X1.A.G7.1

Overview
NameX1.A.G7.1 (AHD24744.1)
Smed IDSMED30000843
Length (bp)787
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 X1.A.G7.1 (SMED30000843) t-SNE clustered cells

Violin plots show distribution of expression levels for X1.A.G7.1 (SMED30000843) 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 X1.A.G7.1 (SMED30000843) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for X1.A.G7.1 (SMED30000843) 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



SMED30000843

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30000843SMESG000070405.1 SmedASXL_012618SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30000843SMESG000070405.1 SmedASXL_012618SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30000843SMESG000070405.1 dd_Smed_v4_4731_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30000843SMESG000070405.1 dd_Smed_v4_4731_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30000843SMESG000070405.1 dd_Smed_v4_4731_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30000843SMESG000070405.1 dd_Smed_v4_4731_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30000843SMESG000070405.1 dd_Smed_v4_4731_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30000843SMESG000070405.1 dd_Smed_v4_4731_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000843SMESG000070405.1 Contig48830newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000843SMESG000070405.1 Contig48830uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
zeta neoblastSMED30000843SMESG000070405.1 dd_Smed_v4_4731_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
Homology
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BLAST of X1.A.G7.1 vs. TrEMBL
Match: V9XRT9 (X1.A.G7.1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 365.925 bits (938), Expect = 3.630e-126
Identity = 201/206 (97.57%), Postives = 204/206 (99.03%), Query Frame = 2 
Query:  104 MSKKDCGDIYDQLSSSPPEYSQQPTNLLMNSTGIHSDQVQDGSVRLVLLESKEIRSGSKFINSKSHRIFGYILIACGVFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKXXXXXXXXXXXXXXXXXXXYGTAFYHRQNGTLIFTVFYGILTMSLLVLLIFNSALICKEICCRQQRMSQVQYVACEQPV 721
            MS+KDCGDIYDQLSSSPPEYSQQPTNLL+NSTGIHSDQVQDG VRLVLLESKEIRSGSKFINSKSHRIFGYILIACG+FVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKILNILALINIGIGILVAILYGTAFYHRQNG LIFTVFYGILTMSLLVLLIFNSALICKEICCRQQRMSQVQYVACEQPV
Sbjct:    1 MSQKDCGDIYDQLSSSPPEYSQQPTNLLINSTGIHSDQVQDGPVRLVLLESKEIRSGSKFINSKSHRIFGYILIACGIFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKILNILALINIGIGILVAILYGTAFYHRQNGILIFTVFYGILTMSLLVLLIFNSALICKEICCRQQRMSQVQYVACEQPV 206
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BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000070405.1 (SMESG000070405.1)

HSP 1 Score: 383.259 bits (983), Expect = 2.029e-136
Identity = 210/210 (100.00%), Postives = 210/210 (100.00%), Query Frame = 2 
Query:   98 MFMSKKDCGDIYDQLSSSPPEYSQQPTNLLMNSTGIHSDQVQDGSVRLVLLESKEIRSGSKFINSKSHRIFGYILIACGVFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKXXXXXXXXXXXXXXXXXXXYGTAFYHRQNGTLIFTVFYGILTMSLLVLLIFNSALICKEICCRQQRMSQVQYVACEQPVNI 727
            MFMSKKDCGDIYDQLSSSPPEYSQQPTNLLMNSTGIHSDQVQDGSVRLVLLESKEIRSGSKFINSKSHRIFGYILIACGVFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKILNILALINIGIGILVAILYGTAFYHRQNGTLIFTVFYGILTMSLLVLLIFNSALICKEICCRQQRMSQVQYVACEQPVNI
Sbjct:    1 MFMSKKDCGDIYDQLSSSPPEYSQQPTNLLMNSTGIHSDQVQDGSVRLVLLESKEIRSGSKFINSKSHRIFGYILIACGVFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKILNILALINIGIGILVAILYGTAFYHRQNGTLIFTVFYGILTMSLLVLLIFNSALICKEICCRQQRMSQVQYVACEQPVNI 210
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BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046775.1 (SMESG000046775.1)

HSP 1 Score: 134.806 bits (338), Expect = 1.300e-38
Identity = 90/201 (44.78%), Postives = 128/201 (63.68%), Query Frame = 2 
Query:  137 QLSSSPPEYSQQPTNLLMNSTGIHSDQVQDGSVRLVLLESKEIRSGSKFINSKSHRIFGYILIACGVFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKXXXXXXXXXXXXXXXXXXXY----------GTAFYHRQNGTLIFT-VFYGILTMSLLVLLIFNSALICKEICCRQQRMSQVQYVA 706
            Q + SPPEYS++   LL N T IH  QV  G + ++L +     S +KF NSK HRI+G ILI  GV ++ +DPLLPIL  YPF+I IAG+F IISG  SIQ V+ N K+YLI A I NIL+LIN GIGI++AI+               Y +    ++ T   + +L+ +L +LLIF++  IC+E+CC++Q+ S++Q+  
Sbjct:   20 QFTLSPPEYSEKSNYLLSNVTDIHPPQVAVGPICMILPQLYAPESQNKFWNSKLHRIYGSILIVFGVIIIILDPLLPILYRYPFTIVIAGIFTIISGCLSIQGVRSNKKVYLISAMIFNILSLINCGIGIIIAIIMVLTHNRFSGPCPRHYSQYCSNMVLTGAIHKVLSFALFLLLIFHTTTICREVCCKRQKASKIQFAT 220
[Close]
BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046786.1 (SMESG000046786.1)

HSP 1 Score: 132.88 bits (333), Expect = 7.203e-38
Identity = 93/204 (45.59%), Postives = 126/204 (61.76%), Query Frame = 2 
Query:  137 QLSSSPPEYSQQPTNLLMNSTGIHSDQVQDGSVRLVLLESKEIRSGSKFINSKSHRIFGYILIACGVFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKXXXXXXXXXX---XXXXXXXXXYGTAFYHRQNGTL-------IFT-VFYGILTMSLLVLLIFNSALICKEICCRQQRMSQVQYVACEQ 715
            Q + SPPEYS++   LL N T I S QV  G + ++L +S    S SKF  SK HRI+G ILI  GV ++ +DPLLPIL  YPF+I IAG+F I+SG  SIQ V+ N K+ LI A ILNIL+LIN     I  ++ +L  T F    N TL       + T    G+L+++L +LLIF++  IC+E+CC++Q+   VQY    Q
Sbjct:   20 QFTLSPPEYSEKSNYLLNNVTDIRSSQVPVGPICIILPQSDASESQSKFHFSKPHRIYGLILIVFGVIIIILDPLLPILYRYPFTIVIAGIFTIVSGSLSIQGVRSNKKVCLISAMILNILSLINCGIGIIVAIIMVLTHTHFTIPCNRTLSDFCSNIVKTGTILGVLSIALFLLLIFDTTTICREVCCKRQKAPNVQYATNVQ 223
[Close]
BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046788.1 (SMESG000046788.1)

HSP 1 Score: 127.102 bits (318), Expect = 7.484e-36
Identity = 89/205 (43.41%), Postives = 129/205 (62.93%), Query Frame = 2 
Query:  104 MSKKDCGDIYDQLSSSPPEYSQQPTNLLMNSTGIHSDQVQDGSVRLVLLESKEIRSGSKFINSKSHRIFGYILIACGVFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKXXXXXXXXXXXXXXXXXXXYGTAFYHRQNGTLIFTVFYGILTMSLLVLLIFNSALICKEICCRQQRMSQVQYVACEQP 718
            MS+K   +I  Q++ +PP YS+   +L+ N   I   QV  G V LVL +     S +KF + + HRIFG   + CG+ VL  DPL+PIL  Y FS+ IAG+FMIISG+FS QAV+RN K +L+ + ILNIL++INIG+GI++AI+         + T +  +F G+L   L +L+IF+S +IC+E    ++   QVQY+   QP
Sbjct:    1 MSEKGYDEIPYQINENPPGYSEHSRSLINNPVHIPPAQVPVGPVHLVLPQPNAAESLNKFHHKRLHRIFGNTFMVCGIIVLLFDPLIPILYGYSFSVCIAGLFMIISGVFSKQAVQRNKKAFLMVSNILNILSMINIGVGIIIAIIIIL------HSTWLLAIFTGLLYGCLFLLIIFDSVIICRE-NFNKKSFPQVQYIPYIQP 198
[Close]
BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046789.1 (SMESG000046789.1)

HSP 1 Score: 121.709 bits (304), Expect = 1.718e-33
Identity = 94/225 (41.78%), Postives = 136/225 (60.44%), Query Frame = 2 
Query:  104 MSKKDCGDIYDQLSSSPPEYSQQPTNLLMNSTGIHSDQVQDGSVRLVLLESKEIRSGSKFINSKSHRIFGYILIACGVFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKXXXXXXXXXXXXXXXXXXXYGTA-----------------FYHRQNGTLIFT--VFYGILTMSLLVLLIFNSALICKEICCRQQRMSQVQYVACEQPV 721
            MS +   +I  +L+  PP YS+   N    ST +   Q   G VR++  E       +KF  +K HRIFG ILIACG+ +L +DPL+P+L   PFSI IAG+FMI SG+ S+ AVKRN+KL +IF+ ILNIL+ +NI IG     ++  +                 F HRQ    IFT  +F+GI  + L++LLIF  ++I +E+CC+++++ +VQYVA EQP+
Sbjct:    1 MSSEISSNIPLKLNPDPPRYSEHQGN----STNVLPAQSSLGLVRILPTEPNSPPQQNKFGYTKLHRIFGQILIACGIIILLLDPLIPLLFGIPFSICIAGLFMIASGVMSLIAVKRNVKLLMIFSNILNILSSVNIAIGTAFHTIWAISYSPRKQCPKSDYVNPHCFEHRQQNLSIFTISIFFGIFNLFLVILLIFYISVINREMCCKKKKIPKVQYVAYEQPL 221
The following BLAST results are available for this feature:
BLAST of X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XRT93.630e-12697.57X1.A.G7.1 (Fragment) OS=Schmidtea mediterranea OX=... [more]
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BLAST of X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000070405.12.029e-136100.00SMESG000070405.1[more]
SMESG000046775.11.300e-3844.78SMESG000046775.1[more]
SMESG000046786.17.203e-3845.59SMESG000046786.1[more]
SMESG000046788.17.484e-3643.41SMESG000046788.1[more]
SMESG000046789.11.718e-3341.78SMESG000046789.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30000843
GenBankAHD24744.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000843 ID=SMED30000843|Name=X1.A.G7.1|organism=Schmidtea mediterranea sexual|type=transcript|length=787bp
ATCTAAACAAAGTCTCAATATTTAGAATTTATACTAAATATCTTGTTTTA
AATCTCTCTGTGGATTTTTATCTATTATATAAAATTTATAAGCGAAAATG
TTTATGTCTAAAAAAGATTGCGGCGATATTTATGACCAACTTAGTTCAAG
TCCGCCAGAATATTCTCAACAGCCAACTAATTTATTGATGAATTCCACTG
GTATTCATTCTGATCAAGTTCAGGATGGTTCAGTTCGATTGGTACTGCTA
GAATCGAAAGAGATTAGAAGTGGTAGTAAATTTATAAACAGTAAATCGCA
TAGAATATTTGGATATATTCTAATTGCTTGTGGGGTTTTTGTACTTTGTA
TTGATCCATTATTGCCAATACTTCTCGAATATCCGTTTTCAATTTCAATC
GCAGGTGTATTTATGATTATCAGTGGAATTTTCTCAATTCAAGCCGTTAA
AAGAAATTTAAAGCTCTATCTAATATTTGCGAAAATATTGAATATTTTGG
CATTGATTAATATTGGAATTGGTATACTTGTAGCTATTCTATATGGAACT
GCTTTCTATCATAGGCAAAATGGAACACTCATCTTTACCGTATTCTATGG
AATTCTAACAATGAGCTTACTAGTTCTGCTCATTTTTAACAGCGCATTAA
TATGCAAAGAGATTTGTTGCCGACAACAAAGAATGTCCCAAGTCCAATAT
GTCGCATGTGAACAACCAGTTAATATATGAAAGTGTAAATAAAATTTGTT
CCAATTTTACTGTTTCATTAAAAATCAATTAAGAAAA
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protein sequence of SMED30000843-orf-1

>SMED30000843-orf-1 ID=SMED30000843-orf-1|Name=SMED30000843-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=211bp
MFMSKKDCGDIYDQLSSSPPEYSQQPTNLLMNSTGIHSDQVQDGSVRLVL
LESKEIRSGSKFINSKSHRIFGYILIACGVFVLCIDPLLPILLEYPFSIS
IAGVFMIISGIFSIQAVKRNLKLYLIFAKILNILALINIGIGILVAILYG
TAFYHRQNGTLIFTVFYGILTMSLLVLLIFNSALICKEICCRQQRMSQVQ
YVACEQPVNI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000099neuron
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 71..93
NoneNo IPR availableTMHMMTMhelixcoord: 162..184
NoneNo IPR availableTMHMMTMhelixcoord: 130..152
NoneNo IPR availableTMHMMTMhelixcoord: 98..117