SMED30005940

Overview
NameSMED30005940
Smed IDSMED30005940
Length (bp)777
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




SMED30005940

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30005940SMESG000062905.1 SMESG000029324.1 Contig499GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005940 Contig4009GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30005940SMESG000008003.1 SmedASXL_013873SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30005940SMESG000008003.1 dd_Smed_v4_5199_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30005940SMESG000008003.1 dd_Smed_v4_5199_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30005940SMESG000008003.1 dd_Smed_v6_5199_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30005940SMESG000008003.1 dd_Smed_v4_5199_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30005940 vs. Planmine SMEST
Match: SMESG000008004.1 (SMESG000008004.1)

HSP 1 Score: 166.777 bits (421), Expect = 5.162e-51
Identity = 129/220 (58.64%), Postives = 154/220 (70.00%), Query Frame = 3
Query:   42 MIFIILTFLFLWNLFGQSSENLSPPSIKSFNSMNFTINCVQNDWENCEKWFDLYKDYPMYKLLNNLNAENKMNIYYMKVKFSDLKGRLNSFRVRTSSNLHYIEKLKSEFQLIQEKSK-IQSFL--------------DIXXXXXXXXXXXXXXQNSDXXXXXXXXXXXXXXXXVNLLDIPPMEDDMALXXXXXXXXXXXXFQTRFNKSMSLLKDLILSMN 656
            MI II TFL L N F QSSENLSPP IKSFN  N   NCVQN  ENCEKW DLY+DYPMYKL+NNLNAENKMN Y MK  FS+ K  LNS RV T + L+  EK KSE QL++EK+K ++S L              ++EK LE  +E  K  +NSDKIIEKI++E+ L EEL+N LD+PPMEDD+ L KI EN +K+ E+Q+ F K   LLKDL+LSMN
Sbjct:    1 MIIIIFTFLLLGNSFAQSSENLSPPFIKSFNCKNIKANCVQNGVENCEKWVDLYEDYPMYKLINNLNAENKMNNYNMKRNFSETKESLNSLRVTTDTMLNKFEKQKSEIQLLKEKTKSLKSLLGKEIDDKGLNKMESELEKHLEKMKETYKRFENSDKIIEKIEKEVTLNEELLNSLDMPPMEDDLVLMKISENKEKLNEYQSHFRKIKLLLKDLLLSMN 220          
BLAST of SMED30005940 vs. Planmine SMEST
Match: SMESG000007998.1 (SMESG000007998.1)

HSP 1 Score: 97.8265 bits (242), Expect = 4.078e-26
Identity = 48/69 (69.57%), Postives = 51/69 (73.91%), Query Frame = 3
Query:   42 MIFIILTFLFLWNLFGQSSENLSPPSIKSFNSMNFTINCVQNDWENCEKWFDLYKDYPMYKLLNNLNAE 248
            MIFIILTFL L N FGQS EN     IKSFN  N   NC+QNDWENCEKW DLYKD PMYKL+NN N +
Sbjct:    1 MIFIILTFLLLGNSFGQSRENRCSSFIKSFNCKNLKANCLQNDWENCEKWVDLYKDNPMYKLMNNCNYD 69          
BLAST of SMED30005940 vs. Planmine SMEST
Match: SMESG000008013.1 (SMESG000008013.1)

HSP 1 Score: 75.8702 bits (185), Expect = 9.688e-17
Identity = 40/109 (36.70%), Postives = 61/109 (55.96%), Query Frame = 3
Query:  102 NLSPPSIKSFNSMNFTINCVQNDWENCEKWFDLYKDYPMYKLLNNLNAENKMNIYYMKVKFSDLKGRLNSFRVR----TSSNLHYIEKLKSEFQLIQEKSKI-QSFLDI 413
            N +  +I+ FN  NF   C+  D   C  WF+ +  YP+++L NNL AENKMN+YY +   S+ K  + S+RV     T  +L   EKL   F+  + + KI + +LD+
Sbjct:    5 NPAGENIEEFNGENFMKYCIGKDRNTCGDWFERFDGYPLFELFNNLGAENKMNVYYSQRNLSEFKDIVQSYRVYSGQLTEGSLQLFEKLDETFKEAENRLKIAEGYLDL 113          
The following BLAST results are available for this feature:
BLAST of SMED30005940 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 SMED30005940 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 SMED30005940 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 SMED30005940 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 SMED30005940 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 SMED30005940 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 SMED30005940 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 SMED30005940 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 SMED30005940 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 SMED30005940 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 SMED30005940 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 SMED30005940 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 SMED30005940 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 SMED30005940 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000008004.15.162e-5158.64SMESG000008004.1[more]
SMESG000007998.14.078e-2669.57SMESG000007998.1[more]
SMESG000008013.19.688e-1736.70SMESG000008013.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005940 ID=SMED30005940|Name=SMED30005940|organism=Schmidtea mediterranea sexual|type=transcript|length=777bp
GTGAAAAATTTTGAAAAATTTCCAAAATTCTTTAAATCGTCATGATATTT
ATCATTTTAACTTTTCTCTTTTTGTGGAATTTATTTGGCCAAAGTAGCGA
GAATCTTTCTCCTCCTTCCATCAAGTCCTTCAATTCCATGAATTTCACAA
TAAATTGTGTGCAAAACGATTGGGAAAATTGTGAAAAATGGTTTGATTTG
TATAAAGATTATCCCATGTATAAATTGCTGAATAATCTGAATGCAGAAAA
TAAAATGAATATCTACTATATGAAAGTAAAGTTCTCAGATCTTAAAGGAC
GTTTAAATTCATTTCGTGTGAGAACAAGCTCAAATTTGCATTATATAGAA
AAACTAAAATCCGAATTTCAATTAATTCAAGAAAAGAGCAAGATACAGTC
GTTTCTTGATATAGAAAAACTTTTAGAAGTTACCGAAGAATTATTGAAAT
TACTACAAAATTCTGATAAGATTATCGAAAAAATTCAACAAGAATTAATA
TTGTTAGAAGAATTGGTTAATTTACTTGATATCCCACCAATGGAAGATGA
CATGGCGTTAAAGAAGATAATGGAAAACATGAAAAAAATAAAAGAATTTC
AAACTCGTTTTAATAAATCAATGTCACTTCTAAAAGATCTGATCTTGTCA
ATGAATTTATCAAAAATATTATAAATATGTGCTTGCAATGAATTTATCAA
AATTCTTATAAATTGAGAACATTCTAAATGTGATATAATTCAAAAACTGA
TCATTTGATATAATTTATTCATTTTAT
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protein sequence of SMED30005940-orf-1

>SMED30005940-orf-1 ID=SMED30005940-orf-1|Name=SMED30005940-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=211bp
MIFIILTFLFLWNLFGQSSENLSPPSIKSFNSMNFTINCVQNDWENCEKW
FDLYKDYPMYKLLNNLNAENKMNIYYMKVKFSDLKGRLNSFRVRTSSNLH
YIEKLKSEFQLIQEKSKIQSFLDIEKLLEVTEELLKLLQNSDKIIEKIQQ
ELILLEELVNLLDIPPMEDDMALKKIMENMKKIKEFQTRFNKSMSLLKDL
ILSMNLSKIL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000418head
PLANA:0002032epidermal cell
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..16
score: 0.832