SMED30030294

Overview
NameSMED30030294
Smed IDSMED30030294
Length (bp)1057
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 SMED30030294 (SMED30030294) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030294 (SMED30030294) 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 SMED30030294 (SMED30030294) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30030294 (SMED30030294) 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



SMED30030294

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30030294SMESG000026870.1 PL04016B2E04ncbi_smed_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
dorsal ventral margin of the whole animalSMED30030294SMESG000026870.1 PL04016B2E04ncbi_smed_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30030294SMESG000026870.1 PL04016B2E04ncbi_smed_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
protonephridiaSMED30030294SMESG000026870.1 dd_Smed_v4_2495_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30030294SMESG000026870.1 dd_Smed_v4_2495_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30030294SMESG000026870.1 dd_Smed_v4_2495_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30030294SMESG000026870.1 dd_Smed_v4_2495_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30030294SMESG000026870.1 dd_Smed_v4_2495_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030294SMESG000078691.1 SMESG000032258.1 SMESG000026870.1 SMESG000010388.1 SMESG000072628.1 SMESG000049466.1 SMESG000043394.1 SMESG000032682.1 SMESG000026600.1 SMESG000022674.1 SMESG000016243.1 Contig5552uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030294SMESG000078691.1 SMESG000032258.1 SMESG000026870.1 SMESG000010388.1 SMESG000072628.1 SMESG000049466.1 SMESG000043394.1 SMESG000032682.1 SMESG000026600.1 SMESG000022674.1 SMESG000016243.1 Contig5552newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030294SMESG000026870.1 Contig6473uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030294SMESG000026870.1 Contig6473newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030294 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005861:184..6507 -3872
Homology
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BLAST of SMED30030294 vs. TrEMBL
Match: A0A1S3HFX6 (syntaxin-7 isoform X1 OS=Lingula unguis OX=7574 GN=LOC106154937 PE=3 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 6.882e-9
Identity = 52/195 (26.67%), Postives = 110/195 (56.41%), Query Frame = 1 
Query:  277 MGGPHDTSQKRNKMXXXXXXXXXXXXFTQSLFESISHMHIYDEASRLTVTRVKEEYEKIVPKYNEVHEKVISKMTQMALEARQSMS---LMTSRNDDQISLMDQMTREDTDVQATEEML---LRVQQ--------LEKNLVQAENLFNEINKIVIESREDVEQIEVNVISANDDVNLGNEKLQQATVYKQKAKEK 819
            +G   D+ + R+++ + + K   ++A T  LF+ +S +   +   +L+V R++ ++++ + +Y+E+ +K   K+  +AL  R   S      + +DD+++LM+Q      ++QA E+++   L V Q        LE +++    +F ++  +V E  E ++ IE +V  A+D+V  GNE+L +A  Y++KA++K
Sbjct:   71 IGSDRDSKELRDRIHETELKTNKIIAETTKLFKQLSGIRGIERQQKLSVERIQNDFKETIQRYSELQKKAAEKVKTIALRQRTQSSEGLGFGASDDDKVALMEQDELRRQELQAQEQLIEDDLAVIQEREERIRELEADILDINEIFRDLGTLVYEQGEMIDNIEDHVSKAHDNVEAGNEQLVKAASYQKKARKK 265
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BLAST of SMED30030294 vs. TrEMBL
Match: A0A1S3HFV1 (syntaxin-7 isoform X2 OS=Lingula unguis OX=7574 GN=LOC106154937 PE=3 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 7.643e-9
Identity = 52/195 (26.67%), Postives = 110/195 (56.41%), Query Frame = 1 
Query:  277 MGGPHDTSQKRNKMXXXXXXXXXXXXFTQSLFESISHMHIYDEASRLTVTRVKEEYEKIVPKYNEVHEKVISKMTQMALEARQSMS---LMTSRNDDQISLMDQMTREDTDVQATEEML---LRVQQ--------LEKNLVQAENLFNEINKIVIESREDVEQIEVNVISANDDVNLGNEKLQQATVYKQKAKEK 819
            +G   D+ + R+++ + + K   ++A T  LF+ +S +   +   +L+V R++ ++++ + +Y+E+ +K   K+  +AL  R   S      + +DD+++LM+Q      ++QA E+++   L V Q        LE +++    +F ++  +V E  E ++ IE +V  A+D+V  GNE+L +A  Y++KA++K
Sbjct:   64 IGSDRDSKELRDRIHETELKTNKIIAETTKLFKQLSGIRGIERQQKLSVERIQNDFKETIQRYSELQKKAAEKVKTIALRQRTQSSEGLGFGASDDDKVALMEQDELRRQELQAQEQLIEDDLAVIQEREERIRELEADILDINEIFRDLGTLVYEQGEMIDNIEDHVSKAHDNVEAGNEQLVKAASYQKKARKK 258
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BLAST of SMED30030294 vs. TrEMBL
Match: A0A1S3J3Y4 (syntaxin-12 OS=Lingula unguis OX=7574 GN=LOC106169883 PE=3 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 3.125e-6
Identity = 57/224 (25.45%), Postives = 106/224 (47.32%), Query Frame = 1 
Query:  202 LVTRITNNLQQIRQITKDLGDLYLIMGGPHDTSQKRNKMXXXXXXXXXXXXFTQSLFESISHMHIYDEAS-----RLTVTRVKEEYEKIVPKYNEVHEKVISKMTQMALEARQSM----SLMTSRNDDQI------SLMDQMT---REDTDVQATEEMLLRVQQLEKNLVQAENLFNEINKIVIESREDVEQIEVNVISANDDVNLGNEKLQQATVYKQKAKEK 819
            L   I+NN+Q+I    K++  +   +G P D+ Q R+++ + Q +  DL   T   F+ ISH+ +    S     ++   R+ E++  ++ ++  +  +  +K       AR +     + +    + QI          Q T    ED D+Q  +E    ++QLE +++    +F ++  +V E  E ++ IE NV SA   V  G E+L +A  Y+ KA+ K
Sbjct:  275 LTQSISNNIQKISNNVKNIRRMVNQIGTPQDSDQLRDRLHESQHQTNDLAKSTTQYFKDISHLPVSSNQSDQRQRKMQRERLMEDFTSLLNEFQTLQREAANKEKASVRRARAASGHDSAFLEGPREQQIIDIGGGPPSRQQTLQMEEDVDLQLIQERETAIKQLESDIMDVNQIFKDLGMLVHEQGEVIDSIEANVESAQIQVEAGTEQLAKARDYQSKARRK 498
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BLAST of SMED30030294 vs. Planmine SMEST
Match: SMESG000026870.1 (SMESG000026870.1)

HSP 1 Score: 417.542 bits (1072), Expect = 6.608e-148
Identity = 220/225 (97.78%), Postives = 223/225 (99.11%), Query Frame = 1 
Query:  145 MAQNYGSVESIDTKDNVQNLVTRITNNLQQIRQITKDLGDLYLIMGGPHDTSQKRNKMXXXXXXXXXXXXFTQSLFESISHMHIYDEASRLTVTRVKEEYEKIVPKYNEVHEKVISKMTQMALEARQSMSLMTSRNDDQISLMDQMTREDTDVQATEEMLLRVQQLEKNLVQAENLFNEINKIVIESREDVEQIEVNVISANDDVNLGNEKLQQATVYKQKAKEK 819
            MAQNYGSVESIDTKDNVQNLVTRITNNLQQIRQITKDLGDLYLIMGGPHDTSQKRNKMLQLQQKAKDLLAFT+SLFESISHMHIYDEASRLTVTRVKEEYEKIVPKYNEVHEKVISKMTQMALEARQSMSLMTSRNDDQISLMDQMTREDTDVQATEEMLLRVQQLEKNLVQAENLFNEINKIVIESREDVEQIEVNVISANDD +LGNEKLQQATVYKQKA +K
Sbjct:    1 MAQNYGSVESIDTKDNVQNLVTRITNNLQQIRQITKDLGDLYLIMGGPHDTSQKRNKMLQLQQKAKDLLAFTKSLFESISHMHIYDEASRLTVTRVKEEYEKIVPKYNEVHEKVISKMTQMALEARQSMSLMTSRNDDQISLMDQMTREDTDVQATEEMLLRVQQLEKNLVQAENLFNEINKIVIESREDVEQIEVNVISANDDEDLGNEKLQQATVYKQKATKK 225
The following BLAST results are available for this feature:
BLAST of SMED30030294 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 SMED30030294 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 SMED30030294 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 SMED30030294 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 SMED30030294 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 SMED30030294 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 SMED30030294 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 SMED30030294 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A1S3HFX66.882e-926.67syntaxin-7 isoform X1 OS=Lingula unguis OX=7574 GN... [more]
A0A1S3HFV17.643e-926.67syntaxin-7 isoform X2 OS=Lingula unguis OX=7574 GN... [more]
A0A1S3J3Y43.125e-625.45syntaxin-12 OS=Lingula unguis OX=7574 GN=LOC106169... [more]
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BLAST of SMED30030294 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 SMED30030294 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 SMED30030294 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 SMED30030294 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 SMED30030294 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 SMED30030294 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000026870.16.608e-14897.78SMESG000026870.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030294 ID=SMED30030294|Name=SMED30030294|organism=Schmidtea mediterranea sexual|type=transcript|length=1057bp
CTGGAATTTTACACATTTGAATTTAACATTATAAATTAATACTTTGGTAG
TTTTATAAAAATATTTTATAACCAATTTAAAATAATTGTTTGAAGAATAT
TAAACTATTGTTCATAACAAATTATAATAACTTTTTATATACATATGGCT
CAAAATTATGGATCAGTAGAGAGTATTGACACCAAAGACAATGTACAAAA
TCTTGTTACTCGAATAACAAATAACTTACAGCAAATTCGTCAAATAACTA
AAGACCTAGGAGATCTCTACTTGATTATGGGTGGACCTCATGATACTTCA
CAGAAAAGAAATAAAATGTTACAATTACAACAAAAAGCCAAAGATCTTTT
GGCTTTTACACAATCCCTTTTTGAAAGTATTTCTCATATGCATATTTATG
ATGAAGCATCTCGACTTACAGTGACAAGAGTGAAAGAAGAGTATGAAAAG
ATTGTGCCAAAATACAATGAAGTTCACGAGAAAGTCATTTCCAAAATGAC
CCAAATGGCTCTCGAAGCCAGACAGTCCATGTCTTTAATGACATCAAGGA
ATGATGATCAGATCTCACTAATGGATCAAATGACTCGGGAAGACACTGAT
GTTCAAGCTACAGAAGAAATGCTACTTAGAGTTCAACAACTTGAGAAAAA
TCTAGTCCAAGCCGAAAACCTTTTCAATGAGATTAACAAGATTGTCATTG
AAAGTCGGGAAGATGTGGAACAAATAGAAGTTAACGTTATTAGTGCCAAT
GATGATGTGAACTTGGGAAATGAAAAGCTGCAACAAGCCACCGTTTATAA
ACAAAAGGCCAAAGAAAAAGATTTGCATAATTGTCACCGTCATAATAGTT
CTGGCCATCATCGGACTGATCATTGGATTGACTGTGAAGAAATAAAGTTT
TTTGATTCGAGTTCTTCCTTATCAGGAAAACAGTTTGAGAAGAATAATGA
TTTGTTTTTTACCAGTGAGCACGACAAATTCTATCTGTTTTCTAATTATA
TTCTATTAATTTTTTATAGTCAGATTCAATAAATTATATTGTATTTTGAA
AAAAAAA
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protein sequence of SMED30030294-orf-1

>SMED30030294-orf-1 ID=SMED30030294-orf-1|Name=SMED30030294-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=296bp
MAQNYGSVESIDTKDNVQNLVTRITNNLQQIRQITKDLGDLYLIMGGPHD
TSQKRNKMLQLQQKAKDLLAFTQSLFESISHMHIYDEASRLTVTRVKEEY
EKIVPKYNEVHEKVISKMTQMALEARQSMSLMTSRNDDQISLMDQMTRED
TDVQATEEMLLRVQQLEKNLVQAENLFNEINKIVIESREDVEQIEVNVIS
ANDDVNLGNEKLQQATVYKQKAKEKDLHNCHRHNSSGHHRTDHWIDCEEI
KFFDSSSSLSGKQFEKNNDLFFTSEHDKFYLFSNYILLIFYSQIQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000026gut
PLANA:0000043dorsal ventral margin of the whole animal
PLANA:0000070intestinal phagocyte
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR000727T_SNARE_dom
IPR010989SNARE
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0005484SNAP receptor activity
Vocabulary: biological process
TermDefinition
GO:0016192vesicle-mediated transport
GO:0006886intracellular protein transport
GO:0061025membrane fusion
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0005622intracellular
GO:0016021integral component of membrane