SMED30011356

Overview
NameSMED30011356
Smed IDSMED30011356
Length (bp)866
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30011356 (SMED30011356) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011356 (SMED30011356) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30011356

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
reproductive organSMED30011356h1SMcG0001616 Contig48952newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30011356h1SMcG0001616 Contig48952uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30011356h1SMcG0001616 Contig44934uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30011356h1SMcG0001616 Contig44934newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011356 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.016021:12419..17733 +3622
Homology
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BLAST of SMED30011356 vs. Planmine SMEST
Match: SMESG000032278.1 (SMESG000032278.1)

HSP 1 Score: 513.457 bits (1321), Expect = 0.000e+0
Identity = 270/270 (100.00%), Postives = 270/270 (100.00%), Query Frame = -3 
Query:   22 MYEIIYILIKIMSKYMLIDLLLYCXXXXXXXXXXXXXXXISEAVGSSNLECARDLRFCNLAIMSPTSNCIPWKLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNTTKNFDVIHLPIAQNISLHGKFNRSVIDVIAIGPVRVINL 831
            MYEIIYILIKIMSKYMLIDLLLYCNIFNIFFNAFFAQANISEAVGSSNLECARDLRFCNLAIMSPTSNCIPWKLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNTTKNFDVIHLPIAQNISLHGKFNRSVIDVIAIGPVRVINL
Sbjct:    1 MYEIIYILIKIMSKYMLIDLLLYCNIFNIFFNAFFAQANISEAVGSSNLECARDLRFCNLAIMSPTSNCIPWKLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNTTKNFDVIHLPIAQNISLHGKFNRSVIDVIAIGPVRVINL 270
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BLAST of SMED30011356 vs. Planmine SMEST
Match: SMESG000032278.1 (SMESG000032278.1)

HSP 1 Score: 492.656 bits (1267), Expect = 1.751e-178
Identity = 259/259 (100.00%), Postives = 259/259 (100.00%), Query Frame = -3 
Query:   22 MSKYMLIDLLLYCXXXXXXXXXXXXXXXISEAVGSSNLECARDLRFCNLAIMSPTSNCIPWKLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNTTKNFDVIHLPIAQNISLHGKFNRSVIDVIAIGPVRVINL 798
            MSKYMLIDLLLYCNIFNIFFNAFFAQANISEAVGSSNLECARDLRFCNLAIMSPTSNCIPWKLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNTTKNFDVIHLPIAQNISLHGKFNRSVIDVIAIGPVRVINL
Sbjct:    1 MSKYMLIDLLLYCNIFNIFFNAFFAQANISEAVGSSNLECARDLRFCNLAIMSPTSNCIPWKLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNTTKNFDVIHLPIAQNISLHGKFNRSVIDVIAIGPVRVINL 259
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BLAST of SMED30011356 vs. Planmine SMEST
Match: SMESG000032278.1 (SMESG000032278.1)

HSP 1 Score: 483.411 bits (1243), Expect = 6.650e-175
Identity = 255/255 (100.00%), Postives = 255/255 (100.00%), Query Frame = -3 
Query:   22 MLIDLLLYCXXXXXXXXXXXXXXXISEAVGSSNLECARDLRFCNLAIMSPTSNCIPWKLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNTTKNFDVIHLPIAQNISLHGKFNRSVIDVIAIGPVRVINL 786
            MLIDLLLYCNIFNIFFNAFFAQANISEAVGSSNLECARDLRFCNLAIMSPTSNCIPWKLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNTTKNFDVIHLPIAQNISLHGKFNRSVIDVIAIGPVRVINL
Sbjct:    1 MLIDLLLYCNIFNIFFNAFFAQANISEAVGSSNLECARDLRFCNLAIMSPTSNCIPWKLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNTTKNFDVIHLPIAQNISLHGKFNRSVIDVIAIGPVRVINL 255
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BLAST of SMED30011356 vs. Planmine SMEST
Match: SMESG000032267.1 (SMESG000032267.1)

HSP 1 Score: 151.369 bits (381), Expect = 4.442e-44
Identity = 77/186 (41.40%), Postives = 119/186 (63.98%), Query Frame = -3 
Query:  139 SNLECARDLRFCNLAIMSPTSNCIPW-KLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNT 693
            SN  C R+ ++C+L   +  S C+ W ++++  KI +I E TT+C K  + Y+C +     D + +++  C  Q CD Y+LC+ G+K+ET  KSIK N+ + +DT+II +KSK +C+ISA C +CES K  I+ +FS CK+L+  N   +   FDNL+P   ++FY+LP+KN  L GSVF V  +T
Sbjct:   32 SNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDT 217
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BLAST of SMED30011356 vs. Planmine SMEST
Match: SMESG000032289.1 (SMESG000032289.1)

HSP 1 Score: 130.954 bits (328), Expect = 1.049e-36
Identity = 76/226 (33.63%), Postives = 122/226 (53.98%), Query Frame = -3 
Query:   22 SSNLECARDLRFCNLAIMSPTSNCIPWKLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCD-TYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNTTKNFDVIHLPIAQNISLHGKFNRSVIDVIAIGPVRVINL 696
            S+  EC RDL +CN+      +NC   K +   +I+ IF+NTTLC+K + GY C   +   ++Q      C   KCD  Y+LCK G+K+E T  S+K  +   +  +I+ +++ S+C+IS+ C +CE VK +I   FS CKLL+      +  +FDNLK N  H FY+LP+ N  ++G VF + F        +H      I+         ++++ +  ++VIN 
Sbjct:    6 SAKFECTRDLDYCNVGQKPNVTNCFAHKPANEMRILNIFKNTTLCKKYEGGYWCPG-LYAFNRQNFFHNYCNKLKCDFPYDLCKDGIKWEATSNSLKLKIPSQFYVLIVKEENLSDCLISSQCQNCELVKGLISNTFSKCKLLQLDG--SKKIIFDNLKQNELHTFYVLPLTNNAIQGFVFKLIFQNGNEIPPMH---KTTIAAEKDSVIKSLNLLMLARLKVINF 225
The following BLAST results are available for this feature:
BLAST of SMED30011356 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 SMED30011356 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 SMED30011356 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 SMED30011356 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 SMED30011356 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 SMED30011356 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 SMED30011356 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 SMED30011356 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 SMED30011356 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 SMED30011356 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 SMED30011356 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 SMED30011356 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 SMED30011356 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 SMED30011356 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000032278.10.000e+0100.00SMESG000032278.1[more]
SMESG000032278.11.751e-178100.00SMESG000032278.1[more]
SMESG000032278.16.650e-175100.00SMESG000032278.1[more]
SMESG000032267.14.442e-4441.40SMESG000032267.1[more]
SMESG000032289.11.049e-3633.63SMESG000032289.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011356 ID=SMED30011356|Name=SMED30011356|organism=Schmidtea mediterranea sexual|type=transcript|length=866bp
CAAAACAAAGTTGTTATATTATAAGTTAATAACACGCACAGGGCCAATTG
CAATAACGTCAATTACGCTGCGATTAAACTTTCCATGTAAGGATATATTC
TGCGCAATCGGGAGATGAATAACATCGAAGTTTTTTGTTGTATTAAATGA
CACAGTGAACACAGACCCTTTTAGTCGCCGATTCTTGATTGGGAGAAGAT
AAAATACGTGATTTGTATTTGGTTTGAGATTGTCGAATAAAGTGGGTTCA
GGTGTAATATTTGTCCCTTTCAATAACTTACAGCCACTGAAATTTATTTT
TATTATATTTTTCACCGATTCACAATCATGACATAGAGCAGATATTATGC
ATTCCGATTTTGATTTCTGCCAAATAATCACCGTGTCATAATCCTGTGAT
AAATTGAACTTGATAGATTTGTAAGTTGTTTCATATTTCATTCCATGTTT
ACATAAATTATATGTATCACACTTCTGGTTGGGACATAGAGTGAAATCCT
TTTTTTGTTTATCCGAAGGAAGTACGTTGGATGCGCACAAATAGCCTTCT
TTTCCTTTCTGGCATAAAGTTGTATTTTCAAATATTTTCATAATTTTAAA
TGATTTAGATAATTTCCATGGAATACAATTTGAAGTGGGAGACATTATAG
CCAGATTGCAGAATCTCAGATCACGAGCACACTCTAAATTTGAAGAACCG
ACAGCTTCACTAATATTCGCCTGTGCAAAGAATGCATTGAAAAAAATATT
GAAAATGTTGCAATATAATAATAAATCTATAAGCATATATTTACTCATAA
TTTTTATTAAAATGTATATGATTTCATACATTTATACGCAGAAATATCCC
CAAAACCACCCAAAAC
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protein sequence of SMED30011356-orf-1

>SMED30011356-orf-1 ID=SMED30011356-orf-1|Name=SMED30011356-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=271bp
MYEIIYILIKIMSKYMLIDLLLYCNIFNIFFNAFFAQANISEAVGSSNLE
CARDLRFCNLAIMSPTSNCIPWKLSKSFKIMKIFENTTLCQKGKEGYLCA
SNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDT
VIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFD
NLKPNTNHVFYLLPIKNRRLKGSVFTVSFNTTKNFDVIHLPIAQNISLHG
KFNRSVIDVIAIGPVRVINL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 21..40