SMED30017873

Overview
NameSMED30017873
Smed IDSMED30017873
Length (bp)369
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



SMED30017873

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
oocyteSMED30017873 Contig21774newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30017873 Contig21774uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30017873 Contig21774newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30017873 Contig21774uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30017873 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014926:12293..12661 -1485
v31.012257:2257..2610 -1462
v31.015591:6253..6621 +1458
v31.000740:36943..37289 +1232
v31.009114:3283..3644 +1214
Homology
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BLAST of SMED30017873 vs. Planmine SMEST
Match: SMESG000031442.1 (SMESG000031442.1)

HSP 1 Score: 153.68 bits (387), Expect = 1.530e-48
Identity = 74/87 (85.06%), Postives = 79/87 (90.80%), Query Frame = 3 
Query:   66 LLRATETTGATSRENDPPPAYQEFEFPDFDPDIVYAPAVTTHSPPPSIYIDLVEEVIETPLLNHSLEQLGLDLEEIAVLSGRVPTSP 326
            LLRATETTGAT RENDPPPAY+EFEFPD DPD+VYA  VT H+PPPSIYIDLVEEVIE P+LNH+LEQ GLDLEEIAVLSG VPTSP
Sbjct:   63 LLRATETTGATIRENDPPPAYEEFEFPDLDPDVVYASGVTIHTPPPSIYIDLVEEVIEAPILNHALEQFGLDLEEIAVLSGLVPTSP 149
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BLAST of SMED30017873 vs. Planmine SMEST
Match: SMESG000070051.1 (SMESG000070051.1)

HSP 1 Score: 156.762 bits (395), Expect = 2.781e-48
Identity = 76/103 (73.79%), Postives = 87/103 (84.47%), Query Frame = 3 
Query:   57 EANLLRATETTGATSRENDPPPAYQEFEFPDFDPDIVYAPAVTTHSPPPSIYIDLVEEVIETPLLNHSLEQLGLDLEEIAVLSGRVPTSPTPASNLRTSTQMG 365
            EANLLRA ETTG TSR NDPPPAYQEFEFPDFDP+I+YAPAVT H+PPPSIYIDLVE+ I+ P L+++L QLGLD+ EI +L+GRVPTSPT      TSTQMG
Sbjct:  146 EANLLRAIETTGTTSRANDPPPAYQEFEFPDFDPNIIYAPAVTIHTPPPSIYIDLVEDAIKVPTLDNALGQLGLDIGEITILTGRVPTSPTLVFAPGTSTQMG 248
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BLAST of SMED30017873 vs. Planmine SMEST
Match: SMESG000056201.1 (SMESG000056201.1)

HSP 1 Score: 139.813 bits (351), Expect = 2.575e-43
Identity = 68/103 (66.02%), Postives = 79/103 (76.70%), Query Frame = 3 
Query:   54 AEANLLRATETTGATSRENDPPPAYQEFEFPDFDPDIVYAPAVTTHSPPPSIYIDLVEEVIETPLLNHSLEQLGLDLEEIAVLSGRVPTSPTPASNLRTSTQM 362
            AEANLLR  E  G   RENDPP  Y+EFEFP+ DPD+VYAPA+T + PPPSIYID VEE+   P+LNHSLEQL L L+EIAVLS RVPT+P P +   TSTQ+
Sbjct:    9 AEANLLRENERIGKNIRENDPPLVYEEFEFPELDPDVVYAPAITVYQPPPSIYIDFVEELKNAPVLNHSLEQLKLKLDEIAVLSDRVPTNPAPINVPETSTQV 111
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BLAST of SMED30017873 vs. Planmine SMEST
Match: SMESG000020775.1 (SMESG000020775.1)

HSP 1 Score: 136.346 bits (342), Expect = 3.858e-40
Identity = 72/103 (69.90%), Postives = 79/103 (76.70%), Query Frame = 3 
Query:   57 EANLLRATETTGATSRENDPPPAYQEFEFPDFDPDIVYAPAVTTHSPPPSIYIDLVEEVIETPLLNHSLEQLGLDLEEIAVLSGRVPTSPTPASNLRTSTQMG 365
            EANLLRA E TG T   ND PPAY+EFEFPD DPD+VYAPAVT + PPPSIYIDL E+  E P+LNHSLEQL L  +EIAVLSGRVPTS T  +   TSTQ G
Sbjct:  138 EANLLRAKERTGGTVEVNDLPPAYEEFEFPDLDPDVVYAPAVTFYPPPPSIYIDLEEDENEAPILNHSLEQLDLAPDEIAVLSGRVPTSLTQTNEPETSTQEG 240
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BLAST of SMED30017873 vs. Planmine SMEST
Match: SMESG000045969.1 (SMESG000045969.1)

HSP 1 Score: 125.561 bits (314), Expect = 1.572e-37
Identity = 63/101 (62.38%), Postives = 79/101 (78.22%), Query Frame = 3 
Query:   60 ANLLRATETTGATSRENDPPPAYQEFEFPDFDPDIVYAPAVTTHSPPPSIYIDLVEEVIETPLLNHSLEQLGLDLEEIAVLSGRVPTSPTPASNLRTSTQM 362
            A+LLRA ET G TS  + PPP YQEFEFP+FDPDI+YAP     +PPPS+YIDLVE++ E P ++ +LE+LGL++EEI++LSG VPTS TP S   TSTQM
Sbjct:   58 ASLLRAIETVGTTSGISGPPPVYQEFEFPEFDPDIIYAPMAVI-TPPPSVYIDLVEDITEAPTVDQALERLGLNVEEISILSGHVPTSRTPTSVPGTSTQM 157
The following BLAST results are available for this feature:
BLAST of SMED30017873 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 SMED30017873 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 SMED30017873 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 SMED30017873 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 SMED30017873 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 SMED30017873 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 SMED30017873 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 SMED30017873 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 SMED30017873 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 SMED30017873 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 SMED30017873 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 SMED30017873 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 SMED30017873 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 SMED30017873 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000031442.11.530e-4885.06SMESG000031442.1[more]
SMESG000070051.12.781e-4873.79SMESG000070051.1[more]
SMESG000056201.12.575e-4366.02SMESG000056201.1[more]
SMESG000020775.13.858e-4069.90SMESG000020775.1[more]
SMESG000045969.11.572e-3762.38SMESG000045969.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017873 ID=SMED30017873|Name=SMED30017873|organism=Schmidtea mediterranea sexual|type=transcript|length=369bp
GAGTATCTCGACGGCGGCCAAATCGAAATCGCCGTCGCCGCCAACGACGC
CGAGCAGAAGCCAATCTGCTTAGGGCGACTGAAACAACGGGAGCAACCAG
CAGAGAAAATGATCCGCCTCCGGCCTACCAAGAGTTTGAATTTCCAGATT
TCGACCCTGATATCGTATACGCCCCGGCCGTAACAACTCACTCTCCACCT
CCATCTATCTATATCGATTTAGTGGAGGAAGTAATCGAAACTCCACTATT
AAATCACTCGTTGGAGCAATTAGGTCTCGATTTAGAAGAAATTGCCGTTC
TTAGTGGACGCGTTCCGACGAGTCCTACCCCTGCTAGTAATCTCAGAACC
TCAACCCAAATGGGACCAA
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protein sequence of SMED30017873-orf-1

>SMED30017873-orf-1 ID=SMED30017873-orf-1|Name=SMED30017873-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=122bp
VSRRRPNRNRRRRQRRRAEANLLRATETTGATSRENDPPPAYQEFEFPDF
DPDIVYAPAVTTHSPPPSIYIDLVEEVIETPLLNHSLEQLGLDLEEIAVL
SGRVPTSPTPASNLRTSTQMGP
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland