SMED30023017

Overview
NameSMED30023017
Smed IDSMED30023017
Length (bp)799
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30023017 (SMED30023017) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023017 (SMED30023017) 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.
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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



SMED30023017

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30023017h1SMcG0002113 SmedASXL_013733SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30023017h1SMcG0002113 dd_Smed_v4_1320_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30023017h1SMcG0002113 dd_1320dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
Smed sexual biotypeSMED30023017h1SMcG0002113 Contig42151uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023017h1SMcG0002113 Contig42151newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023017h1SMcG0002113 Contig4598GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023017h1SMcG0002113 Contig33706newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023017h1SMcG0002113 Contig33706uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023017h1SMcG0016518 Contig4598GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
parapharyngeal regionSMED30023017h1SMcG0002113 dd_Smed_v6_1320_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023017 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014976:14873..15971 +3783
v31.019097:14135..15230 -3670
Homology
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BLAST of SMED30023017 vs. Planmine SMEST
Match: SMESG000065348.1 (SMESG000065348.1)

HSP 1 Score: 342.428 bits (877), Expect = 2.141e-120
Identity = 202/202 (100.00%), Postives = 202/202 (100.00%), Query Frame = 2 
Query:  137 MRMVSKVFILSVIGVILQLCLGQQDFIASDKTDENLQVQLKAFSELQEDNKNKEKQWNNYWTSYPPNNEGRNTDQMSTSDYNWNRGSTASPKVDEITTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKVEQLIKRNNGKNKSSQLIRYLRRVVPNYQRKISLWNRTNCRTYRRSSDFCKIIRDIQSSLGDIARFLKQTQGY 742
            MRMVSKVFILSVIGVILQLCLGQQDFIASDKTDENLQVQLKAFSELQEDNKNKEKQWNNYWTSYPPNNEGRNTDQMSTSDYNWNRGSTASPKVDEITTRASNNSSRNKWRRRIVRIERELRSLRRRISKVEQLIKRNNGKNKSSQLIRYLRRVVPNYQRKISLWNRTNCRTYRRSSDFCKIIRDIQSSLGDIARFLKQTQGY
Sbjct:    1 MRMVSKVFILSVIGVILQLCLGQQDFIASDKTDENLQVQLKAFSELQEDNKNKEKQWNNYWTSYPPNNEGRNTDQMSTSDYNWNRGSTASPKVDEITTRASNNSSRNKWRRRIVRIERELRSLRRRISKVEQLIKRNNGKNKSSQLIRYLRRVVPNYQRKISLWNRTNCRTYRRSSDFCKIIRDIQSSLGDIARFLKQTQGY 202
[Close]
BLAST of SMED30023017 vs. Planmine SMEST
Match: SMESG000065348.1 (SMESG000065348.1)

HSP 1 Score: 337.806 bits (865), Expect = 1.560e-118
Identity = 200/200 (100.00%), Postives = 200/200 (100.00%), Query Frame = 2 
Query:  143 MVSKVFILSVIGVILQLCLGQQDFIASDKTDENLQVQLKAFSELQEDNKNKEKQWNNYWTSYPPNNEGRNTDQMSTSDYNWNRGSTASPKVDEITTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKVEQLIKRNNGKNKSSQLIRYLRRVVPNYQRKISLWNRTNCRTYRRSSDFCKIIRDIQSSLGDIARFLKQTQGY 742
            MVSKVFILSVIGVILQLCLGQQDFIASDKTDENLQVQLKAFSELQEDNKNKEKQWNNYWTSYPPNNEGRNTDQMSTSDYNWNRGSTASPKVDEITTRASNNSSRNKWRRRIVRIERELRSLRRRISKVEQLIKRNNGKNKSSQLIRYLRRVVPNYQRKISLWNRTNCRTYRRSSDFCKIIRDIQSSLGDIARFLKQTQGY
Sbjct:    1 MVSKVFILSVIGVILQLCLGQQDFIASDKTDENLQVQLKAFSELQEDNKNKEKQWNNYWTSYPPNNEGRNTDQMSTSDYNWNRGSTASPKVDEITTRASNNSSRNKWRRRIVRIERELRSLRRRISKVEQLIKRNNGKNKSSQLIRYLRRVVPNYQRKISLWNRTNCRTYRRSSDFCKIIRDIQSSLGDIARFLKQTQGY 200
[Close]
BLAST of SMED30023017 vs. Planmine SMEST
Match: SMESG000065355.1 (SMESG000065355.1)

HSP 1 Score: 55.4546 bits (132), Expect = 2.470e-9
Identity = 50/201 (24.88%), Postives = 90/201 (44.78%), Query Frame = 2 
Query:  128 DSKMRMVSKVFILSVIGVILQLCLGQQDFIASDKTDENLQ--VQLKAFSELQEDNKNKEKQWNNYWTSYPPNNEGRNTDQMSTSDYNWNRGSTASPKVDEITTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKVEQLIKRNNGKNKSSQLIRYLRRVVPNYQRKISLWNRTNCRTYRRSSDFCKIIRDIQSSLGDIARFL 724
            + KM+ ++ +F L+++            F++    D N +  ++LK  +   ++N N+EKQ+  Y+T               TS YN N  +T  P  ++I    S   +                        ++ +I + N  N++  L+ YLRR+VP+Y+R +   NR  C  Y  +   C++IRD+Q  L  ++RFL
Sbjct:   17 NKKMKFINIIFYLAILA-----------FVSCGNYDSNSEEDLELKELTAENDENDNQEKQY--YYT---------------TSLYNRNYRTTP-PTNNKIARLESLLQNIYSRLNY-----------------LQTIINQKN--NRNGPLLGYLRRIVPSYRRSLVQINRKYCGRYSANKGLCQLIRDVQLVLNRVSRFL 169
[Close]
BLAST of SMED30023017 vs. Planmine SMEST
Match: SMESG000065350.1 (SMESG000065350.1)

HSP 1 Score: 57.3806 bits (137), Expect = 2.680e-9
Identity = 25/60 (41.67%), Postives = 38/60 (63.33%), Query Frame = 2 
Query:  545 NNGKNKSSQLIRYLRRVVPNYQRKISLWNRTNCRTYRRSSDFCKIIRDIQSSLGDIARFL 724
            N   N++  L+ YLRR+VP+Y+R +   NR  C  Y  + + CK+IRD+Q  L  ++RFL
Sbjct:  292 NQKNNRNGPLLGYLRRIVPSYRRSLVQINRKYCEQYSANKELCKLIRDVQLVLNRVSRFL 351
[Close]
BLAST of SMED30023017 vs. Planmine SMEST
Match: SMESG000065350.1 (SMESG000065350.1)

HSP 1 Score: 56.9954 bits (136), Expect = 4.906e-9
Identity = 25/60 (41.67%), Postives = 38/60 (63.33%), Query Frame = 2 
Query:  545 NNGKNKSSQLIRYLRRVVPNYQRKISLWNRTNCRTYRRSSDFCKIIRDIQSSLGDIARFL 724
            N   N++  L+ YLRR+VP+Y+R +   NR  C  Y  + + CK+IRD+Q  L  ++RFL
Sbjct:  443 NQKNNRNGPLLGYLRRIVPSYRRSLVQINRKYCEQYSANKELCKLIRDVQLVLNRVSRFL 502
The following BLAST results are available for this feature:
BLAST of SMED30023017 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 SMED30023017 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 SMED30023017 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 SMED30023017 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 SMED30023017 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 SMED30023017 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 SMED30023017 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 SMED30023017 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 SMED30023017 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 SMED30023017 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 SMED30023017 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 SMED30023017 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 SMED30023017 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 SMED30023017 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000065348.12.141e-120100.00SMESG000065348.1[more]
SMESG000065348.11.560e-118100.00SMESG000065348.1[more]
SMESG000065355.12.470e-924.88SMESG000065355.1[more]
SMESG000065350.12.680e-941.67SMESG000065350.1[more]
SMESG000065350.14.906e-941.67SMESG000065350.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023017 ID=SMED30023017|Name=SMED30023017|organism=Schmidtea mediterranea sexual|type=transcript|length=799bp
TACAATCTGAATTTTTGAGCAGATTGATATCAATATTGTTAAAACCGTCT
GAAAAGTCTATCATCTCAATTCTGTCAAGTCAACTGGACTATAATAAAGA
TATAAAAGGTCTTGTTGAAATCAAATAGACAGCAAAATGAGGATGGTATC
GAAGGTATTTATACTATCTGTGATTGGGGTTATTCTCCAGTTATGCTTGG
GGCAGCAGGATTTTATTGCGTCTGATAAGACTGATGAGAACCTACAAGTT
CAACTGAAGGCATTCTCTGAACTCCAGGAAGATAATAAGAATAAGGAGAA
ACAATGGAATAATTATTGGACTTCGTATCCTCCAAATAATGAAGGTCGAA
ACACAGATCAAATGTCAACGTCTGACTATAACTGGAATCGAGGATCTACG
GCCTCTCCAAAAGTAGATGAGATAACAACGAGGGCTTCTAATAATTCTTC
CAGGAATAAATGGAGAAGACGAATAGTGAGAATTGAAAGGGAGCTGCGAT
CGTTAAGAAGGCGAATAAGCAAAGTAGAACAATTGATAAAAAGAAACAAT
GGAAAAAATAAAAGTAGTCAATTAATTAGATATCTTCGTCGAGTAGTACC
AAATTATCAACGTAAAATTTCTCTGTGGAATCGTACTAATTGCAGGACAT
ATAGAAGGTCCAGTGATTTCTGCAAGATAATCAGGGATATTCAATCCTCC
TTGGGTGATATTGCAAGGTTTTTGAAGCAAACTCAAGGATATTAAATGAC
TTAGTTTATCATTAGCAAATAAACATTTTTATTTATTCTTAAAAAAAAA
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protein sequence of SMED30023017-orf-1

>SMED30023017-orf-1 ID=SMED30023017-orf-1|Name=SMED30023017-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=203bp
MRMVSKVFILSVIGVILQLCLGQQDFIASDKTDENLQVQLKAFSELQEDN
KNKEKQWNNYWTSYPPNNEGRNTDQMSTSDYNWNRGSTASPKVDEITTRA
SNNSSRNKWRRRIVRIERELRSLRRRISKVEQLIKRNNGKNKSSQLIRYL
RRVVPNYQRKISLWNRTNCRTYRRSSDFCKIIRDIQSSLGDIARFLKQTQ
GY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000420parapharyngeal region