SMED30029574

Overview
NameSMED30029574
Smed IDSMED30029574
Length (bp)486
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell 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




Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30029574 (SMED30029574) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029574 (SMED30029574) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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




SMED30029574

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
head regionSMED30029574SMESG000009967.1 SMESG000009978.1 SmedASXL_001830SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30029574SMESG000009967.1 SMESG000009978.1 dd_Smed_v4_18817_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029574SMESG000009967.1 SMESG000009978.1 dd_Smed_v4_18817_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30029574SMESG000009967.1 SMESG000009978.1 dd_Smed_v6_18817_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30029574SMESG000009967.1 SMESG000009978.1 OX_Smed_1.0.05170ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30029574 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004437:31914..32392 +1789
Homology
BLAST of SMED30029574 vs. TrEMBL
Match: A0A0L8HJL6 (Uncharacterized protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22013095mg PE=4 SV=1)

HSP 1 Score: 92.0485 bits (227), Expect = 5.964e-21
Identity = 45/93 (48.39%), Postives = 64/93 (68.82%), Query Frame = 2
Query:  125 ESRKYKSCKQNSDCCIHEWCAYGKVCYPKIKCPKFQCPDGECQNGFCMPKDPCDLNRHKSCKLISDSCSLDYNLGYHTCSHNIEIGKILCFMR 403
            + R+Y++C +   CC HE+CAY ++CYPKI C  F CPDG CQ+G C+P  PC    HK    + +SCS+++NLGY+TC +N++IG  LC  R
Sbjct:   26 KRRRYRTCAEG--CCPHEYCAYHRICYPKIHC-HFGCPDGSCQHGVCLPDPPC----HKRACGMGNSCSMNFNLGYNTCQYNLDIGSTLCVDR 111          
BLAST of SMED30029574 vs. TrEMBL
Match: K1Q0A4 (Uncharacterized protein OS=Crassostrea gigas OX=29159 GN=CGI_10019551 PE=4 SV=1)

HSP 1 Score: 90.1225 bits (222), Expect = 4.091e-20
Identity = 47/104 (45.19%), Postives = 60/104 (57.69%), Query Frame = 2
Query:  101 FASFLETTESRKYKSCKQNSDCCIHEWCAYGKVCYPKIKCPKFQCPDGECQNGFCMPKDPCDLNRHKSCKLISDSCSLDYNLGYHTCSHNIEIGKILCFMRRDK 412
              +   T    KYK C +   CC HE+CAY K+CYP I C +  CPDG CQNG C P  PC +N        +++CS +YNLGY TC +N+ IG  LC+ R  K
Sbjct:    1 MTTIKHTASEIKYKYCAEG--CCPHEFCAYHKICYPVIHC-EPTCPDGSCQNGLCFPAKPCKVNTECG---FAEACSYNYNLGYETCQYNLNIGDTLCYDRNGK 98          
BLAST of SMED30029574 vs. TrEMBL
Match: V4A400 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_174113 PE=4 SV=1)

HSP 1 Score: 78.9518 bits (193), Expect = 1.569e-15
Identity = 42/93 (45.16%), Postives = 59/93 (63.44%), Query Frame = 2
Query:  134 KYKSCKQNSDCCIHEWCAYGKVCYPKIKCPKFQCPDGECQNGFCMPKDPCDLNRHKSCKLISDSCSLDYNLGYHTCSHNIEIGKILCFMRRDK 412
            +Y+ C +   CC+HE+CAY  +CYPKI C +F CPDG C N  CMP   C  N  + C + ++ C+  +NLGY TC ++++IGK LC  R  K
Sbjct:   55 EYRYCSEG--CCVHEYCAYHSICYPKIHC-EFSCPDGLCVNEICMPYKKC--NSSQQCGM-ANVCTYHHNLGYDTCQYDLDIGKSLCLDRDGK 141          
The following BLAST results are available for this feature:
BLAST of SMED30029574 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 SMED30029574 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 SMED30029574 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 SMED30029574 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 SMED30029574 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 SMED30029574 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 SMED30029574 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 SMED30029574 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A0L8HJL65.964e-2148.39Uncharacterized protein OS=Octopus bimaculoides OX... [more]
K1Q0A44.091e-2045.19Uncharacterized protein OS=Crassostrea gigas OX=29... [more]
V4A4001.569e-1545.16Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
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BLAST of SMED30029574 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 SMED30029574 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 SMED30029574 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 SMED30029574 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 SMED30029574 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 SMED30029574 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029574 ID=SMED30029574|Name=SMED30029574|organism=Schmidtea mediterranea sexual|type=transcript|length=486bp
ATTTATTACGGAAAATCTCTGGAAATAAATAAAATTCTTTGTCTATAAAA
ATAATAATATACTCATGAAAATAATTTCATATTCTCTACTTGGAATATTA
TTCGCTTCCTTCTTGGAAACAACTGAAAGTAGAAAGTATAAGTCCTGCAA
ACAAAATTCTGATTGTTGTATTCACGAATGGTGTGCTTATGGGAAAGTCT
GTTATCCAAAAATAAAATGTCCGAAATTTCAGTGTCCAGACGGGGAGTGC
CAAAATGGGTTTTGCATGCCTAAAGATCCGTGTGATCTGAACCGTCACAA
ATCTTGTAAACTGATTTCAGATAGTTGTTCACTGGATTACAATCTTGGTT
ATCATACCTGTTCTCACAATATTGAAATTGGTAAAATTCTGTGCTTTATG
CGCAGGGACAAATTCAGAGGCTGACATCAAATTGTCTGAAACCTTTCGAT
TTTGTCAATCAAAATTTTTAGATTAGTTAATAAAAC
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protein sequence of SMED30029574-orf-1

>SMED30029574-orf-1 ID=SMED30029574-orf-1|Name=SMED30029574-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=120bp
MKIISYSLLGILFASFLETTESRKYKSCKQNSDCCIHEWCAYGKVCYPKI
KCPKFQCPDGECQNGFCMPKDPCDLNRHKSCKLISDSCSLDYNLGYHTCS
HNIEIGKILCFMRRDKFRG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
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..22
score: 0.507