SMED30025311

Overview
NameSMED30025311
Smed IDSMED30025311
Length (bp)925
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 SMED30025311 (SMED30025311) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30025311 (SMED30025311) 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




SMED30025311

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30025311SMESG000016276.1 SmedASXL_001121SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30025311SMESG000016276.1 dd_Smed_v4_38236_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30025311SMESG000016276.1 dd_Smed_v4_38236_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30025311SMESG000016276.1 dd_Smed_v6_38236_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
SMED30025311 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004247:11045..12013 +4536
Homology
BLAST of SMED30025311 vs. Planmine SMEST
Match: SMESG000016276.1 (SMESG000016276.1)

HSP 1 Score: 515.768 bits (1327), Expect = 0.000e+0
Identity = 270/284 (95.07%), Postives = 277/284 (97.54%), Query Frame = 3
Query:   33 MLILLYISFVINANAGEIYLAVSSCVFNPMMTIPTQSLTECALKCSELNCKLFYVQPNSSSCYLYAFSEVCQSNTACPNVSGFINNKYNNLFQGDSSEIGYQILQNVNSPFASGTPSAFGILNPQQVFLLTLGRDKKPILAVGKYKNSNLLVFPKAXXXXXXXXXXXQLLLNVLRYFTNGSCTSSLACYVSVANYLNYVGIRGKVFGVNPFTVVNVTNLINLATSMDWHFVVAGTFWSQTATSSVKDLVKLFGLCISSEYGSSDFIIRNNVCVNVTSYTSPSCS 884
            M + +Y+S    ++AGEIYLAVSSCVFNPMMTIPTQSLTECALKCSEL+CKLFYVQPNSSSCYLYAFSEVCQSNTACPNVSGFINNKYNNLFQGDSSEIGYQILQNVNS FASGTPSAFGILNPQQVFLLTLGRDKKPILAVGKYKNSNLLVFPKASTESFTTETTSQLLLNVLRYFTNGSCTSSLACYVSVANYLNYVGIRGKVFGVNPFTVVNVTNLINLATSMDWHFVVAGTFWSQTATSSVKDLVKLFGLCISSEYGSSDFIIRNNVCVNVTSYTSP+CS
Sbjct:    1 MRVPIYLS----SHAGEIYLAVSSCVFNPMMTIPTQSLTECALKCSELHCKLFYVQPNSSSCYLYAFSEVCQSNTACPNVSGFINNKYNNLFQGDSSEIGYQILQNVNSTFASGTPSAFGILNPQQVFLLTLGRDKKPILAVGKYKNSNLLVFPKASTESFTTETTSQLLLNVLRYFTNGSCTSSLACYVSVANYLNYVGIRGKVFGVNPFTVVNVTNLINLATSMDWHFVVAGTFWSQTATSSVKDLVKLFGLCISSEYGSSDFIIRNNVCVNVTSYTSPACS 280          
BLAST of SMED30025311 vs. Planmine SMEST
Match: SMESG000016276.1 (SMESG000016276.1)

HSP 1 Score: 484.182 bits (1245), Expect = 7.642e-175
Identity = 252/255 (98.82%), Postives = 254/255 (99.61%), Query Frame = 3
Query:  120 MMTIPTQSLTECALKCSELNCKLFYVQPNSSSCYLYAFSEVCQSNTACPNVSGFINNKYNNLFQGDSSEIGYQILQNVNSPFASGTPSAFGILNPQQVFLLTLGRDKKPILAVGKYKNSNLLVFPKAXXXXXXXXXXXQLLLNVLRYFTNGSCTSSLACYVSVANYLNYVGIRGKVFGVNPFTVVNVTNLINLATSMDWHFVVAGTFWSQTATSSVKDLVKLFGLCISSEYGSSDFIIRNNVCVNVTSYTSPSCS 884
            MMTIPTQSLTECALKCSEL+CKLFYVQPNSSSCYLYAFSEVCQSNTACPNVSGFINNKYNNLFQGDSSEIGYQILQNVNS FASGTPSAFGILNPQQVFLLTLGRDKKPILAVGKYKNSNLLVFPKASTESFTTETTSQLLLNVLRYFTNGSCTSSLACYVSVANYLNYVGIRGKVFGVNPFTVVNVTNLINLATSMDWHFVVAGTFWSQTATSSVKDLVKLFGLCISSEYGSSDFIIRNNVCVNVTSYTSP+CS
Sbjct:    1 MMTIPTQSLTECALKCSELHCKLFYVQPNSSSCYLYAFSEVCQSNTACPNVSGFINNKYNNLFQGDSSEIGYQILQNVNSTFASGTPSAFGILNPQQVFLLTLGRDKKPILAVGKYKNSNLLVFPKASTESFTTETTSQLLLNVLRYFTNGSCTSSLACYVSVANYLNYVGIRGKVFGVNPFTVVNVTNLINLATSMDWHFVVAGTFWSQTATSSVKDLVKLFGLCISSEYGSSDFIIRNNVCVNVTSYTSPACS 255          
BLAST of SMED30025311 vs. Planmine SMEST
Match: SMESG000016190.1 (SMESG000016190.1)

HSP 1 Score: 236.113 bits (601), Expect = 1.167e-76
Identity = 118/286 (41.26%), Postives = 176/286 (61.54%), Query Frame = 3
Query:   33 MLILLYISFVINANAGEIYLAVSSCVFNPMMTIPTQSLTECALKCSELNCKLFYVQPNSSSCYLYAFSEVCQSNTACPNVSGFINNKYNNLFQGDSSEIGYQILQNVNSPFASGTPSAFGILNPQQVFLLTLGRDKKPILAVGKYKNSNLLVFPKAXXXXXXXXXXXQLLL--NVLRYFTNGSCTSSLACYVSVANYLNYVGIRGKVFGVNPFTVVNVTNLINLATSMDWHFVVAGTFWSQTATSSVKDLVKLFGLCISSEYGSSDFIIRNNVCVNVTSYTSPSCS 884
            ML+++  +F+        Y  +SSCVFN      + S  ECA+KC    CK F      S CYLY F E+CQSNT C N + F+N+++N++F G S    +QIL+N+ +P+ASG PS F I+N  Q F L +      I+A+G   NS L+++PKA  +   T  +   LL  N+L Y T G C+ S  CY SV  Y NY G +G VFG++  ++ N+T+LI +A+  DWHF++AGTFW++T  S V+DL KL+G+CI   Y   +F++  N+C+N+++Y+S  C+
Sbjct:    1 MLLIMLSTFLAPVQGTGYYALISSCVFNAFARHSSDSFIECAVKCDLTECKGFTFFMEISMCYLYRFGEICQSNTNCTNETVFVNDRFNSMFNGYSDGARFQILKNIKAPYASGNPSIFTIVNTSQAFPLIITSGNLIIMALGSLGNSKLVLYPKAFDDQNFTFKSKNNLLAFNILSYLTYGKCSRSFDCYHSVDAYRNYTGSKGLVFGISANSLFNLTDLITMASMYDWHFIIAGTFWTETLLSQVQDLSKLYGMCIIKTYEIDNFLVSGNICLNISTYSSMPCT 286          
BLAST of SMED30025311 vs. Planmine SMEST
Match: SMESG000016190.1 (SMESG000016190.1)

HSP 1 Score: 232.261 bits (591), Expect = 3.862e-75
Identity = 115/268 (42.91%), Postives = 168/268 (62.69%), Query Frame = 3
Query:   87 YLAVSSCVFNPMMTIPTQSLTECALKCSELNCKLFYVQPNSSSCYLYAFSEVCQSNTACPNVSGFINNKYNNLFQGDSSEIGYQILQNVNSPFASGTPSAFGILNPQQVFLLTLGRDKKPILAVGKYKNSNLLVFPKAXXXXXXXXXXXQLLL--NVLRYFTNGSCTSSLACYVSVANYLNYVGIRGKVFGVNPFTVVNVTNLINLATSMDWHFVVAGTFWSQTATSSVKDLVKLFGLCISSEYGSSDFIIRNNVCVNVTSYTSPSCS 884
            Y  +SSCVFN      + S  ECA+KC    CK F      S CYLY F E+CQSNT C N + F+N+++N++F G S    +QIL+N+ +P+ASG PS F I+N  Q F L +      I+A+G   NS L+++PKA  +   T  +   LL  N+L Y T G C+ S  CY SV  Y NY G +G VFG++  ++ N+T+LI +A+  DWHF++AGTFW++T  S V+DL KL+G+CI   Y   +F++  N+C+N+++Y+S  C+
Sbjct:   15 YALISSCVFNAFARHSSDSFIECAVKCDLTECKGFTFFMEISMCYLYRFGEICQSNTNCTNETVFVNDRFNSMFNGYSDGARFQILKNIKAPYASGNPSIFTIVNTSQAFPLIITSGNLIIMALGSLGNSKLVLYPKAFDDQNFTFKSKNNLLAFNILSYLTYGKCSRSFDCYHSVDAYRNYTGSKGLVFGISANSLFNLTDLITMASMYDWHFIIAGTFWTETLLSQVQDLSKLYGMCIIKTYEIDNFLVSGNICLNISTYSSMPCT 282          
BLAST of SMED30025311 vs. Planmine SMEST
Match: SMESG000016184.1 (SMESG000016184.1)

HSP 1 Score: 199.904 bits (507), Expect = 1.186e-62
Identity = 101/266 (37.97%), Postives = 158/266 (59.40%), Query Frame = 3
Query:   87 YLAVSSCVFNPMMTIPTQSLTECALKCSELNCKLFYVQPNSSSCYLYAFSEVCQSNTACPNVSGFINNKYNNLFQGDSSEIGYQILQNVNSPFASGTPSAFGILNPQQVFLLTL-GRDKKPILAVGKYKNSNLLVFPKAXXXXXXXXXXXQLLLNVLRYFTNGSCTSSLACYVSVANYLNYVGIRGKVFGVNPFTVVNVTNLINLATSMDWHFVVAGTFWSQTATSSVKDLVKLFGLCISSEYGSSDFIIRNNVCVNVTSYTSPSC 881
            Y +VSSCVF    +  + SL +C +KC    CK F    N S CYLY F E+CQSNT C N + F+N+++N++F G S    +QI +N+   + +G PS F ILN  Q F L +  R++   LA+G +  S LL++PK    +  ++ ++  ++N++ Y TNG CTS   C   V  Y +YVG +  V G+   +V N+T+LI  AT   W F+V GTFW    ++ V+ + KL+G+CI++  G S F++ +N+C N++++    C
Sbjct:   12 YKSVSSCVFKSFASYSSISLIDCGIKCDLEQCKGFKFYANISMCYLYRFGEICQSNTNCTNETVFVNDRFNSMFNGYSDGARFQIFKNIQYQYETGYPSVFTILNDSQAFPLAVDDRERMVTLAIGTFGTSRLLLYPKGGLINNPSQCST-FVVNIMNYLTNGKCTSDCDCLHLVDYYKDYVGTKNLVIGIQSLSVFNLTDLITQATVNSWSFIVFGTFWYSETSNEVRAIAKLYGMCITTLNGLSQFLVTDNICQNISTFALKDC 276          
The following BLAST results are available for this feature:
BLAST of SMED30025311 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 SMED30025311 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 SMED30025311 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 SMED30025311 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 SMED30025311 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 SMED30025311 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 SMED30025311 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 SMED30025311 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 SMED30025311 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 SMED30025311 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 SMED30025311 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 SMED30025311 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 SMED30025311 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 SMED30025311 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000016276.10.000e+095.07SMESG000016276.1[more]
SMESG000016276.17.642e-17598.82SMESG000016276.1[more]
SMESG000016190.11.167e-7641.26SMESG000016190.1[more]
SMESG000016190.13.862e-7542.91SMESG000016190.1[more]
SMESG000016184.11.186e-6237.97SMESG000016184.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025311 ID=SMED30025311|Name=SMED30025311|organism=Schmidtea mediterranea sexual|type=transcript|length=925bp
TTGTAATGAAAAATATTATTACATTTTGCTTCATGTTAATTTTATTATAC
ATTTCCTTTGTGATCAATGCTAACGCAGGAGAGATTTATCTTGCCGTTAG
CTCTTGCGTTTTCAACCCCATGATGACAATTCCAACGCAATCGCTCACCG
AATGCGCATTGAAATGCAGTGAACTAAATTGTAAATTGTTCTACGTCCAA
CCGAATTCCTCCAGTTGCTATTTGTACGCGTTCAGTGAGGTGTGCCAATC
CAATACGGCTTGTCCAAACGTATCGGGATTCATCAATAATAAATACAACA
ATTTATTTCAAGGAGATTCCAGCGAAATCGGCTATCAGATTCTACAAAAT
GTAAATTCTCCGTTTGCCAGTGGAACGCCTTCAGCATTTGGTATACTGAA
TCCACAACAGGTCTTTCTGTTAACTTTGGGTCGAGATAAAAAACCAATAT
TGGCCGTTGGCAAATACAAAAACAGTAACTTACTGGTCTTTCCGAAAGCC
AGTACAGAATCATTTACTACAGAAACCACTAGTCAATTGTTATTGAATGT
TTTGAGATATTTCACAAATGGGTCTTGTACAAGCAGTTTGGCATGCTACG
TAAGCGTTGCTAATTACCTAAATTATGTTGGGATCAGAGGCAAAGTCTTC
GGAGTGAACCCGTTTACAGTGGTCAATGTAACAAATCTGATAAATTTAGC
AACTTCAATGGATTGGCATTTTGTCGTCGCTGGGACCTTTTGGTCACAAA
CAGCTACTAGCTCTGTAAAGGACCTGGTGAAGTTATTCGGACTATGCATA
AGTTCTGAGTATGGTTCTTCGGACTTCATAATAAGAAACAATGTTTGCGT
CAATGTGACAAGCTACACTTCACCATCTTGTTCCTGAATGTGAACAGTGA
AAACCTTTGAACACATTGAAATTAG
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protein sequence of SMED30025311-orf-1

>SMED30025311-orf-1 ID=SMED30025311-orf-1|Name=SMED30025311-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=295bp
VMKNIITFCFMLILLYISFVINANAGEIYLAVSSCVFNPMMTIPTQSLTE
CALKCSELNCKLFYVQPNSSSCYLYAFSEVCQSNTACPNVSGFINNKYNN
LFQGDSSEIGYQILQNVNSPFASGTPSAFGILNPQQVFLLTLGRDKKPIL
AVGKYKNSNLLVFPKASTESFTTETTSQLLLNVLRYFTNGSCTSSLACYV
SVANYLNYVGIRGKVFGVNPFTVVNVTNLINLATSMDWHFVVAGTFWSQT
ATSSVKDLVKLFGLCISSEYGSSDFIIRNNVCVNVTSYTSPSCS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..25
score: 0.888
NoneNo IPR availableTMHMMTMhelixcoord: 12..34