SMED30029229

Overview
NameSMED30029229
Smed IDSMED30029229
Length (bp)332
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



SMED30029229

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Category 3 cellSMED30029229SMESG000033974.1 dd_Smed_v4_34155_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
Alignments
SMED30029229 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002443:44369..44700 +1660
Homology
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BLAST of SMED30029229 vs. Planmine SMEST
Match: SMESG000033974.1 (SMESG000033974.1)

HSP 1 Score: 182.185 bits (461), Expect = 5.496e-59
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = 1 
Query:    1 RQIFTEKELQARLPDRSITQQLNMIPVQHLPVNLSNCVEWDATNVFTLAPVPSIPXXXXXXXXXXXXXXXXXTENALLQVNLITIENPNVIKIPEVTSYESNEMPANSDL 330
            RQIFTEKELQARLPDRSITQQLNMIPVQHLPVNLSNCVEWDATNVFTLAPVPSIPNRKHKPNKNRRRKEKRRTENALLQVNLITIENPNVIKIPEVTSYESNEMPANSDL
Sbjct:   47 RQIFTEKELQARLPDRSITQQLNMIPVQHLPVNLSNCVEWDATNVFTLAPVPSIPNRKHKPNKNRRRKEKRRTENALLQVNLITIENPNVIKIPEVTSYESNEMPANSDL 156
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BLAST of SMED30029229 vs. Planmine SMEST
Match: SMESG000032225.1 (SMESG000032225.1)

HSP 1 Score: 95.5153 bits (236), Expect = 7.669e-26
Identity = 73/110 (66.36%), Postives = 79/110 (71.82%), Query Frame = 1 
Query:    1 RQIFTEKELQARLPDRSITQQLNMIPVQHLPVNLSNCVEWDATNVFTLAPVPSIPXXXXXXXXXXXXXXXXXTENALLQVNLITIENPNVIKIPEVTSYESNEMPANSDL 330
            RQ+FTEKELQARLP RS  QQLN+I V HLPV  SN +E D TN     PV  I NRKHKPNKN+RR+EKRRTENALLQ NL  IEN   I I E T YE   MPA+SDL
Sbjct:   79 RQLFTEKELQARLPGRSTAQQLNIISVHHLPVYSSNRIERDVTNAVMTRPVLPICNRKHKPNKNQRRREKRRTENALLQANLNAIENVISIGISETTPYEPISMPADSDL 188
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BLAST of SMED30029229 vs. Planmine SMEST
Match: SMESG000026903.1 (SMESG000026903.1)

HSP 1 Score: 87.8113 bits (216), Expect = 3.712e-23
Identity = 64/110 (58.18%), Postives = 76/110 (69.09%), Query Frame = 1 
Query:    1 RQIFTEKELQARLPDRSITQQLNMIPVQHLPVNLSNCVEWDATNVFTLAPVPSIPXXXXXXXXXXXXXXXXXTENALLQVNLITIENPNVIKIPEVTSYESNEMPANSDL 330
            RQIFTEKELQARLP R++ Q+LN+IP  HLP++ SN    D  NV    P  SI NR+HKPNKNRR +EKRR ENA L  NL T+ENPN  ++ E  S E   MP NS+L
Sbjct:   18 RQIFTEKELQARLPGRNMAQRLNIIPSHHLPIDSSNLTRSDDPNVVATIPTSSIQNRRHKPNKNRRIREKRRAENAALHANLSTMENPNSNRMSETISQEPIFMPNNSNL 127
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BLAST of SMED30029229 vs. Planmine SMEST
Match: SMESG000047586.1 (SMESG000047586.1)

HSP 1 Score: 68.1662 bits (165), Expect = 1.490e-15
Identity = 53/110 (48.18%), Postives = 68/110 (61.82%), Query Frame = 1 
Query:    1 RQIFTEKELQARLPDRSITQQLNMIPVQHLPVNLSNCVEWDATNVFTLAPVPSIPXXXXXXXXXXXXXXXXXTENALLQVNLITIENPNVIKIPEVTSYESNEMPANSDL 330
            RQIFTEKELQ+ LP R++ Q+L++I   HL +N SN    D  N  T  P PS  +R+HKPNKN RR++KRR EN   Q NL  IENPN  +  E+   E   M  + +L
Sbjct:   43 RQIFTEKELQSWLPRRNMVQRLDIISTHHLLINSSNLTNNDDANAATAMPAPSTSSRRHKPNKNWRRRQKRRAENGSQQANLGVIENPNPSRTAEIFPLEPTSMHNDKNL 152
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BLAST of SMED30029229 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1)

HSP 1 Score: 66.2402 bits (160), Expect = 4.471e-14
Identity = 51/96 (53.12%), Postives = 69/96 (71.88%), Query Frame = 1 
Query:    1 RQIFTEKELQARLPDRSITQQLNMIPVQHLPVNLSNCVEWDATNVFTLAPVPSIPXXXXXXXXXXXXXXXXXTENALLQVNLITIENPNVIKIPEV 288
            RQIFTEKE QARLP R++TQ+L++IPV HLP N  N  + +  NV T    PS  N++H+PN+NRRR+++R+ ENALLQ NL   EN ++  I E+
Sbjct:   85 RQIFTEKEKQARLPSRNMTQRLDIIPVHHLPTNPKNQRDNNNKNVPTKLTTPSTVNQRHRPNRNRRRRQRRKAENALLQSNLGVRENASLESITEL 180
The following BLAST results are available for this feature:
BLAST of SMED30029229 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 SMED30029229 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 SMED30029229 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 SMED30029229 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 SMED30029229 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 SMED30029229 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 SMED30029229 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 SMED30029229 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 SMED30029229 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 SMED30029229 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 SMED30029229 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 SMED30029229 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 SMED30029229 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 SMED30029229 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000033974.15.496e-59100.00SMESG000033974.1[more]
SMESG000032225.17.669e-2666.36SMESG000032225.1[more]
SMESG000026903.13.712e-2358.18SMESG000026903.1[more]
SMESG000047586.11.490e-1548.18SMESG000047586.1[more]
SMESG000046646.14.471e-1453.13SMESG000046646.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029229 ID=SMED30029229|Name=SMED30029229|organism=Schmidtea mediterranea sexual|type=transcript|length=332bp
AGGCAGATTTTCACAGAGAAAGAGTTGCAGGCGCGGTTACCCGATCGAAG
TATAACCCAACAACTCAACATGATTCCAGTGCAGCATCTGCCGGTTAATT
TGTCAAATTGTGTCGAATGGGACGCCACCAATGTATTCACGTTAGCGCCA
GTTCCATCGATCCCGAATCGAAAACATAAGCCCAACAAAAACCGTCGGAG
AAAAGAGAAAAGGAGGACCGAGAATGCCTTATTACAGGTGAATTTGATTA
CCATTGAAAATCCGAATGTAATTAAGATTCCTGAAGTAACATCATATGAA
TCTAACGAAATGCCGGCCAACTCCGATCTGGA
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protein sequence of SMED30029229-orf-1

>SMED30029229-orf-1 ID=SMED30029229-orf-1|Name=SMED30029229-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=110bp
RQIFTEKELQARLPDRSITQQLNMIPVQHLPVNLSNCVEWDATNVFTLAP
VPSIPNRKHKPNKNRRRKEKRRTENALLQVNLITIENPNVIKIPEVTSYE
SNEMPANSDL
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell