SMED30002352

Overview
NameSMED30002352
Smed IDSMED30002352
Length (bp)1060
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



SMED30002352

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
nervous systemSMED30002352 dd_Smed_v4_23734_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002352 dd_Smed_v4_23734_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30002352 dd_Smed_v4_23734_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30002352 dd_Smed_v4_23734_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
body wall musculatureSMED30002352 dd_Smed_v4_23734_0_1dd_Smed_v4PMID:30471994
Scimone 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 SMED30002352 vs. Planmine SMEST
Match: SMESG000071708.1 (SMESG000071708.1)

HSP 1 Score: 114.005 bits (284), Expect = 4.034e-38
Identity = 89/250 (35.60%), Postives = 120/250 (48.00%), Query Frame = -1 
Query:   26 GHIQIPASLLNKTCXXXXXXXXXXXX*TLI-------KVDGYHINRTSNYNPPDLVFSSSDFPMRLCNIPNFDMQNHSYDEGIVT-DNDDVINTF-------------------------NFVY-----SYHYIAITYFDRLLN--C*TLSGVRIQSKWCHRCLVGFKLDDAFEKHMDLCAKN*LGTTSH----NGYVTNXXXXXXXXXXXXXXXXFEAILSKNDKYFQ*RLPVLIGLLLINSITCDKLY 643
            G I  P SLLNK C  N        F   I        +  +H N T +YN  DL FS SD PM+LC+IP F+ +N +    ++T D +++IN F                         N +      SYHYIA+T  DRLLN    + +  R+QS WCHRCL GF+   +  KH  LC KN LGTT +    N  +       ++    +    FEAIL  +D +FQ  +P+  GLLLIN+ T +K Y
Sbjct: 1326 GFIPTPLSLLNKHCTVNVANSDNLCFIYSILAILNHENIGNHHRNETFSYNTSDLDFSPSDLPMKLCDIPKFEAKNQNLSINVLTYDENNLINDFSNPEVFKHPYVEIIHRSKVVGGQPINLILLESLDSYHYIAVTKLDRLLNYRNHSFTDTRVQSIWCHRCLNGFRNIISLNKHKGLCDKNQLGTTLYTLPLNKNLEFKNWAKTVTPPFVLYADFEAILPSDDIHFQIHMPISAGLLLINNFTGEKSY 1575

HSP 2 Score: 52.7582 bits (125), Expect = 4.034e-38
Identity = 26/41 (63.41%), Postives = 31/41 (75.61%), Query Frame = -2 
Query:  748 HFCIDVKFEKDGEFQYFIISNSSK----PFLDEGIALMKER 858
             FCIDV+FEKDGEFQ FIISNS++     FLDEG  L+ E+
Sbjct: 1250 QFCIDVEFEKDGEFQSFIISNSARIMNDSFLDEGATLLDEK 1290

HSP 3 Score: 31.187 bits (69), Expect = 4.034e-38
Identity = 14/31 (45.16%), Postives = 23/31 (74.19%), Query Frame = -3 
Query:  660 KEITKVRENGGNWMINKIKVNNFKLTKYLKL 752
            ++IT + + G NW+INKIK  +F LTK+ ++
Sbjct: 1289 EKITLINDKGSNWVINKIKEIHFVLTKFSQI 1319
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BLAST of SMED30002352 vs. Planmine SMEST
Match: SMESG000033494.1 (SMESG000033494.1)

HSP 1 Score: 110.923 bits (276), Expect = 3.107e-37
Identity = 87/245 (35.51%), Postives = 117/245 (47.76%), Query Frame = -1 
Query:   41 GHIQIPASLLNKTCXXXXXXXXXXXX*TLI-------KVDGYHINRTSNYNPPDLVFSSSDFPMRLCNIPNFDMQNHSYDEGIVT-DNDDVINTF-------------------------NFVY-----SYHYIAITYFDRLLN--C*TLSGVRIQSKWCHRCLVGFKLDDAFEKHMDLCAKN*LGTTSH----NGYVTNXXXXXXXXXXXXXXXXFEAILSKNDKYFQ*RLPVLIGLLLINSIT 643
            G I  P SLLNK C  N        F   I        +  +H N T +YN  +L FS SD PM+LC+IP F+ +N +    ++T D +++IN F                         N +      SYHYIA+T  DRLLN    + +  R+QS WCHRCL GF+   +  KH  LC KN LGTT +    N  +       ++    +    FEAIL  +D YFQ  +P+  GLLLIN+ T
Sbjct: 1032 GFIPTPLSLLNKHCTVNVANSDNLCFIYSILAILNHENIGNHHRNETFSYNTSELDFSPSDLPMKLCDIPKFEAKNQNLSINVLTYDENNLINDFSNPEIFKHPHVEIIHRSKVVGGQPINLILLESLDSYHYIAVTKLDRLLNYRNHSFTDTRVQSIWCHRCLNGFRNIISLNKHKGLCDKNQLGTTLYTLPLNKNLEFKNWAKTVTPPFVLYADFEAILPSDDIYFQIHMPISAGLLLINNFT 1276

HSP 2 Score: 52.373 bits (124), Expect = 3.107e-37
Identity = 26/41 (63.41%), Postives = 31/41 (75.61%), Query Frame = -2 
Query:  748 HFCIDVKFEKDGEFQYFIISNSSK----PFLDEGIALMKER 858
             FCIDV+FEKDGEFQ FIISNS++     FLDEG  L+ E+
Sbjct:  956 QFCIDVEFEKDGEFQSFIISNSARIMNDSFLDEGATLLDEK 996

HSP 3 Score: 31.187 bits (69), Expect = 3.107e-37
Identity = 14/31 (45.16%), Postives = 23/31 (74.19%), Query Frame = -3 
Query:  660 KEITKVRENGGNWMINKIKVNNFKLTKYLKL 752
            ++IT + + G NW+INKIK  +F LTK+ ++
Sbjct:  995 EKITLINDKGSNWVINKIKEIHFVLTKFSQI 1025
[Close]
BLAST of SMED30002352 vs. Planmine SMEST
Match: SMESG000033494.1 (SMESG000033494.1)

HSP 1 Score: 110.923 bits (276), Expect = 3.108e-37
Identity = 87/246 (35.37%), Postives = 117/246 (47.56%), Query Frame = -1 
Query:   38 GHIQIPASLLNKTCXXXXXXXXXXXX*TLI-------KVDGYHINRTSNYNPPDLVFSSSDFPMRLCNIPNFDMQNHSYDEGIVT-DNDDVINTF-------------------------NFVY-----SYHYIAITYFDRLLN--C*TLSGVRIQSKWCHRCLVGFKLDDAFEKHMDLCAKN*LGTTSH----NGYVTNXXXXXXXXXXXXXXXXFEAILSKNDKYFQ*RLPVLIGLLLINSITC 643
            G I  P SLLNK C  N        F   I        +  +H N T +YN  +L FS SD PM+LC+IP F+ +N +    ++T D +++IN F                         N +      SYHYIA+T  DRLLN    + +  R+QS WCHRCL GF+   +  KH  LC KN LGTT +    N  +       ++    +    FEAIL  +D YFQ  +P+  GLLLIN+ T 
Sbjct: 1032 GFIPTPLSLLNKHCTVNVANSDNLCFIYSILAILNHENIGNHHRNETFSYNTSELDFSPSDLPMKLCDIPKFEAKNQNLSINVLTYDENNLINDFSNPEIFKHPHVEIIHRSKVVGGQPINLILLESLDSYHYIAVTKLDRLLNYRNHSFTDTRVQSIWCHRCLNGFRNIISLNKHKGLCDKNQLGTTLYTLPLNKNLEFKNWAKTVTPPFVLYADFEAILPSDDIYFQIHMPISAGLLLINNFTV 1277

HSP 2 Score: 52.7582 bits (125), Expect = 3.108e-37
Identity = 26/41 (63.41%), Postives = 31/41 (75.61%), Query Frame = -2 
Query:  748 HFCIDVKFEKDGEFQYFIISNSSK----PFLDEGIALMKER 858
             FCIDV+FEKDGEFQ FIISNS++     FLDEG  L+ E+
Sbjct:  956 QFCIDVEFEKDGEFQSFIISNSARIMNDSFLDEGATLLDEK 996

HSP 3 Score: 31.187 bits (69), Expect = 3.108e-37
Identity = 14/31 (45.16%), Postives = 23/31 (74.19%), Query Frame = -3 
Query:  660 KEITKVRENGGNWMINKIKVNNFKLTKYLKL 752
            ++IT + + G NW+INKIK  +F LTK+ ++
Sbjct:  995 EKITLINDKGSNWVINKIKEIHFVLTKFSQI 1025
[Close]
BLAST of SMED30002352 vs. Planmine SMEST
Match: SMESG000008378.1 (SMESG000008378.1)

HSP 1 Score: 109.768 bits (273), Expect = 6.719e-26
Identity = 76/212 (35.85%), Postives = 108/212 (50.94%), Query Frame = -1 
Query:   26 VDGYHINRTSNYNPPDLVFSSSDFPMRLCNIPNFDMQNHSYDEGIVT-DNDDVINTF-------------------------NFVY-----SYHYIAITYFDRLLN--C*TLSGVRIQSKWCHRCLVGFKLDDAFEKHMDLCAKN*LGTTSH----NGYVTNXXXXXXXXXXXXXXXXFEAILSKNDKYFQ*RLPVLIGLLLINSITCDKLY 550
            +  +H N T +YN  +L FS SD PM+LC+IP F+ +N +    ++T D +++IN F                         N +      SYHYIA+T  DRLLN    + +  R+QS WCHRCL GF+   +  KH  LC KN LGTT +    N  +       ++    +    FEAIL  +D +FQ  +P+  GLLLIN+ T +K Y
Sbjct: 1335 IGNHHRNETFSYNTSELDFSPSDLPMKLCDIPKFEAKNQNLSINVLTYDENNLINDFSNPEVFKHPYVEIIHRSKVVGGQPINLILLESLDSYHYIAVTKLDRLLNYRNHSFTDTRVQSIWCHRCLNGFRNIISLNKHKGLCDKNQLGTTLYTLPLNKNLEFKNWAKTVTPPFVLHADFEAILPSDDIHFQIHMPISAGLLLINNFTGEKSY 1546
[Close]
BLAST of SMED30002352 vs. Planmine SMEST
Match: SMESG000072420.1 (SMESG000072420.1)

HSP 1 Score: 92.8189 bits (229), Expect = 1.989e-23
Identity = 76/252 (30.16%), Postives = 112/252 (44.44%), Query Frame = -1 
Query:   26 IECQGHIQIPASLLNKTCXXXXXXXXXX----XX*TLIKVDG---YHINRTSNYNP--PDLVFSSSDFPMRLCNIPNFDMQNH-------SYDEGIVTDNDDVINTFNFV----------------------YSYHYIAITYFDRLLNC*TLSGVRIQSKWCHRCLVGFKLDDAFEKHMDLCAKN*LGTT----SHNGYVTNXXXXXXXXXXXXXXXXFEAILSKNDKYFQ*RLPVLIGLLLINSITCDKLY 655
            +  + +I+ P  L NK CI N              +++K D     H NR  +Y     +L +  +D PM+L  I  F+  N        SYDE    ++DD +    F+                        YHY+ IT  +RLLNC   +  RI+S WCHRCL GF+   A +KH  LC +N LGTT      N ++       ++    +    FE++L K+D + Q  LP+  GLLLIN+     +Y
Sbjct: 1952 LSGRSYIKTPKKLANKYCITNVKDSDNLCFIYSILSILKKDEIVRQHRNRIYSYTKYLNELNYDPNDMPMKLNGIRKFESNNEGLIINIFSYDETAKPEHDDFVLKHPFINIIHRSKITEGTIINLLLLNNGKQYHYVGITSLNRLLNCKDKTTERIRSLWCHRCLNGFRNKKALDKHEILCMRNQLGTTLYTFPENKFIKFTDWSKTVTPPYVIYADFESVLPKDDVHHQIHLPISAGLLLINNFDGSTIY 2203

HSP 2 Score: 35.039 bits (79), Expect = 1.989e-23
Identity = 18/41 (43.90%), Postives = 27/41 (65.85%), Query Frame = -2 
Query:  748 HFCIDVKFEKDGEFQYFIISNSSKP----FLDEGIALMKER 858
             F I+++FEKDGE +   ISNS++P    F D+GI  + E+
Sbjct: 1880 QFGIEIEFEKDGEIKLNNISNSARPLTQSFFDDGIQKINEK 1920
The following BLAST results are available for this feature:
BLAST of SMED30002352 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 SMED30002352 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 SMED30002352 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 SMED30002352 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 SMED30002352 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 SMED30002352 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 SMED30002352 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 SMED30002352 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 SMED30002352 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 SMED30002352 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 SMED30002352 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 SMED30002352 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 SMED30002352 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 SMED30002352 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000071708.14.034e-3835.60SMESG000071708.1[more]
SMESG000033494.13.107e-3735.51SMESG000033494.1[more]
SMESG000033494.13.108e-3735.37SMESG000033494.1[more]
SMESG000008378.16.719e-2635.85SMESG000008378.1[more]
SMESG000072420.11.989e-2330.16SMESG000072420.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002352 ID=SMED30002352|Name=SMED30002352|organism=Schmidtea mediterranea sexual|type=transcript|length=1060bp
TATATGTATATGTGTGTATATATATATATAATTTGTCACAAGTAATACTA
TTTATTAATAATAAACCAATTAAAACAGGCAAGCGTCACTGGAAATATTT
ATCATTTTTAGATAAAATAGCCTCGAAACACAACAAAAAGAGGAGTAGCG
ATCTTAGACTAATAATTAAACGACAATTCGTTACATAACCATTATGTGAC
GTTGTTCCTAACTAATTTTTTGCACATAAATCCATATGTTTCTCAAAAGC
ATCATCCAATTTAAAACCAACCAAGCATCGATGACACCATTTACTCTGAA
TTCTAACACCGGAAAGAGTCTAACAATTCAACAATCTATCAAAATAAGTG
ATTGCTATGTAGTGATAGGAATAAACAAAATTAAATGTATTAATTACATC
ATCATTATCTGTAACAATTCCTTCATCGTAACTATGATTTTGCATATCAA
AATTGGGAATATTACAGAGTCGCATTGGGAAATCGGAAGAACTAAAAACA
AGGTCAGGTGGGTTATAATTAGACGTTCTATTTATATGATAACCATCAAC
CTTTATCAAGGTTCAAAATTTCTAAAATATTATAAAAAACTAATTAAATA
TGCAAGTTTTATTTAATAAGGATGCCGGAATTTGAATATGACCCTGACAC
TCAATCTACTAATTTTAAATATTTTGTCAATTTAAAATTATTTACTTTAA
TTTTGTTAATCATCCAGTTGCCACCATTTTCTCTTACTTTAGTAATTTCT
TTCCTTCATAAGAGCAATACCTTCATCTAAGAAAGGTTTGGACGAGTTTG
AAATTATAAAATATTGGAATTCTCCATCCTTTTCAAATTTAACATCAATA
CAGAAGTGGAAGTTACTCGGTTATAGAATTCATCATCATCATGGGAACTG
TTTTGACAGTAAACAGGGTATAAATTACGTTAATTGAGGAAAATTTAAAT
ACATAAATTTGTTTTAATTAAAAGTTTGTTCACTCATAAAATTATTTAAA
AATTGGTGCGAATTATTTTTAAATTATAGAAAACGATTAAGAAAAAGATT
AATAAAATAA
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protein sequence of SMED30002352-orf-1

>SMED30002352-orf-1 ID=SMED30002352-orf-1|Name=SMED30002352-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=127bp
MFLKSIIQFKTNQASMTPFTLNSNTGKSLTIQQSIKISDCYVVIGINKIK
CINYIIIICNNSFIVTMILHIKIGNITESHWEIGRTKNKVRWVIIRRSIY
MITINLYQGSKFLKYYKKLIKYASFI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000240body wall musculature