SMED30026355

Overview
NameSMED30026355
Smed IDSMED30026355
Length (bp)1500
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 SMED30026355 (SMED30026355) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026355 (SMED30026355) 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 SMED30026355 (SMED30026355) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026355 (SMED30026355) 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



SMED30026355

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30026355SMESG000076739.1 SmedASXL_014599SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30026355 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001456:53049..68396 +7376
Homology
[Close]
BLAST of SMED30026355 vs. TrEMBL
Match: R7T3K3 (Uncharacterized protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_171728 PE=4 SV=1)

HSP 1 Score: 68.5514 bits (166), Expect = 1.304e-8
Identity = 59/270 (21.85%), Postives = 111/270 (41.11%), Query Frame = 2 
Query:  461 DNNYIFPVFTIKQRDALFEYASQLGFGSELIEEIVGQTLSEYILKQIEESTRVKASVKTQSTNIAVLLSKCNASVYATSVARYLIRKNCHLVVFIDENKTTDINYKVDIEISRLKKLLSEFSTIHGYNIITHKIRDLANKTFDYIISGVESDACDNNRP--SSQLKTWCVNQTSHILCINPPSISYLTWKSAVFIGVPTFSYSNLNIKID-SNINVVCSNINRKVNLEKITKKPDGLILLCNINFPDKVFSFLNLNYRSSFTNRKWLRLY 1261
            D   + P  + + R  L + A+  G   E   E VG++ +E IL+ +  + R+      Q   + VL         A + AR+L      +  F+    +T  + +   E+S L+   +        NI+T+   DL +   + ++SG++   CDN+    ++ +  W     +  L I+PP     T      +GVP +    L+I +     +  CS +                  LC+++ P  VFS  ++ Y S F ++  + L+
Sbjct:  234 DAGLLVPSVSHELRSRLMKSAADCGLSCERQVEAVGRSAAEMILQLLGGNHRLTPQNAHQRPRVTVLCGPHMQGAQALNCARHLAMHTVQVTAFVPSQLSTLASPESQSELSLLRMTKT--------NIVTNP-NDLPSSGVEMVVSGLDGHDCDNSHEPWAAAVVEWYATIKASALAIDPP-----TGPGGSSLGVPKW---GLSIALPLHGAHTTCSQM-----------------YLCDLSLPTGVFSAASVKYTSPFGHKFVIPLH 469
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BLAST of SMED30026355 vs. TrEMBL
Match: E0VJ09 (YjeF domain-containing protein, putative OS=Pediculus humanus subsp. corporis OX=121224 GN=8230378 PE=4 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 2.563e-8
Identity = 76/328 (23.17%), Postives = 130/328 (39.63%), Query Frame = 2 
Query:  323 SQQPDLVREITQQLNQDHIGISGRCP-----VISVNRTTNDFSKFNEYWNLDNNYIFPVFTIKQRDALFEYASQLGFGSELIEEIVGQTLSEYILKQIEESTRVKASVKTQSTNIAVLLSKCNASVYATSVARYLIRKNCHLVVFIDE--NKTTDINYKVDIEISRLKKLLSEFSTIHGYNIITHKIRDLANKTFDYIISGVESDACDNNRPSSQLKTWCVNQTSHILCINPP--SISYLTWKSAVFIGVPTFSYSNLNIKIDSNINVVCSNINRKVNLEKITKKPDGLILLCNINFPDKVFSFLNL-NYRSSFTNRKWLRLYSDNDL 1276
            + +PD+VR      N D  G   RC        SVN+      K +  +  D+  I P    + R  L   A + G   E   EI+G+  +E  L  +  + R+    + Q  NIAVL           + AR L  +    +V+I +  + TT++ +++      L ++ S        N +T  ++DLA+ + D II  +           +   +W  N  + +L I+PP      +T K ++   +P  +Y   N                            G I LCNIN P +VF+ +    Y S F  + ++ L+ ++ L
Sbjct:  176 ASKPDVVR------NADKKGARYRCDENILNSKSVNKRIIVPLKDSIEYVTDSGLIVPSLPPELRKKLLALAERFGLSFERQSEIIGRACTEMALLLVGGARRLNPQNQHQCPNIAVLCGSHRTGSQGVNCARQLASQGVKTIVYIQDPVDLTTEMTHELG-----LYRMTS--------NKVTTNLQDLASTSVDLIILALLDSKSTTENIITPAASWANNNRAQVLAIDPPKHGTPGVTAKYSLVPALP-LAYDACN----------------------------GKIYLCNINIPLQVFTDVGFTEYASPFGPKFFMVLHPNDSL 455
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BLAST of SMED30026355 vs. TrEMBL
Match: A0A482V7J8 (YjeF N, FDF, and/or LSM14 domain containing protein OS=Asbolus verrucosus OX=1661398 GN=BDFB_007574 PE=4 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 2.735e-7
Identity = 71/328 (21.65%), Postives = 132/328 (40.24%), Query Frame = 2 
Query:  317 NYSQQPDLVREI-----TQQLNQDHIGISGRCPVISVNRTTNDFSKFNEYWNLDNNYIFPVFTIKQRDALFEYASQLGFGSELIEEIVGQTLSEYILKQIEESTRVKASVKTQSTNIAVLLSKCNASVYATSVARYLIRKNCHLVVFIDENKTTDINYKVDIEISRLKKLLSEFSTIHGYNIITHKIRDLANKTFDYIISGVESDACDNNRPSSQLKTWCVNQTSHILCINPPSISYLTWKSAVFIGVPTFSYSNLNIKIDSNINVVCSNINRKVNLEKITKKP----DGLILLCNINFPDKVFSFLNLNYRSSFTNRKWLRLYSDND 1273
            N SQ+PD++R +     ++  + +++  S       +     DF ++      D+  I P  +   R  L+E A ++G   E   E++G+  +E  ++ +    R+      Q   + VL           + AR L     H +V+I           V  E++ +KK LS +  +   N + + + +L N   D II  +  D  +N +    L  W     + I+ ++PPSI           G+P                     I  K +L  +   P    +G + LCN+ FP +VF+ + + Y+S F  +  + L+  +D
Sbjct:  180 NNSQKPDVIRNLDSKKPSKYRHDENVIASTPATYRQIIVPKQDFCEYV----TDDGLIIPSVSRSLRKKLWEVADRVGLTWEKRVELLGRAAAEICIQLLGGGHRLNPHNSHQFPTVVVLCGPHKQGAMGINAARQLASHGVHTIVYI-----------VSSEVAIIKKELSLY--LLTKNSVVYSVCNLPNFA-DLIIMALCEDT-ENPKSYPDLCDWANRNRAPIMALDPPSI-----------GIP--------------------GITPKFSLLPVLPLPHSPKNGKLYLCNLGFPLEVFNEVGIKYKSPFGPKFVIPLHPKDD 457
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BLAST of SMED30026355 vs. Planmine SMEST
Match: SMESG000076739.1 (SMESG000076739.1)

HSP 1 Score: 835.869 bits (2158), Expect = 0.000e+0
Identity = 409/412 (99.27%), Postives = 411/412 (99.76%), Query Frame = 2 
Query:   53 GSDSNESVGIKMNFQSKKYRSNTFSFNAEDFSSYDEGHSKSVSQSKPTTSLWESSPSKRDIFNALQEIGVIPSKNRNDNYPKSSQFSQNYSQQPDLVREITQQLNQDHIGISGRCPVISVNRTTNDFSKFNEYWNLDNNYIFPVFTIKQRDALFEYASQLGFGSELIEEIVGQTLSEYILKQIEESTRVKASVKTQSTNIAVLLSKCNASVYATSVARYLIRKNCHLVVFIDENKTTDINYKVDIEISRLKKLLSEFSTIHGYNIITHKIRDLANKTFDYIISGVESDACDNNRPSSQLKTWCVNQTSHILCINPPSISYLTWKSAVFIGVPTFSYSNLNIKIDSNINVVCSNINRKVNLEKITKKPDGLILLCNINFPDKVFSFLNLNYRSSFTNRKWLRLYSDNDLCLVE 1288
            GSDSNESVGIKMNFQSKKYRSNTFSFNAEDFSSYDEGHSKSVSQSKPTTSLWESSPSKRDIFNALQEIGVIPSKNRNDNYPKSSQFSQNYSQQPDLVREITQQLNQDHIG+SGRCPVISVN TTNDFSKFNEYWNLDNNYIFPVFTIKQRDALFEYASQLGFGSELIEEIVGQTLSEYILKQIEESTRVKASVKTQSTNIAVLLSKCNASVYATSVARYLIRKNCHLVVFIDENKTTDINYKVDIEISRLKKLLSEFSTIHGYNIITHKIRDLANKTFDYIISGVESDACDNNRPSSQLKTWCVNQTSHILCINPPSISYLTWKSAVFIGVPTFSYSNLNIKIDSNINVVCSNINRKVNLEKITKKPDGLILLCNINFPDKVFSFLNLNYRSSF+NRKWLRLYSDNDLCLVE
Sbjct:  186 GSDSNESVGIKMNFQSKKYRSNTFSFNAEDFSSYDEGHSKSVSQSKPTTSLWESSPSKRDIFNALQEIGVIPSKNRNDNYPKSSQFSQNYSQQPDLVREITQQLNQDHIGLSGRCPVISVNTTTNDFSKFNEYWNLDNNYIFPVFTIKQRDALFEYASQLGFGSELIEEIVGQTLSEYILKQIEESTRVKASVKTQSTNIAVLLSKCNASVYATSVARYLIRKNCHLVVFIDENKTTDINYKVDIEISRLKKLLSEFSTIHGYNIITHKIRDLANKTFDYIISGVESDACDNNRPSSQLKTWCVNQTSHILCINPPSISYLTWKSAVFIGVPTFSYSNLNIKIDSNINVVCSNINRKVNLEKITKKPDGLILLCNINFPDKVFSFLNLNYRSSFSNRKWLRLYSDNDLCLVE 597
The following BLAST results are available for this feature:
BLAST of SMED30026355 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 SMED30026355 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 SMED30026355 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 SMED30026355 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 SMED30026355 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 SMED30026355 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 SMED30026355 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 SMED30026355 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
R7T3K31.304e-821.85Uncharacterized protein OS=Capitella teleta OX=283... [more]
E0VJ092.563e-823.17YjeF domain-containing protein, putative OS=Pedicu... [more]
A0A482V7J82.735e-721.65YjeF N, FDF, and/or LSM14 domain containing protei... [more]
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BLAST of SMED30026355 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 SMED30026355 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 SMED30026355 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 SMED30026355 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 SMED30026355 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 SMED30026355 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000076739.10.000e+099.27SMESG000076739.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026355 ID=SMED30026355|Name=SMED30026355|organism=Schmidtea mediterranea sexual|type=transcript|length=1500bp
TGGTTAAAATATTCCACGAATTGTCGGAGTTCTTACAACAAATTTGATTT
TAGGTTCGGATTCTAATGAATCAGTAGGTATAAAAATGAATTTCCAATCA
AAAAAATACCGAAGCAACACATTTAGTTTTAACGCTGAAGATTTTTCCAG
TTACGATGAAGGTCACTCTAAATCAGTTTCTCAATCAAAACCAACAACCA
GTTTATGGGAATCCTCACCAAGCAAGCGGGATATATTTAATGCTTTGCAA
GAAATCGGAGTCATTCCGTCCAAAAATCGTAATGACAATTATCCAAAATC
CTCGCAATTTAGCCAAAATTACTCACAACAGCCAGATTTAGTTCGTGAAA
TCACCCAGCAATTAAACCAAGATCACATTGGCATATCTGGGCGATGTCCT
GTCATATCTGTGAATAGAACTACCAACGATTTCAGCAAATTCAACGAGTA
TTGGAATTTGGACAATAATTATATTTTCCCAGTATTTACTATTAAACAAC
GCGACGCGTTATTTGAATATGCCAGCCAACTGGGATTTGGTAGTGAGTTA
ATCGAGGAAATAGTTGGCCAGACCCTTTCGGAGTATATTTTAAAACAAAT
TGAAGAATCTACCAGAGTTAAGGCTTCGGTAAAAACTCAAAGCACAAATA
TTGCGGTTTTATTAAGTAAATGCAACGCATCAGTCTATGCGACATCAGTT
GCCAGATATTTGATAAGAAAAAACTGCCATTTGGTTGTGTTCATAGATGA
AAATAAAACAACTGACATTAACTACAAAGTTGATATTGAAATTTCTCGGC
TCAAGAAATTATTATCCGAATTTAGCACAATTCATGGATATAATATTATA
ACTCATAAAATTAGAGATTTAGCAAACAAAACCTTTGATTACATCATATC
TGGAGTAGAATCCGACGCCTGTGACAACAATCGTCCGAGTTCCCAGCTAA
AAACCTGGTGTGTCAATCAAACGTCGCACATTCTATGTATTAATCCCCCA
TCGATTAGCTATCTAACGTGGAAAAGTGCAGTATTTATTGGGGTGCCTAC
ATTTAGCTACAGCAATCTCAACATTAAAATTGACAGCAACATTAATGTTG
TTTGCTCTAACATTAATCGAAAAGTGAATTTAGAAAAAATCACAAAGAAA
CCAGATGGACTCATTTTATTGTGTAATATTAATTTCCCTGATAAAGTGTT
TTCTTTTTTAAATTTAAATTATCGCTCATCTTTTACCAATAGAAAGTGGT
TAAGGTTATACAGTGATAATGACCTCTGTTTGGTGGAGTAGATAAAATAG
CTGTGCTGATTAATTGATGGATGCATTTATAATAGCTATTTTTATGAGTA
TTTATCTATTTTAATTACAATTTTATTGCATGGGTTTTTTACTGTTTTTC
TTTTATTATCATTATTATAATTATAATTATTAGAGGTTTTCTATTTTTTA
AAACTGTTTAATGTGAACAATGAATTGGTAGGAATCTATGTCGATATCGC
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protein sequence of SMED30026355-orf-1

>SMED30026355-orf-1 ID=SMED30026355-orf-1|Name=SMED30026355-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=402bp
MNFQSKKYRSNTFSFNAEDFSSYDEGHSKSVSQSKPTTSLWESSPSKRDI
FNALQEIGVIPSKNRNDNYPKSSQFSQNYSQQPDLVREITQQLNQDHIGI
SGRCPVISVNRTTNDFSKFNEYWNLDNNYIFPVFTIKQRDALFEYASQLG
FGSELIEEIVGQTLSEYILKQIEESTRVKASVKTQSTNIAVLLSKCNASV
YATSVARYLIRKNCHLVVFIDENKTTDINYKVDIEISRLKKLLSEFSTIH
GYNIITHKIRDLANKTFDYIISGVESDACDNNRPSSQLKTWCVNQTSHIL
CINPPSISYLTWKSAVFIGVPTFSYSNLNIKIDSNINVVCSNINRKVNLE
KITKKPDGLILLCNINFPDKVFSFLNLNYRSSFTNRKWLRLYSDNDLCLV
E*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR036652YjeF_N_dom_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036652YjeF N-terminal domain superfamilyGENE3DG3DSA:3.40.50.10260coord: 104..393
e-value: 2.9E-26
score: 94.2
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 22..44
NoneNo IPR availablePANTHERPTHR13612UNCHARACTERIZEDcoord: 124..389