SMED30023917

Overview
NameSMED30023917
Smed IDSMED30023917
Length (bp)395
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



SMED30023917

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30023917SMESG000058631.1 SmedASXL_005301SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
cephalic gangliaSMED30023917SMESG000058631.1 BK007024.1smed_ncbi_20200123PMID:22451003
González-Sastre et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
nervous systemSMED30023917SMESG000058631.1 dd_Smed_v4_4624_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023917SMESG000058631.1 dd_Smed_v4_4624_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30023917SMESG000058631.1 dd_Smed_v4_4624_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30023917SMESG000058631.1 dd_Smed_v4_4624_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30023917SMESG000058631.1 dd_Smed_v4_4624_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023917SMESG000058631.1 Contig50786newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023917SMESG000058631.1 Contig50786uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30023917SMESG000058631.1 dd_Smed_v6_4624_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30023917SMESG000058631.1 BK007024smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30023917SMESG000058631.1 BK007024smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30023917SMESG000058631.1 BK007024smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30023917 vs. TrEMBL
Match: E3CTJ9 (EYE53-2 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 148.288 bits (373), Expect = 4.100e-44
Identity = 74/75 (98.67%), Postives = 75/75 (100.00%), Query Frame = -2 
Query:  128 MIIALVSAVIIGLTQGEYRSSRNSGRNDWSLLKSSHIKRALVPDAWDDWEIKRSEHKKRAVVPDAWDDWEIKRAI 352
            MIIALVSAVIIGLTQGEYRSS+NSGRNDWSLLKSSHIKRALVPDAWDDWEIKRSEHKKRAVVPDAWDDWEIKRAI
Sbjct:    1 MIIALVSAVIIGLTQGEYRSSKNSGRNDWSLLKSSHIKRALVPDAWDDWEIKRSEHKKRAVVPDAWDDWEIKRAI 75
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BLAST of SMED30023917 vs. TrEMBL
Match: A0A193PE55 (Neuropeptide-9 (Fragment) OS=Dugesia japonica OX=6161 GN=DjNp9 PE=2 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 5.738e-15
Identity = 36/46 (78.26%), Postives = 42/46 (91.30%), Query Frame = -2 
Query:  128 SLLKSSHIKRALVPDAWDDWEIKRSEHKKRAVVPDAWDDWEIKRAI 265
            +L+K S+ KRALVPDAWDDWE+KRS +KKRAVVPDAWDDW+IKR I
Sbjct:    1 NLIKESNSKRALVPDAWDDWELKRSFNKKRAVVPDAWDDWDIKRRI 46
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BLAST of SMED30023917 vs. Planmine SMEST
Match: SMESG000058631.1 (SMESG000058631.1)

HSP 1 Score: 166.777 bits (421), Expect = 6.330e-55
Identity = 82/83 (98.80%), Postives = 83/83 (100.00%), Query Frame = -2 
Query:  128 MKTIGNCVMIIALVSAVIIGLTQGEYRSSRNSGRNDWSLLKSSHIKRALVPDAWDDWEIKRSEHKKRAVVPDAWDDWEIKRAI 376
            MKTIGNCVMIIALVSAVIIGLTQGEYRSS+NSGRNDWSLLKSSHIKRALVPDAWDDWEIKRSEHKKRAVVPDAWDDWEIKRAI
Sbjct:    1 MKTIGNCVMIIALVSAVIIGLTQGEYRSSKNSGRNDWSLLKSSHIKRALVPDAWDDWEIKRSEHKKRAVVPDAWDDWEIKRAI 83
The following BLAST results are available for this feature:
BLAST of SMED30023917 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 SMED30023917 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 SMED30023917 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 SMED30023917 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 SMED30023917 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 SMED30023917 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 SMED30023917 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 SMED30023917 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
E3CTJ94.100e-4498.67EYE53-2 OS=Schmidtea mediterranea OX=79327 PE=2 SV... [more]
A0A193PE555.738e-1578.26Neuropeptide-9 (Fragment) OS=Dugesia japonica OX=6... [more]
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BLAST of SMED30023917 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 SMED30023917 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 SMED30023917 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 SMED30023917 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 SMED30023917 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 SMED30023917 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000058631.16.330e-5598.80SMESG000058631.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023917 ID=SMED30023917|Name=SMED30023917|organism=Schmidtea mediterranea sexual|type=transcript|length=395bp
TCAACGCAGAGTTGAAATAAAAAACTAGTTATATTTTATATATATTAAAA
AGATATTTCTTCCACAAAATGAATGTTAATCATTTGTATTCTGTTGATAC
AGTTAATGGTGAAGAGAATTCTCGTCAGATTGCTCTTTTAATTTCCCAAT
CATCCCATGCGTCTGGAACTACAGCTCGCTTTTTGTGTTCACTTCGTTTT
ATTTCCCAATCATCCCAGGCATCAGGGACCAGCGCTCGTTTTATGTGCGA
CGATTTCAATAAACTCCAGTCATTTCTGCCCGAATTTCTAGAACTTCTGT
ATTCTCCTTGTGTGAGACCAATGATCACTGCTGATACCAATGCTATTATC
ATCACGCAATTTCCAATAGTTTTCATTGAGAATTACAGATTTTAA
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protein sequence of SMED30023917-orf-1

>SMED30023917-orf-1 ID=SMED30023917-orf-1|Name=SMED30023917-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
MNVNHLYSVDTVNGEENSRQIALLISQSSHASGTTARFLCSLRFISQSSQ
ASGTSARFMCDDFNKLQSFLPEFLELLYSPCVRPMITADTNAIIITQFPI
VFIENYRF*
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Aliases
The feature 'SMED30023917' has the following synonyms
Synonym
EYE53-2
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000044cephalic ganglia
PLANA:0000097ventral nerve cord
PLANA:0000099neuron
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..24
score: 0.823
NoneNo IPR availableTMHMMTMhelixcoord: 4..21