SMED30031396

Overview
NameSMED30031396
Smed IDSMED30031396
Length (bp)1229
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.
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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



SMED30031396

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



PAGE Curations: 20

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30031396h1SMcG0020996 Contig17129newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031396h1SMcG0020996 Contig17129uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031396h1SMcG0020999 Contig17129newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031396h1SMcG0020999 Contig17129uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031396h1SMcG0020998 Contig17129newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031396h1SMcG0020998 Contig17129uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031396h1SMcG0020997 Contig17129newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031396h1SMcG0020997 Contig17129uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031396h1SMcG0020995 Contig17129newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031396h1SMcG0020995 Contig17129uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
reproductive organSMED30031396h1SMcG0020996 Contig17129newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30031396h1SMcG0020996 Contig17129uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30031396h1SMcG0020999 Contig17129newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30031396h1SMcG0020999 Contig17129uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30031396h1SMcG0020998 Contig17129newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30031396h1SMcG0020998 Contig17129uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30031396h1SMcG0020997 Contig17129newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30031396h1SMcG0020997 Contig17129uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30031396h1SMcG0020995 Contig17129newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30031396h1SMcG0020995 Contig17129uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30031396 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003196:26165..27392 +6131
Homology
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BLAST of SMED30031396 vs. TrEMBL
Match: A0A3P7REC1 (Uncharacterized protein OS=Dibothriocephalus latus OX=60516 GN=DILT_LOCUS17755 PE=4 SV=1)

HSP 1 Score: 90.8929 bits (224), Expect = 5.720e-18
Identity = 52/146 (35.62%), Postives = 75/146 (51.37%), Query Frame = 2 
Query:   56 IYRNPNGLYPVNPFPEDYPKRISAEKQDSTI-LKLDWSKCRMEKQREWHGYTGAIGYLPEPPLPSYSRYVAHSTCPPLMAGIKYHEFRRGKPVRESAPNTQYDYCQMGALSGPEIMTRIIPRMVHSIRDDIPDSRQWRFDGRDHQL 490
            I RNP+GL P++ FPEDYP           I L L+ S   +  +  WHGYTGA  +  + P+PS ++++      P   G+        KPV +  P+       + A++G + MT +I    H I+ D+ DSR WRFDGRDH  
Sbjct:   12 IRRNPHGLQPLSTFPEDYPPMGRLNYNVPPIKLTLEDSPTALIPEPFWHGYTGARTHFVQQPMPSNAQFLLTGGYAPRRGGMSAVVTESPKPVHDLPPSVPCSTVTVAAMAGKDSMTTVIRPQTHPIQVDVSDSRLWRFDGRDHTF 157
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BLAST of SMED30031396 vs. TrEMBL
Match: A0A183TGC0 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS15518 PE=4 SV=1)

HSP 1 Score: 89.7373 bits (221), Expect = 1.353e-17
Identity = 50/146 (34.25%), Postives = 76/146 (52.05%), Query Frame = 2 
Query:   56 IYRNPNGLYPVNPFPEDYPKRISAEKQDSTI-LKLDWSKCRMEKQREWHGYTGAIGYLPEPPLPSYSRYVAHSTCPPLMAGIKYHEFRRGKPVRESAPNTQYDYCQMGALSGPEIMTRIIPRMVHSIRDDIPDSRQWRFDGRDHQL 490
            + RNP+GL P++ +PEDYP           I L L+ S   +  +  WHGYTGA  +  + P+PS ++++      P   G+        KPV +  P+       + A++G + MT +I   +H I+ D+ DSR WRFDGRDH  
Sbjct:   12 VRRNPHGLQPLSTYPEDYPPMGRLNYNVPPIRLTLEDSPTALIPEPFWHGYTGARTHFVQQPMPSNAQFLLTGGYAPRREGVSAVVTESPKPVHDLPPSVPCSTVTVAAMAGKDSMTTVIRPQIHPIQVDVSDSRLWRFDGRDHTF 157
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BLAST of SMED30031396 vs. TrEMBL
Match: A0A075ADM2 (Uncharacterized protein OS=Opisthorchis viverrini OX=6198 GN=T265_00161 PE=4 SV=1)

HSP 1 Score: 87.8113 bits (216), Expect = 5.442e-17
Identity = 50/145 (34.48%), Postives = 74/145 (51.03%), Query Frame = 2 
Query:   59 YRNPNGLYPVNPFPEDYPKRISAEKQDSTI-LKLDWSKCRMEKQREWHGYTGAIGYLPEPPLPSYSRYVAHSTCPPLMAGIKYHEFRRGKPVRESAPNTQYDYCQMGALSGPEIMTRIIPRMVHSIRDDIPDSRQWRFDGRDHQL 490
            YRNPNGL P + F EDY KR +       + L+ +  +  + + + WHGYTGA  +    PLPS +R+  +    P    IK +       ++++A    Y+     AL G   M R     +H ++ D+PDSR WRFDGR+H  
Sbjct:    7 YRNPNGLQPFSMFTEDYLKRGTIHYNIPPVRLERETLESVVVEPKYWHGYTGAKTFFTHQPLPSTTRFSVYGGTTPSRISIKSYIPSVEPAIQDTACGIPYNVTSAAALHGASAMGRPQRPQIHPMQIDVPDSRLWRFDGRNHTF 151
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BLAST of SMED30031396 vs. TrEMBL
Match: A0A183VRL8 (Uncharacterized protein OS=Trichobilharzia regenti OX=157069 GN=TRE_LOCUS3124 PE=4 SV=1)

HSP 1 Score: 72.4034 bits (176), Expect = 1.605e-11
Identity = 48/145 (33.10%), Postives = 64/145 (44.14%), Query Frame = 2 
Query:   62 RNPNGLYPVNPFPEDYPKRISAEKQ--DSTILKLDWSKCRMEKQREWHGYTGAIGYLPEPPLPSYSRYVAHSTCPPLMAGIKYHEFRRGKPVRESAPNTQYDYCQMGALSGPEIMTRIIPRMVHSIRDDIPDSRQWRFDGRDHQL 490
            RNPNG    + FPEDYPK+ S         +LK        E  + WHGY GA  +    PLPS + +  +    P    +  +    G   R S  +T ++   M  L G     +      H I+ D PDSR WRFDGR+H  
Sbjct:    8 RNPNGWQHYSAFPEDYPKKGSLHYNIPPVRLLKETLEDVVFEP-KYWHGYVGAKTFFTHQPLPSTTYFSVYGGTAPKRNDVNAYIPSTGDATRYSTLSTPHNIVAMADLYGAFGKNQPHRPQAHPIQVDAPDSRFWRFDGRNHTF 151
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BLAST of SMED30031396 vs. TrEMBL
Match: A0A1I8GL57 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig022535g1 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 1.104e-6
Identity = 30/76 (39.47%), Postives = 40/76 (52.63%), Query Frame = 2 
Query:  188 REWHGYTGAIGYLPEPPLPSYSRYVAHSTCPPLMA----GIKYHEFRRGKPVRESAPNTQYDYCQMGALSGPEIMT 403
            R W GYTGAIGY PE P P+  RY AH   PP        ++Y E R  +      P   ++  Q+ AL GP++M+
Sbjct:   57 RNWRGYTGAIGYFPEQPAPTNRRYFAHGLEPPEAGRRDCALRYQEIRAYRGSTAPPPGVPFNDAQLAALWGPQLMS 132
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BLAST of SMED30031396 vs. Planmine SMEST
Match: SMESG000016750.1 (SMESG000016750.1)

HSP 1 Score: 315.079 bits (806), Expect = 5.096e-108
Identity = 150/150 (100.00%), Postives = 150/150 (100.00%), Query Frame = 2 
Query:   44 RFVRIYRNPNGLYPVNPFPEDYPKRISAEKQDSTILKLDWSKCRMEKQREWHGYTGAIGYLPEPPLPSYSRYVAHSTCPPLMAGIKYHEFRRGKPVRESAPNTQYDYCQMGALSGPEIMTRIIPRMVHSIRDDIPDSRQWRFDGRDHQLY 493
            RFVRIYRNPNGLYPVNPFPEDYPKRISAEKQDSTILKLDWSKCRMEKQREWHGYTGAIGYLPEPPLPSYSRYVAHSTCPPLMAGIKYHEFRRGKPVRESAPNTQYDYCQMGALSGPEIMTRIIPRMVHSIRDDIPDSRQWRFDGRDHQLY
Sbjct:    7 RFVRIYRNPNGLYPVNPFPEDYPKRISAEKQDSTILKLDWSKCRMEKQREWHGYTGAIGYLPEPPLPSYSRYVAHSTCPPLMAGIKYHEFRRGKPVRESAPNTQYDYCQMGALSGPEIMTRIIPRMVHSIRDDIPDSRQWRFDGRDHQLY 156
[Close]
BLAST of SMED30031396 vs. Planmine SMEST
Match: SMESG000035386.1 (SMESG000035386.1)

HSP 1 Score: 75.485 bits (184), Expect = 3.196e-16
Identity = 53/149 (35.57%), Postives = 73/149 (48.99%), Query Frame = 2 
Query:   56 IYRNPNGLYPVNPFPEDYPKRISAEKQDSTILKLDWSKCRMEKQR-EWHGYTGAIGYLPEPPLPSYSRYVAHSTCPPLMAGIKYHEFRRGKPVRESAPNTQYDYCQMGALSGPEIM---TRIIPRMVHSIRDDIPDSRQWRFDGRDHQL 490
            I RNP GLYPVN FPEDYP ++  +K       +DWS C  +     W GYTGA     E    S   Y  H +  P  A   + E R  +  ++++P+  Y+  Q+  L   EI     R I ++  S       S+ WR+DGRDH+L
Sbjct:    4 IQRNPTGLYPVNIFPEDYPVKMPVQKISIGPSDIDWSNCYQQHNLGSWRGYTGAKLLGKEQQGFSRKLYNTHKSVDP-RAYQTFPEIRDYEFYKDNSPSVPYNIIQLQNLRKSEIHLENKRDIFKLNSS-------SKIWRYDGRDHEL 144
[Close]
BLAST of SMED30031396 vs. Planmine SMEST
Match: SMESG000035386.1 (SMESG000035386.1)

HSP 1 Score: 75.8702 bits (185), Expect = 3.758e-16
Identity = 53/149 (35.57%), Postives = 73/149 (48.99%), Query Frame = 2 
Query:   56 IYRNPNGLYPVNPFPEDYPKRISAEKQDSTILKLDWSKCRMEKQR-EWHGYTGAIGYLPEPPLPSYSRYVAHSTCPPLMAGIKYHEFRRGKPVRESAPNTQYDYCQMGALSGPEIMT---RIIPRMVHSIRDDIPDSRQWRFDGRDHQL 490
            I RNP GLYPVN FPEDYP ++  +K       +DWS C  +     W GYTGA     E    S   Y  H +  P  A   + E R  +  ++++P+  Y+  Q+  L   EI     R I ++  S       S+ WR+DGRDH+L
Sbjct:   15 IQRNPTGLYPVNIFPEDYPVKMPVQKISIGPSDIDWSNCYQQHNLGSWRGYTGAKLLGKEQQGFSRKLYNTHKSVDP-RAYQTFPEIRDYEFYKDNSPSVPYNIIQLQNLRKSEIHLENKRDIFKLNSS-------SKIWRYDGRDHEL 155
The following BLAST results are available for this feature:
BLAST of SMED30031396 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 SMED30031396 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 SMED30031396 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 SMED30031396 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 SMED30031396 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 SMED30031396 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 SMED30031396 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 SMED30031396 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3P7REC15.720e-1835.62Uncharacterized protein OS=Dibothriocephalus latus... [more]
A0A183TGC01.353e-1734.25Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A075ADM25.442e-1734.48Uncharacterized protein OS=Opisthorchis viverrini ... [more]
A0A183VRL81.605e-1133.10Uncharacterized protein OS=Trichobilharzia regenti... [more]
A0A1I8GL571.104e-639.47Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30031396 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 SMED30031396 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 SMED30031396 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 SMED30031396 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 SMED30031396 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 SMED30031396 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000016750.15.096e-108100.00SMESG000016750.1[more]
SMESG000035386.13.196e-1635.57SMESG000035386.1[more]
SMESG000035386.13.758e-1635.57SMESG000035386.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031396 ID=SMED30031396|Name=SMED30031396|organism=Schmidtea mediterranea sexual|type=transcript|length=1229bp
CAATACTACAAACACTAATTAACAAATGGAAAACAATGAAGAGAGATTTG
TTCGAATTTATAGGAATCCTAACGGTTTGTATCCCGTAAATCCGTTTCCC
GAAGACTATCCGAAAAGAATTAGTGCTGAAAAGCAAGACAGTACGATATT
GAAATTGGACTGGTCAAAATGCAGAATGGAAAAGCAAAGAGAATGGCACG
GTTATACCGGGGCAATTGGATATCTCCCGGAACCCCCATTGCCATCATAT
AGTCGTTATGTTGCGCATAGTACTTGCCCACCATTAATGGCAGGCATCAA
ATATCATGAATTTCGTCGGGGAAAACCAGTTAGAGAATCTGCACCCAATA
CTCAATATGATTATTGTCAAATGGGAGCTCTATCTGGACCTGAAATTATG
ACAAGAATAATTCCACGCATGGTACATTCAATTAGAGATGATATTCCTGA
TTCCAGGCAGTGGCGTTTTGACGGAAGAGATCATCAATTATATTGATACT
CCTTTCAAATAAATTTTCTTTTTTGGAAAAATTAAATATTTTCTCATTCT
TTATAAATTTTTATTTCATTAACTTGAATTTTTAACTCAAAAAATGAAAC
TAAAACAAACACATTCGGTTAGCAGGGATTAACATTATGGACGGAAAATT
TTTCGCCAGATTTGGAAAGTATAGAAAGAAAAATTAATTGGGGAAAATAA
TATAAAAGTGTATTTCAACAAAACAAATGGCCAGTGTGTAAGGTAAAAGA
AATTGATATCTATTCGTATCCAAGAAGATAGTGTTATAATTTCAAAGAAA
GGAATGGATTAGCAACCAATGTGACGAGATGTAAGAGAGTTATGAAAGTG
AAATTTCCTATTTAAAGGTTTAGGAGAGTTTTTTGTGATGAAAATCATAC
ATCTTCAGAATAAAGTCCTTAAAACTGCTAATTAAATATTGTGCATCTAC
ATTAAGTTTTGAATACATGGAAATTTATTACGAATTGAATCAGCTTTTAT
ATCAAACGCTAAGTTTTTGGTAATTTGTGGGAAAAACTCAGACATACTCT
TAGAGTCCTTCTGAGCTGAAGTGTTTGAGTACTCAATAAAAACCAAGAAT
TGACGTCCAACAACTGAATACCATCGTCCAACGAGGAGAAAATTTCACGG
AAAATCTTATTATTTTTAGTGAAAATAGTGCGTACTTGAACTTGAAACTT
GTTTTCCTCCAATAATTTTGACACTATAG
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protein sequence of SMED30031396-orf-1

>SMED30031396-orf-1 ID=SMED30031396-orf-1|Name=SMED30031396-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=157bp
MENNEERFVRIYRNPNGLYPVNPFPEDYPKRISAEKQDSTILKLDWSKCR
MEKQREWHGYTGAIGYLPEPPLPSYSRYVAHSTCPPLMAGIKYHEFRRGK
PVRESAPNTQYDYCQMGALSGPEIMTRIIPRMVHSIRDDIPDSRQWRFDG
RDHQLY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ