM-dependent_MTases
Vocabulary: molecular function
TermDefinition
GO:0016740transferase activity