SMED30011995

Overview
NameSMED30011995
Smed IDSMED30011995
Length (bp)902
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30011995 (SMED30011995) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011995 (SMED30011995) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30011995

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
testisSMED30011995SMESG000079965.1 Contig1552_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
early male germ cellSMED30011995SMESG000079965.1 Contig1552_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism asexual adult cDNA to DNA expression microarray evidence
testis primordiumSMED30011995SMESG000079965.1 Contig1552_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011995 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000445:35941..36841 +4496
v31.000142:7737..8638 +4436
Homology
[Close]
BLAST of SMED30011995 vs. TrEMBL
Match: A0A183T530 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS11578 PE=4 SV=1)

HSP 1 Score: 100.908 bits (250), Expect = 1.339e-21
Identity = 60/223 (26.91%), Postives = 112/223 (50.22%), Query Frame = 1 
Query:   28 SKCFQFKQTFGKLVLYIRVKKKMNMMVICSGFILFLSDLILTVGIISGHGWGCYINQKNKTECHMDLGYRWASSDKKSAGINISGALAYIGLITLFGGCVLMILTGTRLRIGMIRPILITRLILCMIANFVIIVTTIIYIGSYARLKYSTDGYPNLVDDYGISFYMSIIGWLILVIAIVYDGMGVVIPYGFESPTDIFLWDWLEKYYKYNRTKYLILKKKDFP 696
            SK  +FKQ  GKLV Y R++ +   + I    + ++ DL+LT  +     W C+    N T+C++D G+ W   + + AGI  +   A  G   +  GC+++ L+             + R     +  +++  + +I++    R+K   D Y  L+ +Y     + +IGW ++V+A   D +G V+PY  ++P D ++W WL ++Y Y++ + L  K +  P
Sbjct:    5 SKALRFKQGLGKLVFYFRIQCREERIWIYVCLLAWIGDLLLTYSLFVDKTWSCW-EAGNLTQCNLDYGFEW-PIESQPAGITTAVVFAICGQALISIGCLILGLSLPSALCTQPASFYVLRATCLTVGVYLMGFSLMIHVIVAERIK--MDFY-KLITNYSSGLLLFLIGWTLIVVADTVDMVGCVLPYALQNPADRYIWLWLRRHYIYHKHRLLEEKYRIVP 222
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BLAST of SMED30011995 vs. TrEMBL
Match: A0A3P7LLH4 (Uncharacterized protein OS=Dibothriocephalus latus OX=60516 GN=DILT_LOCUS8378 PE=4 SV=1)

HSP 1 Score: 97.4413 bits (241), Expect = 3.368e-20
Identity = 58/223 (26.01%), Postives = 109/223 (48.88%), Query Frame = 1 
Query:   28 SKCFQFKQTFGKLVLYIRVKKKMNMMVICSGFILFLSDLILTVGIISGHGWGCYINQKNKTECHMDLGYRWASSDKKSAGINISGALAYIGLITLFGGCVLMILTGTRLRIGMIRPILITRLILCMIANFVIIVTTIIYIGSYARLKYSTDGYPNLVDDYGISFYMSIIGWLILVIAIVYDGMGVVIPYGFESPTDIFLWDWLEKYYKYNRTKYLILKKKDFP 696
            S+  +FKQ FGKL  Y RV+ +   +      + ++ DL+LT  +     WGC+    N T+C++D G+ W   D + AGI  +   A  G   +   C +  L+   +         + R +      +++  + +I++    R+K   D Y  LV +Y     + + GW ++++A   D +G V+PY  ++PTD ++W WL ++Y + + + L  + +  P
Sbjct:    5 SRALRFKQGFGKLEFYFRVQCREERIWTYVCLLAWVGDLLLTYSLFVDKTWGCW-EAGNSTQCNLDYGFEW-PIDSQPAGITTAVVFATCGQALITIACAIQGLSMLSMLCVQPASFYVFRAVCLTTGVYLLGFSLMIHVIVAERIK--MDFY-KLVTNYSSGLLLFLFGWSLVIVADTVDMVGCVLPYALQNPTDRYIWLWLHRHYIFYKYRLLYERYRIVP 222
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BLAST of SMED30011995 vs. Planmine SMEST
Match: SMESG000079965.1 (SMESG000079965.1)

HSP 1 Score: 489.96 bits (1260), Expect = 8.720e-173
Identity = 241/241 (100.00%), Postives = 241/241 (100.00%), Query Frame = 1 
Query:   10 EIFMSESKCFQFKQTFGKLVLYIRVKKKMNMMVICSGFILFLSDLILTVGIISGHGWGCYINQKNKTECHMDLGYRWASSDKKSAGINISGALAYIGLITLFGGCVLMILTGTRLRIGMIRPILITRLILCMIANFVIIVTTIIYIGSYARLKYSTDGYPNLVDDYGISFYMSIIGWLILVIAIVYDGMGVVIPYGFESPTDIFLWDWLEKYYKYNRTKYLILKKKDFPTMDVTELGVVFE 732
            EIFMSESKCFQFKQTFGKLVLYIRVKKKMNMMVICSGFILFLSDLILTVGIISGHGWGCYINQKNKTECHMDLGYRWASSDKKSAGINISGALAYIGLITLFGGCVLMILTGTRLRIGMIRPILITRLILCMIANFVIIVTTIIYIGSYARLKYSTDGYPNLVDDYGISFYMSIIGWLILVIAIVYDGMGVVIPYGFESPTDIFLWDWLEKYYKYNRTKYLILKKKDFPTMDVTELGVVFE
Sbjct:  314 EIFMSESKCFQFKQTFGKLVLYIRVKKKMNMMVICSGFILFLSDLILTVGIISGHGWGCYINQKNKTECHMDLGYRWASSDKKSAGINISGALAYIGLITLFGGCVLMILTGTRLRIGMIRPILITRLILCMIANFVIIVTTIIYIGSYARLKYSTDGYPNLVDDYGISFYMSIIGWLILVIAIVYDGMGVVIPYGFESPTDIFLWDWLEKYYKYNRTKYLILKKKDFPTMDVTELGVVFE 554
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BLAST of SMED30011995 vs. Planmine SMEST
Match: SMESG000080031.1 (SMESG000080031.1)

HSP 1 Score: 321.627 bits (823), Expect = 5.262e-111
Identity = 152/235 (64.68%), Postives = 188/235 (80.00%), Query Frame = 1 
Query:   19 MSESKCFQFKQTFGKLVLYIRVKKKMNMMVICSGFILFLSDLILTVGIISGHGWGCYINQKNKTECHMDLGYRWASSDKKSAGINISGALAYIGLITLFGGCVLMILTGTRLRIGMIRPILITRLILCMIANFVIIVTTIIYIGSYARLK-YSTDGYPNLVDDYGISFYMSIIGWLILVIAIVYDGMGVVIPYGFESPTDIFLWDWLEKYYKYNRTKYLILKKKDFPTMDVTELG 720
            M ESK  +FKQ FGK++LY R+K+KMNMM+ICS   LF +DLILTVG+ISG GWGCY N KN TEC +DLGYRW  +D+K+AGI I+ AL   GLI LF GC+LMI+TGT L IGM R +L+TRL+LC++A + +IVT ++Y+GSYARLK  ST GYPN++DDYG SFY++++GWL+L IAI YDGMG+VIPYGFES TDIFL  WLEK+Y Y R KY+ILK KD P MDV +L 
Sbjct:    1 MFESKSLRFKQAFGKILLYTRMKRKMNMMIICSSLTLFTADLILTVGLISGSGWGCYRNTKNTTECKLDLGYRWTRTDEKTAGITIAEALGIAGLIALFLGCILMIVTGTLLAIGMTRYVLVTRLVLCILACYFVIVTIVMYVGSYARLKSSSTYGYPNIIDDYGGSFYITVVGWLMLAIAITYDGMGIVIPYGFESTTDIFLRKWLEKHYMYQRKKYVILKDKDMPDMDVQQLA 235
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BLAST of SMED30011995 vs. Planmine SMEST
Match: SMESG000002560.1 (SMESG000002560.1)

HSP 1 Score: 187.963 bits (476), Expect = 1.525e-58
Identity = 99/234 (42.31%), Postives = 154/234 (65.81%), Query Frame = 1 
Query:   19 MSESKCFQFKQTFGKLVLYIRVKKKMNMMVICSGFILFLSDLILTVGIISGHGWGCYINQKNKTECHMDLGYRWASSDKKSAGINISGALAYIGLITLFGGCVLMILTGTRLRIGMIRPILITRLILCMIANFVIIVTTIIYIGSYARLKYSTDG-YPNLVDDYGISFYMSIIGWLILVIAIVYDGMGVVIPYGFESPTDIFLWDWLEKYYKYNRTKYLILKKKDFPTMDVTEL 717
            M ES+ F+FKQ FG+++L+  +KKK N MV+ +  +++ SDL+LT G+++G GWGCY      TEC MDLG+RW S  +KS+ I +   L  IGL+++F   +L+I  G   ++ M++  L+ RL   +   + IIV  ++YI +Y R+K +    YPN++DD+G +FY+S+ GW +L +A++ DG+G++IPYGFE  +DIF   WLEK+Y + R KY+  +  D P   V EL
Sbjct:    1 MFESRSFRFKQLFGRILLHTYLKKKSNFMVLATALMMWTSDLLLTGGLLAGSGWGCYYLNDRSTECKMDLGFRWKSVSEKSSEIIVVEVLVIIGLLSIFLSSILLIFNGLFPQVIMMKGFLLIRLFFDISGCYFIIVGILLYISTYNRMKITNKNIYPNIIDDFGFAFYVSMTGWFLLSLAVILDGVGIIIPYGFEGKSDIFFRKWLEKHYFFMRKKYVYKRDYDMPPTHVDEL 234
[Close]
BLAST of SMED30011995 vs. Planmine SMEST
Match: SMESG000033583.1 (SMESG000033583.1)

HSP 1 Score: 147.132 bits (370), Expect = 1.775e-42
Identity = 72/232 (31.03%), Postives = 142/232 (61.21%), Query Frame = 1 
Query:   25 ESKCFQFKQTFGKLVLYIRVKKKMNMMVICSGFILFLSDLILTVGIISGHGWGCYINQKNKTECHMDLGYRWASSDKKSAGINISGALAYIGLITLFGGCVLMILTGTRLRIGMIRPILITRLILCMIANFVIIVTTIIYIGSYARLKYSTDG-YPNLVDDYGISFYMSIIGWLILVIAIVYDGMGVVIPYGFESPTDIFLWDWLEKYYKYNRTKYLILKKKDFPTMDVTEL 717
            +S+ F++KQ + KL L+I + KK+  M+ICS   L++SD ++T G++SG GW CY N++N T+C +D+G+RW           +  AL  + L+T+ G  ++ +++     +G+ +  L+T ++L + +  ++I+  ++Y+ +  +L  S    YPN+ ++YG SF+++IIGW+IL I++  + MG++    F+   D ++  +LEK+Y++   KY+    +D P + + + 
Sbjct:    6 QSRSFKYKQDYAKLKLHIHINKKLLKMIICSRLTLWVSDCLITFGLVSGSGWACYKNEQNDTKCDLDIGFRWKHHSASGISFTVFLALCSLILLTIIG--IMHLISNVNTYLGLRKRFLMTLILLTVTSALLLILALVLYMSAIVKLCRSRKPVYPNIRNEYGTSFFVTIIGWVILCISVSVEFMGIINVRCFQGWLDQYIVSFLEKHYEFMYKKYIEFNTRDIPIISLEKF 235
[Close]
BLAST of SMED30011995 vs. Planmine SMEST
Match: SMESG000033060.1 (SMESG000033060.1)

HSP 1 Score: 142.51 bits (358), Expect = 6.136e-41
Identity = 77/228 (33.77%), Postives = 130/228 (57.02%), Query Frame = 1 
Query:   19 MSESKCFQFKQTFGKLVLYIRVKKKMNMMVICSGFILFLSDLILTVGIISGHGWGCY-INQKNKTECHMDLGYRWASSDKKSAGINISGALAYIGLITLFGGCVLMILTGTRLRIGMIRPILITRLILCMIANFVIIVTTIIYIGSYARLKYST-DGYPNLVDDYGISFYMSIIGWLILVIAIVYDGMGVVIPYGFESPTDIFLWDWLEKYYKYNRTKYLILKKKDFP 696
            MS  +     +T  KL L+I +++K ++ +    F+    DL+ TVG ++G GWGCY +    +  C +D G RW     KS  I  +  L  IGL+ +    +L+I T     + +++P L+ R IL ++  F+IIV  I+YIG Y RL+    D +P +V+ +G S Y+S  GW+ +V+A+ +D   +++P  +E+ TD F  +WL+++YKY   KY++  + D P
Sbjct:    1 MSVQRHHYLLETIAKLTLFITMERKKSIQMFIVYFLYVCGDLLTTVGFLNGTGWGCYNVTGSVQIACDVDFGIRW---KWKSEIIYCAVVLGIIGLVMMTFVMILIISTTMMSNLSIMKPFLMARFILAILGAFLIIVAMILYIGGYPRLETMVLDEFPYVVNTFGRSVYISYAGWIFIVLAVTFDAQSLILPIYYETETDYFFRNWLQRFYKYLYNKYMLYNQFDIP 225
The following BLAST results are available for this feature:
BLAST of SMED30011995 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 SMED30011995 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 SMED30011995 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 SMED30011995 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 SMED30011995 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 SMED30011995 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 SMED30011995 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 SMED30011995 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A183T5301.339e-2126.91Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A3P7LLH43.368e-2026.01Uncharacterized protein OS=Dibothriocephalus latus... [more]
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BLAST of SMED30011995 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 SMED30011995 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 SMED30011995 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 SMED30011995 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 SMED30011995 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 SMED30011995 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000079965.18.720e-173100.00SMESG000079965.1[more]
SMESG000080031.15.262e-11164.68SMESG000080031.1[more]
SMESG000002560.11.525e-5842.31SMESG000002560.1[more]
SMESG000033583.11.775e-4231.03SMESG000033583.1[more]
SMESG000033060.16.136e-4133.77SMESG000033060.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011995 ID=SMED30011995|Name=SMED30011995|organism=Schmidtea mediterranea sexual|type=transcript|length=902bp
AATCATTAAGAAATTTTCATGTCTGAAAGTAAATGTTTCCAATTCAAACA
AACATTTGGAAAATTAGTTTTATACATAAGAGTGAAAAAGAAAATGAATA
TGATGGTGATTTGTAGTGGATTTATACTGTTTTTATCTGATCTCATTCTC
ACTGTCGGAATCATATCTGGTCACGGATGGGGCTGTTATATCAACCAGAA
AAATAAAACCGAATGTCACATGGATTTGGGCTATCGATGGGCGTCTAGTG
ACAAAAAGTCTGCTGGAATTAATATTTCCGGAGCACTTGCGTATATTGGA
TTAATTACATTGTTTGGTGGATGCGTTTTAATGATATTGACTGGGACGAG
ACTACGAATCGGAATGATTAGACCTATTTTAATAACAAGATTAATATTAT
GCATGATAGCTAACTTTGTTATCATTGTAACGACAATAATATACATTGGC
AGTTACGCTCGACTGAAATATTCGACGGATGGATATCCCAATCTGGTGGA
TGATTATGGCATTTCCTTTTATATGTCAATAATAGGTTGGTTAATCTTGG
TCATTGCAATAGTATATGATGGAATGGGGGTTGTTATTCCGTACGGATTT
GAGAGTCCAACTGATATATTTTTATGGGACTGGTTAGAAAAGTATTATAA
GTATAACCGAACAAAATATTTAATTTTGAAGAAAAAAGATTTTCCTACAA
TGGATGTCACTGAACTAGGGGTTGTGTTCGAATAAAGTCGGAGGGCCTTT
AGTATTTTCTTAAGCGGTCATTTGCAACATACTTTTAGATTTGGTTTATT
CCTTGAGAAGAATTATCTGCCAATGAGCTTATTTGAATCAAACTAAGTTG
GCAAAACAAAATTGTTCATAGGCATCTCCAAATCATGACATCTTTATTTC
AG
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protein sequence of SMED30011995-orf-1

>SMED30011995-orf-1 ID=SMED30011995-orf-1|Name=SMED30011995-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=239bp
MSESKCFQFKQTFGKLVLYIRVKKKMNMMVICSGFILFLSDLILTVGIIS
GHGWGCYINQKNKTECHMDLGYRWASSDKKSAGINISGALAYIGLITLFG
GCVLMILTGTRLRIGMIRPILITRLILCMIANFVIIVTTIIYIGSYARLK
YSTDGYPNLVDDYGISFYMSIIGWLILVIAIVYDGMGVVIPYGFESPTDI
FLWDWLEKYYKYNRTKYLILKKKDFPTMDVTELGVVFE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0002030early male germ cell
PLANA:0003304testis primordium
Vocabulary: INTERPRO
TermDefinition
IPR019774Aromatic-AA_hydroxylase_C
Vocabulary: biological process
TermDefinition
GO:0055114oxidation-reduction process
Vocabulary: molecular function
TermDefinition
GO:0016714oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 86..108
NoneNo IPR availableTMHMMTMhelixcoord: 29..51
NoneNo IPR availableTMHMMTMhelixcoord: 163..182
NoneNo IPR availableTMHMMTMhelixcoord: 121..143