SMED30003403

Overview
NameSMED30003403
Smed IDSMED30003403
Length (bp)1768
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 SMED30003403 (SMED30003403) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003403 (SMED30003403) 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 SMED30003403 (SMED30003403) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003403 (SMED30003403) 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




SMED30003403

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
muscle cellSMED30003403SMESG000074733.1 dd_Smed_v4_9825_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
anterior region of the whole animalSMED30003403SMESG000074733.1 dd_Smed_v4_9825_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30003403SMESG000074733.1 dd_Smed_v4_9825_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30003403 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002302:340..3567 +7512
Homology
BLAST of SMED30003403 vs. TrEMBL
Match: A0A419PXR0 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CSKR_10682s PE=4 SV=1)

HSP 1 Score: 63.1586 bits (152), Expect = 1.404e-6
Identity = 70/240 (29.17%), Postives = 113/240 (47.08%), Query Frame = 2
Query:  368 FSTV-LKCPFTDNHLCYLDC-------DALCYAENCLP-MISSCSKNQTNTT-IKLTWIIDITKVNKTGDWSCSY-GSHGSKPAK---VERYVMTTGQ--TDKSLEMITSTTXXXXXXXXXXXXXXXSTTTHA------------MQQ---TQEIYQENPNEFWLFITNPNXXXXXXXXXXXXXXFNIFFLIRCALLRSLIDQFVQSHKISESCLYRCFCIWINNGLPKSHQNFTSKPNP 994
             STV L CP     +CY+DC       D  C     +  +I+ C   + N T + + ++ID+  +N TG W+C+Y G H S+P +   VER  +TT +  T     M  +T      +          +T  A            M+Q   +Q I QE+ +E  + +T P +V++L+ V+ +SLLFN+   +RCAL ++ +D    S    +S L R  C    +   KS Q +++ P P
Sbjct:  102 MSTVYLLCPQISTSICYMDCTPNCVLGDRGCTVPQAISQVINRCDYKRINATRLLVDYVIDLEALNNTGQWNCAYRGQHASRPLELRAVERRPVTTARFSTPDQTGMSATTMNPPKSSTPTGNGLKSPSTRKASGGTYSNRSINTMEQASGSQRIRQESGHE-TIKLTRPELVVILLIVLAISLLFNVILSVRCALTKTFLDNM--SRGKVDSTLSRLLCFRQKS---KSIQLYSNSPCP 335          
BLAST of SMED30003403 vs. TrEMBL
Match: G7YTW0 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CLF_110789 PE=4 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 2.051e-6
Identity = 70/240 (29.17%), Postives = 118/240 (49.17%), Query Frame = 2
Query:  368 FSTV-LKCPFTDNHLCYLDC-------DALCYAENCLP-MISSCSKNQTNTT-IKLTWIIDITKVNKTGDWSCSY-GSHGSKPAK---VERYVMTTGQ-TDKSLEMITSTTXXXXXXXXXXXXXXXSTTT-------------HAMQQ---TQEIYQENPNEFWLFITNPNXXXXXXXXXXXXXXFNIFFLIRCALLRSLIDQFVQSHKISESCLYRCFCIWINNGLPKSHQNFTSKPNP 994
             STV L CP     +CY+DC       D  C     +  +I+ C   + N T + + ++ID+  +N TG W+C+Y G H S+P +   VER  +TT + +      +++TT N   +       + S +T             + M+Q   +Q I QE+ +E  + +T P +V++L+ V+ +SLLFN+   +RCAL ++ +D    S    +S L R  C    +   KS Q +++ P P
Sbjct:  102 MSTVYLLCPQISTSICYMDCTPNCVLGDRGCTVPQAISQVINRCDYKRINATRLLVDYVIDLEALNNTGQWNCAYRGQHASRPLELRAVERRPVTTARFSTPDQTGMSATTMNPPKSSTPTGNGLKSPSTRKVSGGTYSNRSINTMEQASGSQRIRQESGHE-TIKLTRPELVVILLIVLAISLLFNVILSVRCALTKTFLDNM--SRGKVDSTLSRLLCFRQKS---KSIQLYSNSPCP 335          
BLAST of SMED30003403 vs. Planmine SMEST
Match: SMESG000074733.1 (SMESG000074733.1)

HSP 1 Score: 908.286 bits (2346), Expect = 0.000e+0
Identity = 469/469 (100.00%), Postives = 469/469 (100.00%), Query Frame = 2
Query:  203 MIVIQCIFLYGFLVNTLASDPTNKLLNVSPRFTVTYSYVKIVLECDVKYDIKDNNFSTVLKCPFTDNHLCYLDCDALCYAENCLPMISSCSKNQTNTTIKLTWIIDITKVNKTGDWSCSYGSHGSKPAKVERYVMTTGQTDKSLEMITSTTXXXXXXXXXXXXXXXSTTTHAMQQTQEIYQENPNEFWLFITNPNXXXXXXXXXXXXXXFNIFFLIRCALLRSLIDQFVQSHKISESCLYRCFCIWINNGLPKSHQNFTSKPNPGNSFVGYHREDVYDDMSASSQADRHLINNYSQYELEQDSLLARKYWAGSDGSQSIMARQPQFIYATQPKSNYVIVSGPVCANRGHGPFITPSNTSFLSNSQRTCITDEISRPSSNEYVCNESIIYSQPIKNRPKSYGQFTDGDIVKMTESFPPAPPIRTCTDAQCFRSSTPCADNMQQSITMKNVDLIEHCAHSGVKNTSIENVS 1609
            MIVIQCIFLYGFLVNTLASDPTNKLLNVSPRFTVTYSYVKIVLECDVKYDIKDNNFSTVLKCPFTDNHLCYLDCDALCYAENCLPMISSCSKNQTNTTIKLTWIIDITKVNKTGDWSCSYGSHGSKPAKVERYVMTTGQTDKSLEMITSTTKNVIPNKIVNIPNVISTTTHAMQQTQEIYQENPNEFWLFITNPNVVLVLVCVITVSLLFNIFFLIRCALLRSLIDQFVQSHKISESCLYRCFCIWINNGLPKSHQNFTSKPNPGNSFVGYHREDVYDDMSASSQADRHLINNYSQYELEQDSLLARKYWAGSDGSQSIMARQPQFIYATQPKSNYVIVSGPVCANRGHGPFITPSNTSFLSNSQRTCITDEISRPSSNEYVCNESIIYSQPIKNRPKSYGQFTDGDIVKMTESFPPAPPIRTCTDAQCFRSSTPCADNMQQSITMKNVDLIEHCAHSGVKNTSIENVS
Sbjct:    1 MIVIQCIFLYGFLVNTLASDPTNKLLNVSPRFTVTYSYVKIVLECDVKYDIKDNNFSTVLKCPFTDNHLCYLDCDALCYAENCLPMISSCSKNQTNTTIKLTWIIDITKVNKTGDWSCSYGSHGSKPAKVERYVMTTGQTDKSLEMITSTTKNVIPNKIVNIPNVISTTTHAMQQTQEIYQENPNEFWLFITNPNVVLVLVCVITVSLLFNIFFLIRCALLRSLIDQFVQSHKISESCLYRCFCIWINNGLPKSHQNFTSKPNPGNSFVGYHREDVYDDMSASSQADRHLINNYSQYELEQDSLLARKYWAGSDGSQSIMARQPQFIYATQPKSNYVIVSGPVCANRGHGPFITPSNTSFLSNSQRTCITDEISRPSSNEYVCNESIIYSQPIKNRPKSYGQFTDGDIVKMTESFPPAPPIRTCTDAQCFRSSTPCADNMQQSITMKNVDLIEHCAHSGVKNTSIENVS 469          
BLAST of SMED30003403 vs. Planmine SMEST
Match: SMESG000057504.1 (SMESG000057504.1)

HSP 1 Score: 68.1662 bits (165), Expect = 2.860e-12
Identity = 42/111 (37.84%), Postives = 58/111 (52.25%), Query Frame = 2
Query:  269 NKLLNVSPRFTVTYSYVKIVLECDVKYDIKDNNFSTVLKCPFTDNHLCYLDCDALCYAENCLPMISSCSKNQTNTTIKLTWIIDITKVNKTGDWSCSYGSHGSKPAKVERY 601
            NKLL      T TYS   I L C  K +  +  F   LKCPFTD+ +C+ DCDA     +   +I+ C K+ T  T  +T+ I+I +V  TGDW C Y  + S    + +Y
Sbjct:  170 NKLL-----ITSTYSSAHIKLTCSTKIETGER-FQIHLKCPFTDSEMCFTDCDAT-DGNSLKQIITKCEKSSTYDTFSITYQINIAQVTVTGDWYCIYRGNKSIRIPISKY 273          

HSP 2 Score: 60.077 bits (144), Expect = 1.467e-9
Identity = 46/132 (34.85%), Postives = 61/132 (46.21%), Query Frame = 2
Query:  212 IQCIFLYGFLVNTLASDPTNKLLNVSPRFTVTYSYVKIVLECDVKYDIKDNNFSTVLKCPFTDNHLCYLDCDA-LCYAENCLP-MISSCSKNQTNTTIKLTWIIDITKVNKTGDWSCSYGSHGSKPAKVERY 601
            I  + + G +  T A D   KLL        TYS   I L C  K    +  F   LKCPFTD+ +C+ DC   L    N L  MI+ C    T  T  +T+ I+I +V  TGDW C Y  + S    + +Y
Sbjct:    6 IAIVLVCGIIGRTSAED---KLL-----INATYSSAHIKLTCSTKIGTGER-FQIHLKCPFTDSEICFTDCSGNLTTDGNSLKQMITKCDIISTYDTYSVTYQINIAQVTVTGDWYCIYRGNKSIRIPISKY 128          
BLAST of SMED30003403 vs. Planmine SMEST
Match: SMESG000017122.1 (SMESG000017122.1)

HSP 1 Score: 59.3066 bits (142), Expect = 4.191e-9
Identity = 43/128 (33.59%), Postives = 63/128 (49.22%), Query Frame = 2
Query:  296 FTVTYSYVKIVLECDVKYDIKD-NNFSTV-LKCPFTDNHLCYLDCDALCY--AENCLPMISSCSKNQTN-TTIKLTWIIDITKVNKTGDWSCSYGSHGSKPAKVERYVM---TTGQTDKSLEMITSTT 655
            F+   S  K+ L C V   IK  N+ + + L CPF D   CY++CD  C      C  + +SC+    N +TI L + +D+  VN TG W C Y    S P ++ +YV    T+  T K  +   S+T
Sbjct:   35 FSYNISENKMGLHCSVSTHIKSFNDINKIHLFCPFLDGSSCYINCDNQCLYGVGPCRKVFTSCNYVSNNESTINLYYQLDMRFVNVTGQWICQYDEQKSLPIEISKYVQPMETSTATQKITQKYESST 162          
The following BLAST results are available for this feature:
BLAST of SMED30003403 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 SMED30003403 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 SMED30003403 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 SMED30003403 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 SMED30003403 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 SMED30003403 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 SMED30003403 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 SMED30003403 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A419PXR01.404e-629.17Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
G7YTW02.051e-629.17Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
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BLAST of SMED30003403 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 SMED30003403 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 SMED30003403 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 SMED30003403 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 SMED30003403 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 SMED30003403 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000074733.10.000e+0100.00SMESG000074733.1[more]
SMESG000057504.12.860e-1237.84SMESG000057504.1[more]
SMESG000017122.14.191e-933.59SMESG000017122.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003403 ID=SMED30003403|Name=SMED30003403|organism=Schmidtea mediterranea sexual|type=transcript|length=1768bp
ACTGTAAACCAATTTCTTAGGCACTAACCTGATTACCGGACCAATCAAAA
TCGTTTGTGTCTTAACCACCCACACACAGTTTTCAGTTATATGCCTACAT
CATTGGTTGATATTTATAGCAATTTATGGGCGAATAGTTAACAATTTTCA
TGGAATTTTAAATCAAATATCAATTAAACCAGTAATTTTTTTATTGTTGG
AAATGATCGTAATACAATGCATTTTTCTATATGGATTTTTGGTTAACACT
TTAGCATCAGATCCAACTAATAAGCTCCTAAATGTCAGCCCTCGGTTTAC
AGTGACATATTCTTACGTGAAAATCGTACTTGAATGCGATGTCAAATACG
ATATTAAAGACAATAACTTTTCGACAGTATTGAAATGTCCATTTACTGAC
AATCATTTATGTTATCTGGACTGCGATGCGTTATGCTACGCTGAAAATTG
TTTACCGATGATATCTTCATGTTCGAAAAACCAAACAAATACCACCATCA
AACTTACTTGGATAATTGATATCACAAAAGTCAACAAAACAGGAGACTGG
TCATGCAGTTATGGTTCGCATGGGTCAAAACCAGCAAAGGTTGAAAGATA
CGTAATGACAACTGGTCAGACGGATAAAAGTCTAGAAATGATCACATCGA
CGACTAAAAATGTTATCCCAAATAAAATTGTGAATATTCCAAATGTGATT
TCAACGACTACACATGCCATGCAACAAACTCAAGAGATTTATCAAGAAAA
CCCAAATGAATTTTGGCTCTTTATCACAAATCCAAATGTCGTTTTGGTGC
TAGTCTGCGTCATTACTGTGTCTTTGCTGTTCAACATTTTCTTCCTGATC
CGGTGCGCATTATTGCGTTCCTTAATTGATCAATTTGTACAATCTCACAA
AATATCCGAGTCGTGTTTGTATCGTTGTTTCTGTATTTGGATTAACAATG
GCCTTCCTAAGTCCCATCAAAATTTTACTAGTAAACCGAACCCAGGAAAC
TCATTCGTTGGCTATCACCGGGAAGACGTTTATGATGATATGAGTGCAAG
TTCACAGGCTGACAGGCACTTGATAAATAACTATTCACAATACGAATTGG
AACAAGATTCACTATTAGCCCGTAAATATTGGGCAGGATCAGATGGATCC
CAAAGCATTATGGCAAGACAGCCTCAGTTTATCTATGCAACTCAACCAAA
AAGCAACTATGTTATTGTGTCTGGACCTGTTTGTGCAAATAGAGGCCATG
GGCCGTTTATAACACCTTCAAATACAAGTTTTCTCTCTAACAGTCAAAGG
ACATGCATTACTGATGAAATCAGTCGACCATCTTCTAACGAGTATGTGTG
TAATGAGTCCATTATTTATTCTCAACCAATCAAAAATCGACCGAAATCGT
ACGGCCAATTCACTGACGGAGATATTGTCAAAATGACTGAATCGTTTCCT
CCAGCACCTCCAATAAGAACTTGTACCGATGCTCAATGTTTTCGGAGTTC
GACTCCCTGCGCAGATAATATGCAACAATCAATCACTATGAAAAATGTCG
ATCTTATCGAGCACTGTGCTCATTCTGGAGTCAAAAATACATCTATTGAA
AATGTTTCTTAAAGATATTACATAACCGTTTGAATTTCTTTTTGGAACTA
CACAAAGAAAAGAACTCAAAGATTATGTTTTAGTTAGAATCTCTTGTAAA
TAGAATTTGTCCATATTTATGTGTTTATGTTTTTAAATGTTTGTTTTAAA
AAAACAACCTTGAGTGCC
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protein sequence of SMED30003403-orf-1

>SMED30003403-orf-1 ID=SMED30003403-orf-1|Name=SMED30003403-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=470bp
MIVIQCIFLYGFLVNTLASDPTNKLLNVSPRFTVTYSYVKIVLECDVKYD
IKDNNFSTVLKCPFTDNHLCYLDCDALCYAENCLPMISSCSKNQTNTTIK
LTWIIDITKVNKTGDWSCSYGSHGSKPAKVERYVMTTGQTDKSLEMITST
TKNVIPNKIVNIPNVISTTTHAMQQTQEIYQENPNEFWLFITNPNVVLVL
VCVITVSLLFNIFFLIRCALLRSLIDQFVQSHKISESCLYRCFCIWINNG
LPKSHQNFTSKPNPGNSFVGYHREDVYDDMSASSQADRHLINNYSQYELE
QDSLLARKYWAGSDGSQSIMARQPQFIYATQPKSNYVIVSGPVCANRGHG
PFITPSNTSFLSNSQRTCITDEISRPSSNEYVCNESIIYSQPIKNRPKSY
GQFTDGDIVKMTESFPPAPPIRTCTDAQCFRSSTPCADNMQQSITMKNVD
LIEHCAHSGVKNTSIENVS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 257..279
NoneNo IPR availableTMHMMTMhelixcoord: 57..79
NoneNo IPR availableTMHMMTMhelixcoord: 20..42