SMED30013552

Overview
NameSMED30013552
Smed IDSMED30013552
Length (bp)2603
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 SMED30013552 (SMED30013552) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013552 (SMED30013552) 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 SMED30013552 (SMED30013552) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30013552 (SMED30013552) 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




SMED30013552

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30013552SMESG000020773.1 dd_Smed_v4_6775_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30013552SMESG000020773.1 dd_Smed_v4_6775_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30013552SMESG000020773.1 dd_Smed_v4_6775_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
Alignments
SMED30013552 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002172:9493..12171 -12801
Homology
BLAST of SMED30013552 vs. Ensembl Fly
Match: EloA (gene:FBgn0039066 transcript:FBtr0084375)

HSP 1 Score: 50.447 bits (119), Expect = 6.210e-6
Identity = 26/100 (26.00%), Postives = 56/100 (56.00%), Query Frame = 3
Query: 1524 VLETEIAQFSYEKLLAFDADSRKIQRKTEIFWEKLFKKNHKCANRRDGETWREAYLRNQRDQDIRLKQISERLKKTTEESANAVTKAKLLINSNLAKPKR 1823
            VL   + + + ++LL F+  +  +   +++ W++  +++ +   R + ETWRE +LR Q ++D +L  ++E +K + + S   V K +L    ++ KP R
Sbjct:  388 VLRPVLERATPQQLLNFEEYNPYLMDDSDVLWQQHVQRHCRSQRREEMETWREMFLRCQEEKDRKLSILAESIKASQKISEAPVRKTQLAFVDSMVKPPR 487          
BLAST of SMED30013552 vs. Ensembl Fly
Match: EloA (gene:FBgn0039066 transcript:FBtr0084374)

HSP 1 Score: 50.447 bits (119), Expect = 6.884e-6
Identity = 26/100 (26.00%), Postives = 56/100 (56.00%), Query Frame = 3
Query: 1524 VLETEIAQFSYEKLLAFDADSRKIQRKTEIFWEKLFKKNHKCANRRDGETWREAYLRNQRDQDIRLKQISERLKKTTEESANAVTKAKLLINSNLAKPKR 1823
            VL   + + + ++LL F+  +  +   +++ W++  +++ +   R + ETWRE +LR Q ++D +L  ++E +K + + S   V K +L    ++ KP R
Sbjct:  465 VLRPVLERATPQQLLNFEEYNPYLMDDSDVLWQQHVQRHCRSQRREEMETWREMFLRCQEEKDRKLSILAESIKASQKISEAPVRKTQLAFVDSMVKPPR 564          
BLAST of SMED30013552 vs. Planmine SMEST
Match: SMESG000020773.1 (SMESG000020773.1)

HSP 1 Score: 903.664 bits (2334), Expect = 0.000e+0
Identity = 593/600 (98.83%), Postives = 596/600 (99.33%), Query Frame = 3
Query:   45 KYRTLKALREMEVSVEDIRITNLGKIVKKCTKLEGKPGILAENIIKEWKEMLYKTIHXXXXXXXXXXXEHSQNDKNIKSTKTQFVNNSKIPNKQSVLEPTSDSQSEDCNERDNRSKNYQTKSVMVENHKQKPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHSKNNKLSKEIEIRKISKTRVTNXXXXXXXXCEEFIEMLSXXXXXXXXXXXXXPTXXXXXXXXXXXXXXXXXXXXXXXXXXXXQXXXXXXXXXXXXYINYLESAQEQIXXXXXXXXXXXXAPLGFLVPINENKNQKRVIKSELNNGNVKKEFKDEKPVYYDQKKPSISKTTFNNNIKPEINKHKSRKSEMKSGTSFEDFIIGSAMNKPVEINSRKRKSETVSVQIENKKKNLTNFIPADLTNCPALNSSLSNSDMDEQSVYNRTDIIFQKKDSHINVVKEDVDCTTKYSSERKIWTPKSRNDGMKPEVEENLRTINGVLETEIAQFSYEKLLAFDADSRKIQRKTEIFWEKLFKKNHKCANRRDGETWREAYLRNQRDQDIRLKQISERLKKTTEESANAVTKAKLLINSNLAKPKRRMTDMRR 1844
            KYRTLKALREMEVSVEDIRITNLGKIVKKCTKLEGKPGILAENIIKEWKEMLYKTIHVNDVKKKNNDNEHSQNDKNIKSTKTQFVNNSKIPNKQ++LEPTSDSQSE CNERDNRSKNYQTKSVMVENHKQKPKSNYNKSNDSSTNSSTDENYNSKLSNNNRRSISSSEEENPIPLNHSKNNKLSKEIEIRKISKTRVTNSSDDDSSDCEEFIEMLSKN+KKLNKNNLNKPTKYSSNEESSDNECESNKSKIPNKSIKEIQSKSDSSSDSD DYINYLESAQEQINSKKPNN KPSNAPLGFLVPINENKNQKRVIKSELNNGNVKKEFKDEKPVYYDQKKPSISKTTFNNNIKPEINKHKSRKSEMKSGTSFEDFIIGSAMNKPVEINSRKRKSETVSVQIENKKKNLTNFIPADLTNCPALNSSLSNSDMDEQSVYNRTDIIFQKKDSHINVVKEDVDCTTKYSSERKIWTPKSRNDGMKPEVEENLRTINGVLETEIAQFSYEKLLAFDADSRKIQRKTEIFWEKLFKKNHKCANRRDGETWREAYLRNQRDQDIRLKQISERLKKTTEESANAVTKAKLLINSN AKPKRRMTDMRR
Sbjct:   25 KYRTLKALREMEVSVEDIRITNLGKIVKKCTKLEGKPGILAENIIKEWKEMLYKTIHVNDVKKKNNDNEHSQNDKNIKSTKTQFVNNSKIPNKQNILEPTSDSQSEGCNERDNRSKNYQTKSVMVENHKQKPKSNYNKSNDSSTNSSTDENYNSKLSNNNRRSISSSEEENPIPLNHSKNNKLSKEIEIRKISKTRVTNSSDDDSSDCEEFIEMLSKNQKKLNKNNLNKPTKYSSNEESSDNECESNKSKIPNKSIKEIQSKSDSSSDSDKDYINYLESAQEQINSKKPNNSKPSNAPLGFLVPINENKNQKRVIKSELNNGNVKKEFKDEKPVYYDQKKPSISKTTFNNNIKPEINKHKSRKSEMKSGTSFEDFIIGSAMNKPVEINSRKRKSETVSVQIENKKKNLTNFIPADLTNCPALNSSLSNSDMDEQSVYNRTDIIFQKKDSHINVVKEDVDCTTKYSSERKIWTPKSRNDGMKPEVEENLRTINGVLETEIAQFSYEKLLAFDADSRKIQRKTEIFWEKLFKKNHKCANRRDGETWREAYLRNQRDQDIRLKQISERLKKTTEESANAVTKAKLLINSNFAKPKRRMTDMRR 624          
The following BLAST results are available for this feature:
BLAST of SMED30013552 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 SMED30013552 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 SMED30013552 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 2
Match NameE-valueIdentityDescription
EloA6.210e-626.00gene:FBgn0039066 transcript:FBtr0084375[more]
EloA6.884e-626.00gene:FBgn0039066 transcript:FBtr0084374[more]
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BLAST of SMED30013552 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 SMED30013552 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 SMED30013552 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 SMED30013552 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 SMED30013552 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 SMED30013552 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 SMED30013552 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 SMED30013552 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 SMED30013552 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 SMED30013552 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 SMED30013552 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000020773.10.000e+098.83SMESG000020773.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013552 ID=SMED30013552|Name=SMED30013552|organism=Schmidtea mediterranea sexual|type=transcript|length=2603bp
CTCTTCCGATCTGATTAATCGTAATTTTTTAAAATAATTTTTAGAAATAC
AGAACTCTTAAAGCACTTAGAGAAATGGAAGTTTCTGTAGAAGATATACG
AATTACTAATTTAGGTAAAATAGTTAAAAAATGTACTAAACTTGAAGGGA
AACCAGGAATACTAGCTGAGAATATAATAAAGGAATGGAAAGAGATGTTA
TACAAAACCATCCATGTTAATGATGTAAAAAAGAAAAATAATGATAATGA
ACATTCTCAAAATGATAAAAATATAAAATCGACCAAAACTCAATTCGTAA
ATAATTCAAAAATTCCTAATAAACAAAGCGTCTTAGAACCGACTTCAGAT
AGTCAATCTGAAGATTGTAATGAAAGAGATAATAGGAGTAAAAATTATCA
AACTAAATCGGTAATGGTTGAAAACCACAAGCAAAAGCCAAAATCAAATT
ATAATAAATCTAACGACTCTTCAACTAATTCATCAACTGATGAAAATTAC
AATTCCAAATTATCAAATAATAATAGAAGATCAATATCTAGCAGTGAAGA
AGAAAATCCTATTCCGTTGAATCATTCAAAAAATAATAAATTATCGAAAG
AAATTGAAATTCGAAAAATCAGTAAAACTCGAGTTACTAATAGCAGTGAT
GATGATTCTTCAGACTGTGAAGAATTCATAGAAATGTTATCTAAAAACAA
AAAGAAATTAAACAAAAATAATTTAAATAAACCAACTAAATATTCTAGCA
ATGAGGAATCTTCTGATAATGAATGTGAATCGAATAAAAGTAAAATACCG
AACAAATCTATAAAAGAAATACAGTCTAAAAGTGATAGCAGTAGTGACAG
TGATATGGACTATATTAATTATCTAGAGTCGGCACAAGAGCAAATTAATT
CCAAAAAACCTAACAATCCCAAACCTTCAAATGCACCATTAGGATTTTTA
GTTCCAATAAATGAAAATAAGAATCAGAAAAGAGTCATTAAATCAGAACT
GAATAATGGAAATGTAAAAAAAGAATTCAAAGATGAGAAGCCGGTCTATT
ATGATCAGAAAAAACCATCCATTTCAAAGACGACATTTAATAACAACATA
AAACCAGAAATTAATAAGCATAAATCCAGAAAATCAGAAATGAAATCAGG
CACCTCTTTTGAAGATTTTATAATAGGTAGCGCAATGAACAAACCCGTAG
AAATAAATTCTAGAAAACGAAAATCCGAAACTGTTTCTGTTCAAATCGAA
AACAAAAAGAAAAATTTAACCAATTTCATTCCGGCTGACCTAACAAATTG
TCCGGCATTAAATTCATCTCTCTCGAATTCCGACATGGATGAACAATCGG
TCTACAACAGAACCGACATAATATTCCAAAAGAAAGACAGCCATATCAAT
GTAGTGAAAGAAGATGTCGATTGCACAACTAAATACTCATCGGAACGAAA
AATCTGGACCCCAAAAAGTAGAAATGATGGAATGAAACCCGAAGTCGAAG
AAAACCTCAGAACGATTAATGGAGTTCTAGAAACAGAAATTGCTCAATTC
AGCTACGAGAAATTGTTGGCATTCGATGCAGACAGTCGGAAAATCCAAAG
AAAAACGGAAATTTTCTGGGAGAAATTATTCAAAAAAAATCACAAATGCG
CCAATCGCCGCGACGGGGAAACCTGGCGAGAGGCGTACTTGCGCAACCAG
CGGGATCAGGACATCAGATTGAAACAGATATCAGAACGGTTGAAGAAAAC
GACAGAAGAAAGCGCGAATGCAGTTACTAAAGCTAAACTGCTTATCAACA
GTAATCTTGCGAAGCCGAAAAGACGGATGACCGATATGAGGCGCTGAAAG
CAGGGCAAATGTGATGGTGATCGTCGCGGAATTTGATTTCGTCAACCGAA
TGAATTATAATATTCTACTTTTGTCTTTAACATGAATGTGTATGTGTGCG
AGTCTGTATTTCATAATTGGAGTTGATTGGTTGTCGAGAATTGTTCGATT
GGACGGTTGTGCATTCTGTACTTTATCTAGAGATTTATCTATTTTGTGCT
TTATTCAATCAATATTTTTCAATTGCCCGACTGTTATCGATCATTCTATA
CGCTGAACAGACATGTGTGCACTCGAGGCGCTGAGTTTATTGATTATTTT
TAAAGAAAAATTTCATCGGCTCTTGCGTGTGGGTGTTTGTCTGCTTACTT
ATTATGATTTATTGGGTTATGTTTTGTATTTTGAAACATGTTTCAGTTTA
TTATGAACATCTCATCACTATTGATATCATTATTTTTAAACTGCTTTATT
GGAGTTATTAAAATGAGGAAAAAATGATTTTGGTGATGACGGTGTTTTAT
TTTTAAATGATTTAAAATTAAAATGGGCTTCGTCTTTAATTTATTTTATT
TTTAATAAGTTGGGACTATAATTTTATTAATATTATGAATTTTATTTTTG
AAAATTTTTCAAATTTATTACTTATACTCCCAACTTGTCATTCATTTTCA
ATAATTACTTTATAGACATTTCATGTATTTTTAGATGATTATTTTAATTT
TTGTATTTATTACTGTTTATTGACAGTAGATTCGCGCTATTTTTATGAAT
GAG
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protein sequence of SMED30013552-orf-1

>SMED30013552-orf-1 ID=SMED30013552-orf-1|Name=SMED30013552-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=591bp
MEVSVEDIRITNLGKIVKKCTKLEGKPGILAENIIKEWKEMLYKTIHVND
VKKKNNDNEHSQNDKNIKSTKTQFVNNSKIPNKQSVLEPTSDSQSEDCNE
RDNRSKNYQTKSVMVENHKQKPKSNYNKSNDSSTNSSTDENYNSKLSNNN
RRSISSSEEENPIPLNHSKNNKLSKEIEIRKISKTRVTNSSDDDSSDCEE
FIEMLSKNKKKLNKNNLNKPTKYSSNEESSDNECESNKSKIPNKSIKEIQ
SKSDSSSDSDMDYINYLESAQEQINSKKPNNPKPSNAPLGFLVPINENKN
QKRVIKSELNNGNVKKEFKDEKPVYYDQKKPSISKTTFNNNIKPEINKHK
SRKSEMKSGTSFEDFIIGSAMNKPVEINSRKRKSETVSVQIENKKKNLTN
FIPADLTNCPALNSSLSNSDMDEQSVYNRTDIIFQKKDSHINVVKEDVDC
TTKYSSERKIWTPKSRNDGMKPEVEENLRTINGVLETEIAQFSYEKLLAF
DADSRKIQRKTEIFWEKLFKKNHKCANRRDGETWREAYLRNQRDQDIRLK
QISERLKKTTEESANAVTKAKLLINSNLAKPKRRMTDMRR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000099neuron
Vocabulary: INTERPRO
TermDefinition
IPR017923TFIIS_N
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
Vocabulary: biological process
TermDefinition
GO:0006351transcription, DNA-templated
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 549..569
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 126..170
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 212..260
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 67..94
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 226..260
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 53..177
NoneNo IPR availablePANTHERPTHR15141:SF76TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 3coord: 2..158
NoneNo IPR availablePANTHERPTHR15141TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 3coord: 2..158
coord: 492..585
NoneNo IPR availablePANTHERPTHR15141:SF76TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 3coord: 492..585
IPR017923Transcription factor IIS, N-terminalPROSITEPS51319TFIIS_Ncoord: 1..45
score: 10.34