SMED30021909

Overview
NameSMED30021909
Smed IDSMED30021909
Length (bp)1170
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 SMED30021909 (SMED30021909) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021909 (SMED30021909) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

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 SMED30021909 (SMED30021909) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021909 (SMED30021909) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top


 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30021909

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
cilated neuronSMED30021909h1SMcG0016820 dd_Smed_v4_14838_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30021909h1SMcG0016820 dd_Smed_v6_14838_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
SMED30021909 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000468:50697..61727 +4477
Homology
BLAST of SMED30021909 vs. Planmine SMEST
Match: SMESG000077557.1 (SMESG000077557.1)

HSP 1 Score: 675.241 bits (1741), Expect = 0.000e+0
Identity = 345/345 (100.00%), Postives = 345/345 (100.00%), Query Frame = 1
Query:   79 MESVSNIIKDLKTLEKMFEVVRKLGISKIKCNLYSNICNSPQHHGNCDNIMENYYSHAKNTFTYFICPTCFSTTFLGGFGNIWFSFLVYRNYWNKINYRILFWIMILDISCDLVFIPFEVLQTYWYFEFNSLLGTTLFCQIESLFFNISLMGSIFGKFVAASVRGWSIFFPISYRKFVSMRFINIIIATLIFGFSTLIHLAFFKWALEYDMDPVFGDCYSIHHFKWTDVLRSSIFTYFPLTASXXXXXXXXXXXXXMKSSEKGQIMKLTKGSGAVFCSIIIYGACVLPLWIGYDSSNHYNKMSWSIWNKFIFRFSYAIDPLFYLALDSNMRRATLKYFKKSEEKL 1113
            MESVSNIIKDLKTLEKMFEVVRKLGISKIKCNLYSNICNSPQHHGNCDNIMENYYSHAKNTFTYFICPTCFSTTFLGGFGNIWFSFLVYRNYWNKINYRILFWIMILDISCDLVFIPFEVLQTYWYFEFNSLLGTTLFCQIESLFFNISLMGSIFGKFVAASVRGWSIFFPISYRKFVSMRFINIIIATLIFGFSTLIHLAFFKWALEYDMDPVFGDCYSIHHFKWTDVLRSSIFTYFPLTASFLIYLLIFLKIIFMKSSEKGQIMKLTKGSGAVFCSIIIYGACVLPLWIGYDSSNHYNKMSWSIWNKFIFRFSYAIDPLFYLALDSNMRRATLKYFKKSEEKL
Sbjct:    1 MESVSNIIKDLKTLEKMFEVVRKLGISKIKCNLYSNICNSPQHHGNCDNIMENYYSHAKNTFTYFICPTCFSTTFLGGFGNIWFSFLVYRNYWNKINYRILFWIMILDISCDLVFIPFEVLQTYWYFEFNSLLGTTLFCQIESLFFNISLMGSIFGKFVAASVRGWSIFFPISYRKFVSMRFINIIIATLIFGFSTLIHLAFFKWALEYDMDPVFGDCYSIHHFKWTDVLRSSIFTYFPLTASFLIYLLIFLKIIFMKSSEKGQIMKLTKGSGAVFCSIIIYGACVLPLWIGYDSSNHYNKMSWSIWNKFIFRFSYAIDPLFYLALDSNMRRATLKYFKKSEEKL 345          
BLAST of SMED30021909 vs. Planmine SMEST
Match: SMESG000077556.1 (SMESG000077556.1)

HSP 1 Score: 363.614 bits (932), Expect = 1.885e-120
Identity = 183/270 (67.78%), Postives = 217/270 (80.37%), Query Frame = 1
Query:  295 TTFLGGFGNIWFSFLVYRNYWNKINYRILFWIMILDISCDLVFIPFEVLQTYWYFEFNSLLGTTLFCQIESLFFNISLMGSIFGKFVAASVRGWSIFFPISYRKFVSMRFINIIIATLIFGFSTLIHLAFFKWALEYDMDPVFGDCYSIHHFKWTDVLRSSIFTYFPLTASXXXXXXXXXXXXXMKSSEKGQIMKLTKGSGAVFCSIIIYGACVLPLWIGYDSSNHYNKMSWSIWNKFIFRFSYAIDPLFYLALDSNMRRATLKYFKKSE 1104
             TFLGGFGNIWFSF+V + +W K NYRILFWIMILD+ CD +FIPFEV+QT++Y  FN  LGT LFC+IESL FN++L  SIFG+F+AA VRGWSIF PISYRK VSMR IN+II   + GFS++ HL  FKW L++ MDP+FGDC SIHH+K TD +RS IFTYFPL+A FLIYL+IFLKIIFMKS+EKG++ KL++GSGAVFCSIIIYGACVLPLWIGY S  HYN MSWSIWNKFIFRFS+AI+P  ++ L    +   L   K  E
Sbjct:   17 ATFLGGFGNIWFSFIVIKGFWKKANYRILFWIMILDVICDFIFIPFEVIQTHFYLTFNVSLGTDLFCEIESLLFNMTLHSSIFGRFIAAFVRGWSIFLPISYRKIVSMRLINVIIGIFVIGFSSIFHLIIFKWGLDFKMDPIFGDCTSIHHYKSTDTIRSIIFTYFPLSACFLIYLMIFLKIIFMKSNEKGEMRKLSRGSGAVFCSIIIYGACVLPLWIGYSSEKHYNAMSWSIWNKFIFRFSFAINP--FVKLPKGRKNGKLPPLKDEE 284          
BLAST of SMED30021909 vs. Planmine SMEST
Match: SMESG000056526.1 (SMESG000056526.1)

HSP 1 Score: 140.969 bits (354), Expect = 1.751e-38
Identity = 88/282 (31.21%), Postives = 149/282 (52.84%), Query Frame = 1
Query:  307 GGFGNIWFSFLV--YRNYWNKINYRILFWIMILDISCDLVFIPFEVLQTYWYFEFNSLLGTTLFCQIESLFFNISLMGSIFGKFVAASVRGWSIFFPISYRKFVSMRFINIIIATLIFGFSTLIHLAFFKWALEYDMDPVFGDCYSIHHFKWTDVLRSSIFTYFPLTASXXXXXXXXXXX--XXMKSSEKGQIMKLTKGSGAVFCSIIIYGACVLPLWIGYDSSNHYNKMSWSIWNKFIFRFSYAIDPLFYLALDSNMRRATLKYFKKSEEKL*NICILAIF 1140
            G  GN+W   L+  ++N WN+  YR++  I+I +   + + IP+E  Q+Y     N +LGT L C IE   F +++  S F + + A  R  ++  PI +++  + R + I++ ++      +  +        Y + P+ GDC      K  D  R+S+F + P+  S L Y  I ++I    + S+++  ++K  KGS A+   ++IY  C++  W  Y+S N+ + +  S W KF  R SY  +PLFY+ LDSNMR ++LK  + +  K   I IL IF
Sbjct:   32 GTLGNLWCGLLIIFFKNLWNRPIYRLILGIIIPNFVSNSICIPYEATQSYSLISLNQILGTDLGCAIEGTVFILAMSISNFNQMIVACYRFCAVVSPILFKRISTNRMVLILMLSISVAPVLIYFIGGINTLFWYRVQPLIGDCSENSVSKEIDYFRNSLFLFTPIIVSVLAYAGIIIRILFAGLDSNKRRTLLKRAKGSMALGICMVIYSTCIILYWTDYNSQNYGSNIDISFWKKFANRASYGFNPLFYVTLDSNMRESSLKIIRFANSKKKEI-ILQIF 312          
BLAST of SMED30021909 vs. Planmine SMEST
Match: SMESG000056541.1 (SMESG000056541.1)

HSP 1 Score: 132.494 bits (332), Expect = 2.453e-35
Identity = 84/268 (31.34%), Postives = 145/268 (54.10%), Query Frame = 1
Query:  307 GGFGNIWFSFLVY--RNYWNKINYRILFWIMILDISCDLVFIPFEVLQTYWYFEFNSLLGTTLFCQIESLFFNISLMGSIFGKFVAASVRGWSIFFPISYRKFVSMRFINIIIATLIFGFSTLIHLAFFKWALEYDMDPVFGDCYSIHHFKWTDVLRSSIFTYFPLTASXXXXXXXXXXXXXMK--SSEKGQIMKLTKGSGAVFCSIIIYGACVLPLWIGYDSSNHYNKMSWSIWNKFIFRFSYAIDPLFYLALDSNMRRATLKYFKK 1098
            G  GN+W   +++  ++ W    YRI+F I   D+  +   I +E  QT++       LGT L C  E+  F+I++  S     +AA  R +++  PI +++F + R + I++ +       L  LA   W + Y+     GDC  I   K    LR+++F + P++ S L Y +IF+KI+F+   +S++ +I+   KGS A+  + IIYG+C++  WI Y+S ++   +   +W KF  R SY  +P+FYL +D N+  A  K F++
Sbjct:   31 GIVGNLWTCIVIFFVKSLWKLPAYRIIFSIAFPDLLMNAFCITYESTQTFYLMTKKEYLGTILICMFEATLFSITMSLSNVNSMIAAVFRMFAVITPIRFKRFSTNRIVAIVVVSTSVFPICLYFLAGIPWLITYEFHKTVGDCTEIAPIKGMAELRTTLFQFLPISVSALAYFVIFMKILFVSFDNSQRIEILHRAKGSMALCINTIIYGSCIIMYWIVYNSGDYGIDIQTDLWRKFAIRASYGSNPVFYLTMDKNIMIANGKIFRR 298          
BLAST of SMED30021909 vs. Planmine SMEST
Match: SMESG000056512.1 (SMESG000056512.1)

HSP 1 Score: 129.798 bits (325), Expect = 2.187e-34
Identity = 86/301 (28.57%), Postives = 151/301 (50.17%), Query Frame = 1
Query:  232 ENYYSHAKNT-FTYFI---CPTCFSTTFLGGFGNIW--FSFLVYRNYWNKINYRILFWIMILDISCDLVFIPFEVLQTYWYFEFNSLLGTTLFCQIESLFFNISLMGSIFGKFVAASVRGWSIFFPISYRKFVSMRFINIIIATLIFGFSTLIHLAFFKWALEYDMDPVFGDCYSIHHFKWTDVLRSSIFTYFPLTASXXXXXXXX--XXXXXMKSSEKGQIMKLTKGSGAVFCSIIIYGACVLPLWIGYDSSNHYNKMSWSIWNKFIFRFSYAIDPLFYLALDSNMRRATLKYFKKSEEK 1110
             +Y +  +N+ FTY I     +   +TF G  GN+W   + ++ +  WN+  YR++  I+I D   + + IP+E  Q+Y     N ++G+ + C +E   F I++  S   + + A  R  ++  PI +R   + R + I++ ++      +  +        Y + P+ GDC     F   D  R+S F + P   S L Y+ I   +    + S+ +  ++K  KGS A+  S+ IY  C++  WI Y+S+N+   +  S W KF  R SY + PLFY+ LD+N+R ++L   K +  K
Sbjct:    4 SSYENTTRNSEFTYIIPWYIASIIISTF-GTIGNLWCGSTIIICKRLWNRPIYRLILGIIIPDFVTNSICIPYEATQSYSLIFLNRIIGSDISCAVEGTVFIIAMSMSNINQMIVACYRFCAVVSPIRFRGISTNRMVLILMLSISVAPVLIYFIGGINTLFWYRVQPLIGDCSEYSLFIEIDNFRNSFFQFIPTLISVLAYIGIIFRILFAGLDSNTRKTLLKRAKGSLALGLSMAIYSTCIIVYWIDYNSNNYGYNIDNSFWKKFAIRASYGLTPLFYVTLDNNIRESSLHVIKHTNNK 303          
The following BLAST results are available for this feature:
BLAST of SMED30021909 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021909 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000077557.10.000e+0100.00SMESG000077557.1[more]
SMESG000077556.11.885e-12067.78SMESG000077556.1[more]
SMESG000056526.11.751e-3831.21SMESG000056526.1[more]
SMESG000056541.12.453e-3531.34SMESG000056541.1[more]
SMESG000056512.12.187e-3428.57SMESG000056512.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021909 ID=SMED30021909|Name=SMED30021909|organism=Schmidtea mediterranea sexual|type=transcript|length=1170bp
GTAATTAAAAGAAAACGCTAGGATGAAGGTTATAATCATTACCAGACTAC
GCAACAGATTATATAGAAATTAAAGAAAATGGAATCCGTCAGCAACATAA
TCAAAGATTTAAAAACCTTAGAAAAAATGTTCGAAGTGGTAAGAAAACTA
GGAATATCAAAAATAAAATGTAATCTATACTCCAATATTTGCAATTCTCC
ACAACATCATGGAAATTGTGATAACATTATGGAGAATTATTATTCTCATG
CGAAAAACACCTTCACCTACTTCATTTGCCCCACATGCTTTTCAACAACA
TTCTTAGGAGGCTTTGGAAATATTTGGTTCAGTTTTTTGGTTTATAGAAA
TTACTGGAACAAAATAAATTATAGGATTCTGTTTTGGATAATGATCCTTG
ACATTTCATGTGATCTAGTGTTTATTCCATTTGAAGTCTTGCAAACATAT
TGGTATTTTGAGTTCAATTCTCTTCTGGGAACAACACTTTTTTGTCAAAT
TGAATCACTATTTTTCAACATTAGTTTGATGGGGTCAATTTTCGGTAAAT
TTGTCGCGGCATCTGTCAGAGGTTGGTCTATATTTTTCCCAATTAGCTAT
CGTAAATTTGTTTCAATGCGTTTCATAAATATTATTATTGCAACTTTAAT
TTTTGGATTTTCAACCCTTATCCATTTGGCCTTTTTCAAATGGGCCTTGG
AATATGATATGGACCCGGTCTTTGGTGATTGCTATAGCATTCATCATTTC
AAATGGACAGATGTTTTGCGATCGTCTATTTTTACGTATTTTCCCCTGAC
AGCTAGTTTCTTAATTTATTTGTTGATATTTTTAAAAATAATTTTTATGA
AATCAAGTGAAAAGGGTCAAATAATGAAGTTGACAAAAGGTAGCGGTGCA
GTGTTTTGCAGCATAATAATTTATGGTGCATGCGTTTTGCCATTGTGGAT
CGGATACGACTCTTCAAATCATTATAATAAAATGTCATGGAGCATCTGGA
ATAAATTTATATTTCGATTCAGTTATGCGATTGATCCACTATTTTACCTG
GCTTTGGATTCTAACATGAGAAGAGCAACTTTGAAATATTTCAAGAAATC
TGAAGAGAAATTATGAAACATTTGTATTCTTGCCATTTTTTGTTGAAATT
CATTTTAATTTGAACAGTAT
back to top

protein sequence of SMED30021909-orf-1

>SMED30021909-orf-1 ID=SMED30021909-orf-1|Name=SMED30021909-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=346bp
MESVSNIIKDLKTLEKMFEVVRKLGISKIKCNLYSNICNSPQHHGNCDNI
MENYYSHAKNTFTYFICPTCFSTTFLGGFGNIWFSFLVYRNYWNKINYRI
LFWIMILDISCDLVFIPFEVLQTYWYFEFNSLLGTTLFCQIESLFFNISL
MGSIFGKFVAASVRGWSIFFPISYRKFVSMRFINIIIATLIFGFSTLIHL
AFFKWALEYDMDPVFGDCYSIHHFKWTDVLRSSIFTYFPLTASFLIYLLI
FLKIIFMKSSEKGQIMKLTKGSGAVFCSIIIYGACVLPLWIGYDSSNHYN
KMSWSIWNKFIFRFSYAIDPLFYLALDSNMRRATLKYFKKSEEKL*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR017452GPCR_Rhodpsn_7TM
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane