SMED30014766

Overview
NameSMED30014766
Smed IDSMED30014766
Length (bp)552
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30014766

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30014766h1SMcG0012649 SmedASXL_000510SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30014766h1SMcG0012649 SmedASXL_019401SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30014766h1SMcG0012649 dd_Smed_v4_19769_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30014766h1SMcG0012649 dd_Smed_v6_15797_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30014766h1SMcG0012649 dd_Smed_v6_19769_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
SMED30014766 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002389:34232..38141 +2746
Homology
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BLAST of SMED30014766 vs. Planmine SMEST
Match: SMESG000074227.1 (SMESG000074227.1)

HSP 1 Score: 364.77 bits (935), Expect = 1.046e-122
Identity = 184/184 (100.00%), Postives = 184/184 (100.00%), Query Frame = 1 
Query:    1 EGDVNKLNQNQESIFDIANTLKNESFVNVMLDHCNQPLKLSVTKSFEVILSNLVESENWNLLSQIIGHAHVDEISNKYLISLSISVLKKQNTTELFDKIMSLCLYKNIILCGGETVVTAVIKSGIPSSTMVSILERKIFDTNKTNLENEAPLILACKFLLFDVVNVLVALNCDLKRYRHEAIES 552
            EGDVNKLNQNQESIFDIANTLKNESFVNVMLDHCNQPLKLSVTKSFEVILSNLVESENWNLLSQIIGHAHVDEISNKYLISLSISVLKKQNTTELFDKIMSLCLYKNIILCGGETVVTAVIKSGIPSSTMVSILERKIFDTNKTNLENEAPLILACKFLLFDVVNVLVALNCDLKRYRHEAIES
Sbjct:  533 EGDVNKLNQNQESIFDIANTLKNESFVNVMLDHCNQPLKLSVTKSFEVILSNLVESENWNLLSQIIGHAHVDEISNKYLISLSISVLKKQNTTELFDKIMSLCLYKNIILCGGETVVTAVIKSGIPSSTMVSILERKIFDTNKTNLENEAPLILACKFLLFDVVNVLVALNCDLKRYRHEAIES 716
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BLAST of SMED30014766 vs. Planmine SMEST
Match: SMESG000074227.1 (SMESG000074227.1)

HSP 1 Score: 365.155 bits (936), Expect = 1.287e-122
Identity = 184/184 (100.00%), Postives = 184/184 (100.00%), Query Frame = 1 
Query:    1 EGDVNKLNQNQESIFDIANTLKNESFVNVMLDHCNQPLKLSVTKSFEVILSNLVESENWNLLSQIIGHAHVDEISNKYLISLSISVLKKQNTTELFDKIMSLCLYKNIILCGGETVVTAVIKSGIPSSTMVSILERKIFDTNKTNLENEAPLILACKFLLFDVVNVLVALNCDLKRYRHEAIES 552
            EGDVNKLNQNQESIFDIANTLKNESFVNVMLDHCNQPLKLSVTKSFEVILSNLVESENWNLLSQIIGHAHVDEISNKYLISLSISVLKKQNTTELFDKIMSLCLYKNIILCGGETVVTAVIKSGIPSSTMVSILERKIFDTNKTNLENEAPLILACKFLLFDVVNVLVALNCDLKRYRHEAIES
Sbjct:  556 EGDVNKLNQNQESIFDIANTLKNESFVNVMLDHCNQPLKLSVTKSFEVILSNLVESENWNLLSQIIGHAHVDEISNKYLISLSISVLKKQNTTELFDKIMSLCLYKNIILCGGETVVTAVIKSGIPSSTMVSILERKIFDTNKTNLENEAPLILACKFLLFDVVNVLVALNCDLKRYRHEAIES 739
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BLAST of SMED30014766 vs. Planmine SMEST
Match: SMESG000007087.1 (SMESG000007087.1)

HSP 1 Score: 284.648 bits (727), Expect = 6.420e-89
Identity = 155/184 (84.24%), Postives = 166/184 (90.22%), Query Frame = 1 
Query:    1 EGDVNKLNQNQESIFDIANTLKNESFVNVMLDHCNQPLKLSVTKSFEVILSNLVESENWNLLSQIIGHAHVDEISNKYLISLSISVLKKQNTTELFDKIMSLCLYKNIILCGGETVVTAVIKSGIPSSTMVSILERKIFDTNKTNLENEAPLILACKFLLFDVVNVLVALNCDLKRYRHEAIES 552
            EGDVNKLN NQ+SIFDIAN L+NESFVNVMLDHC QPL+LSVTKSFE+ILSNLVESENW+LLSQII +A VDEISNKYL+SLSISVLKKQ T ELFDKIMSLCL KNII CGGET VTA+IKSGI SSTMVSIL RK+FD NKTNL NE PL+LAC+ LL DVV VLVALNCDLKRYRHEAIES
Sbjct: 1500 EGDVNKLNTNQDSIFDIANNLRNESFVNVMLDHCKQPLELSVTKSFEMILSNLVESENWDLLSQIIDNARVDEISNKYLMSLSISVLKKQKTAELFDKIMSLCLDKNIIFCGGETFVTALIKSGIHSSTMVSILARKLFDINKTNLGNETPLVLACEGLLLDVVKVLVALNCDLKRYRHEAIES 1683
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BLAST of SMED30014766 vs. Planmine SMEST
Match: SMESG000007100.1 (SMESG000007100.1)

HSP 1 Score: 231.491 bits (589), Expect = 3.792e-74
Identity = 119/184 (64.67%), Postives = 149/184 (80.98%), Query Frame = 1 
Query:    1 EGDVNKLNQNQESIFDIANTLKNESFVNVMLDHCNQPLKLSVTKSFEVILSNLVESENWNLLSQIIGHAHVDEISNKYLISLSISVLKKQNTTELFDKIMSLCLYKNIILCGGETVVTAVIKSGIPSSTMVSILERKIFDTNKTNLENEAPLILACKFLLFDVVNVLVALNCDLKRYRHEAIES 552
            EG+VN L++N ESIFDIA  L+NE+F+ +MLDHC Q L+LSVTKS E+ILSNLV+SENW+LL Q+I +A VDEISN+YL+ L ISVL+K+NT ELFD+I+S+C  KN IL  GET VTA++KS I  +TMVSIL RK+FD NK NL  + PLILAC+ LLF VVN L+ LNCDLK ++ +AIES
Sbjct:  240 EGNVNHLDENNESIFDIARKLRNENFIYLMLDHCKQRLELSVTKSMEIILSNLVDSENWDLLFQVIDNAKVDEISNEYLLFLCISVLRKRNTLELFDEIISICTDKNAILHNGETFVTALLKSDINPATMVSILNRKLFDINKANLHKQVPLILACENLLFVVVNALLKLNCDLKYHKSQAIES 423
[Close]
BLAST of SMED30014766 vs. Planmine SMEST
Match: SMESG000007103.1 (SMESG000007103.1)

HSP 1 Score: 75.0998 bits (183), Expect = 6.776e-16
Identity = 53/184 (28.80%), Postives = 100/184 (54.35%), Query Frame = 1 
Query:    1 EGDVNKLNQNQESIFDIANTLKNESFVNVMLDHCNQPLKLSVTKSFEVILSNLVESENWNLLSQIIGHAHVDEISNKYLISLSISVLKKQNTTELFDKIMSLCLYKNIILCGGETVVTAVIKSGIPSSTMVSILERKIFDTNKTNLENEAPLILACKFLLFDVVNVLVALNCDLKRYRHEAIES 552
            EGD+ K N    S   +A  +K++ + N++L+ C + ++L   +     L  +V  +  ++LS  +    + +   ++L+ L +  LK Q + +++  I+  C  K+IIL  GET +T ++K+    S +  I+  K FD NK NL NE+ L++AC+ L  ++V  LV   CD+    + A+++
Sbjct:   30 EGDIIKTNAMNNSALSLAYKIKDKKYYNLLLN-CFKSIELLSDEFGRNFLRQIV-IDKADVLSNTLDKCLIKDCHTEFLLDLGLMALK-QKSNDIYKNILDHCKTKDIILKNGETFLTNLVKNKEDISIITDIVTSKYFDINKVNLRNESILMIACEQLNENIVKFLVRSGCDVTYNSYGAVQA 210

HSP 2 Score: 66.2402 bits (160), Expect = 7.962e-13
Identity = 43/161 (26.71%), Postives = 86/161 (53.42%), Query Frame = 1 
Query:   64 KNESFVNVMLDHCNQPLKLSVTKSFEVILSNLVESENWNLLSQIIGHAHVDEISNKYLISLSISVLKKQNTTELFDKIMSLCLYKNIILCGGETVVTAVIKSGIPSSTMVSILERKIFDTNKTNLENEAPLILACKFLLFDVVNVLVALNCDLKRYRHEAI 546
            +++S+ + +L+ C   L++   +S   +L  L        L  I+    +   SN+ L+ L++ VLK     E ++KI+ +C+  + I   GET ++++ K+ +  S + S++E  +FD  KTN + E  L+LAC  L+  V+ +L+   C++    + A+
Sbjct:  321 QDKSYFSQLLERCPGNLQILSNESGIKLLFKLSSETKLKALEFILSKIEMAGNSNENLLKLAVQVLK-NGGIETYNKIIKMCIEFDAIFDDGETFISSLFKNNVKESIIKSVIESGLFDAKKTNNKAENALMLACSRLMTTVIPILLNQGCEIAYSGYNAV 480
The following BLAST results are available for this feature:
BLAST of SMED30014766 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 SMED30014766 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 SMED30014766 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 SMED30014766 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 SMED30014766 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 SMED30014766 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 SMED30014766 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 SMED30014766 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 SMED30014766 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 SMED30014766 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 SMED30014766 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 SMED30014766 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 SMED30014766 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 SMED30014766 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000074227.11.046e-122100.00SMESG000074227.1[more]
SMESG000074227.11.287e-122100.00SMESG000074227.1[more]
SMESG000007087.16.420e-8984.24SMESG000007087.1[more]
SMESG000007100.13.792e-7464.67SMESG000007100.1[more]
SMESG000007103.16.776e-1628.80SMESG000007103.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014766 ID=SMED30014766|Name=SMED30014766|organism=Schmidtea mediterranea sexual|type=transcript|length=552bp
GAAGGAGATGTGAACAAATTGAACCAAAATCAAGAGAGCATATTTGATAT
TGCAAATACTTTAAAAAATGAAAGTTTTGTTAATGTTATGCTGGACCATT
GCAACCAGCCATTGAAATTGTCAGTTACCAAATCATTTGAAGTGATCTTG
TCTAATTTGGTCGAATCTGAAAATTGGAATTTATTATCTCAAATAATTGG
CCATGCTCATGTTGATGAAATAAGCAATAAATATCTCATATCCCTTTCCA
TATCTGTTCTTAAGAAACAAAATACAACAGAATTATTTGACAAGATAATG
TCTCTATGCCTTTATAAAAATATTATTCTTTGTGGAGGAGAAACCGTCGT
AACTGCTGTGATAAAGTCCGGTATTCCCTCATCGACAATGGTTAGCATTT
TGGAAAGGAAAATATTCGACACCAATAAGACAAATCTTGAAAATGAAGCG
CCATTAATCCTTGCTTGTAAATTTTTGCTATTTGATGTGGTGAACGTTCT
TGTTGCTTTGAATTGTGATCTGAAACGCTATAGACACGAGGCTATTGAAT
CT
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protein sequence of SMED30014766-orf-1

>SMED30014766-orf-1 ID=SMED30014766-orf-1|Name=SMED30014766-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=184bp
EGDVNKLNQNQESIFDIANTLKNESFVNVMLDHCNQPLKLSVTKSFEVIL
SNLVESENWNLLSQIIGHAHVDEISNKYLISLSISVLKKQNTTELFDKIM
SLCLYKNIILCGGETVVTAVIKSGIPSSTMVSILERKIFDTNKTNLENEA
PLILACKFLLFDVVNVLVALNCDLKRYRHEAIES
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR036770Ankyrin_rpt-contain_sf
IPR020683Ankyrin_rpt-contain_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036770Ankyrin repeat-containing domain superfamilySUPERFAMILYSSF48403Ankyrin repeatcoord: 3..175