SMED30001690

Overview
NameSMED30001690
Smed IDSMED30001690
Length (bp)457
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



SMED30001690

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30001690SMESG000069322.1 dd_Smed_v4_12571_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
central nervous systemSMED30001690SMESG000069322.1 dd_Smed_v4_12571_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
nervous systemSMED30001690SMESG000069322.1 dd_Smed_v4_12571_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001690SMESG000069322.1 dd_Smed_v4_12571_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30001690SMESG000069322.1 dd_Smed_v4_12571_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30001690SMESG000069322.1 dd_Smed_v4_12571_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30001690SMESG000069322.1 dd_Smed_v4_12571_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynx musculatureSMED30001690SMESG000069322.1 dd_Smed_v4_12571_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001690 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000179:204759..205350 +2173
Homology
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BLAST of SMED30001690 vs. Planmine SMEST
Match: SMESG000081659.1 (SMESG000081659.1)

HSP 1 Score: 80.8777 bits (198), Expect = 4.640e-24
Identity = 35/44 (79.55%), Postives = 39/44 (88.64%), Query Frame = 3 
Query:    3 NLRNNEYLEATEHRGPSCVEDVAHELDEEIIYASVQPFFSHSTP 134
            NLR+NEY EATEHRGPS VEDVAHELD+EIIYA +QP FSH +P
Sbjct:  146 NLRSNEYSEATEHRGPSYVEDVAHELDKEIIYAPIQPLFSHKSP 189

HSP 2 Score: 47.3654 bits (111), Expect = 4.640e-24
Identity = 25/37 (67.57%), Postives = 26/37 (70.27%), Query Frame = 1 
Query:  136 HKSLLTPPVVSLLFALTSPLRLTRWW*KSNK*ADDHF 246
            HKS LTPPVVSL F L S  RL RWW KS+K ADD  
Sbjct:  186 HKSPLTPPVVSLRFTLKSLPRLMRWWEKSSKQADDEL 222
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BLAST of SMED30001690 vs. Planmine SMEST
Match: SMESG000043502.1 (SMESG000043502.1)

HSP 1 Score: 91.2781 bits (225), Expect = 6.651e-24
Identity = 49/78 (62.82%), Postives = 58/78 (74.36%), Query Frame = 3 
Query:    9 RNNEYLEATEHRGPSCVEDVAHELDEEIIYASVQPFFSHSTPTQITINTSGSESPVRINIAITSNAMVVEEQQISGRS 242
            R+NEY EATE+RGPS  E   +  D EI+YA VQP FSH+ PTQITI+ SGSESPV INIA  SNA++ E+   SGRS
Sbjct:   35 RSNEYSEATEYRGPSYEE--VNTPDTEILYAPVQPIFSHTVPTQITISMSGSESPVYINIATASNAIMGEKYPTSGRS 110
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BLAST of SMED30001690 vs. Planmine SMEST
Match: SMESG000075367.1 (SMESG000075367.1)

HSP 1 Score: 72.0182 bits (175), Expect = 1.475e-15
Identity = 41/82 (50.00%), Postives = 52/82 (63.41%), Query Frame = 3 
Query:    3 NLRNNEYLEATEHRGPSCVEDVAHELDEE--IIYASVQPFFSHSTPTQITINTSGSESPVRINIAITSNAMVVEEQQISGRS 242
            NLR + + E  E   P  +E +A   +++  IIYA VQP FSH  P QITIN +G ESP+ I+IA TS  M+ EE Q SGRS
Sbjct:  191 NLRTDGHSELREVPNPISLEHIAPRFEDDLGIIYAPVQPDFSHPAPAQITINANGHESPINIHIATTSRVMLEEEGQSSGRS 272
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BLAST of SMED30001690 vs. Planmine SMEST
Match: SMESG000064552.1 (SMESG000064552.1)

HSP 1 Score: 66.2402 bits (160), Expect = 1.773e-14
Identity = 33/54 (61.11%), Postives = 40/54 (74.07%), Query Frame = 3 
Query:   81 DEEIIYASVQPFFSHSTPTQITINTSGSESPVRINIAITSNAMVVEEQQISGRS 242
            D +IIYA VQP FSH  P QI IN +G ESP+ I+IA TS A++ EE+Q SGRS
Sbjct:   11 DLDIIYAPVQPEFSHPAPAQIKINANGHESPINIHIATTSRAILEEERQSSGRS 64
[Close]
BLAST of SMED30001690 vs. Planmine SMEST
Match: SMESG000044502.1 (SMESG000044502.1)

HSP 1 Score: 66.6254 bits (161), Expect = 8.716e-14
Identity = 39/80 (48.75%), Postives = 48/80 (60.00%), Query Frame = 3 
Query:    3 NLRNNEYLEATEHRGPSCVEDVAHELDEEIIYASVQPFFSHSTPTQITINTSGSESPVRINIAITSNAMVVEEQQISGRS 242
            NL  N  +E TE R  S  E        EIIYA VQPFFSH +  QITINT+G ESP ++NI+   N  ++E +  SGRS
Sbjct:  165 NLGPNGCVEMTEFRDVSNEEKNRRASYLEIIYAPVQPFFSHPSSAQITINTTGIESPTQVNISKMLNPPLIEREPTSGRS 244
The following BLAST results are available for this feature:
BLAST of SMED30001690 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 SMED30001690 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 SMED30001690 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 SMED30001690 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 SMED30001690 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 SMED30001690 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 SMED30001690 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 SMED30001690 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 SMED30001690 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 SMED30001690 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 SMED30001690 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 SMED30001690 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 SMED30001690 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 SMED30001690 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000081659.14.640e-2479.55SMESG000081659.1[more]
SMESG000043502.16.651e-2462.82SMESG000043502.1[more]
SMESG000075367.11.475e-1550.00SMESG000075367.1[more]
SMESG000064552.11.773e-1461.11SMESG000064552.1[more]
SMESG000044502.18.716e-1448.75SMESG000044502.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001690 ID=SMED30001690|Name=SMED30001690|organism=Schmidtea mediterranea sexual|type=transcript|length=457bp
CCAATTTGAGGAATAACGAATATTTGGAGGCGACGGAACACCGAGGTCCA
TCCTGTGTGGAAGATGTCGCTCATGAACTCGACGAGGAAATAATATATGC
ATCCGTTCAACCCTTCTTCTCGCACTCCACTCCAACACAAATCACTATTA
ACACCTCCGGTAGTGAGTCTCCTGTTCGCATTAACATCGCCATTACGTCT
AACGCGATGGTGGTAGAAGAGCAACAAATAAGCGGACGATCATTTCAGTG
GTGGAACCAACAATACCTCTAGATCGGAGAACCAGATTTCCAAGGCAACC
TTCATCTAATCTGACATCGCGATGTCCCAAGCGCCATACACATTATATCA
TACACATTACCAACATGGATTAACCCATGGGTGTCTGATGGTAATCAGCA
AATTATGTACTGATATTCTGCCGTCTTTTTGGTTTTAAATTATATTATTC
GTGATTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000101muscle cell
PLANA:0000103central nervous system
PLANA:0000478pharynx musculature
PLANA:0003116parenchymal cell