SMED30009139

Overview
NameSMED30009139
Smed IDSMED30009139
Length (bp)1417
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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30009139

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
testis primordiumSMED30009139SMESG000038387.1 Contig5108_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009139 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009327:6871..13375 +6926
Homology
BLAST of SMED30009139 vs. Planmine SMEST
Match: SMESG000038387.1 (SMESG000038387.1)

HSP 1 Score: 805.823 bits (2080), Expect = 0.000e+0
Identity = 432/432 (100.00%), Postives = 432/432 (100.00%), Query Frame = 3
Query:   24 MIELRNAFNHIQNDLIILRQKISEENNGIFNEINSMISFIRQNENYLEKNPFVNELQVTXXXXXXXXXXXXALWKCYKEVLLQIFPTFNSISGLSFQDLSKVQNNEYDLAQNSYLQSKIYFPLQQTLNGSNWSQICNQLNSDNITMISPGTNSVNVADNKNSFRNHIFTQNKISPNVNELFSMHGAGDTIGLHRTKLPPQPEKDIEEIQQTISMQLKLQQHHSKNRYKFQQTHRAWPITPEINVVFQGNSSTNQFPIQNQLFSSNSDPQIFTPNTIVGLHTQYQSQQPNVSQLLNHSLATSNNSFYGFNNAYTNQLTNTQILQANDSEFAQLPSSMFGFLNNSSTNRMVXXXXXXXXXXXXXXXXXVDCPDSPEVTNSQNSYIINNSFASKTCENPSLSKICDPKSNLINYQIKPPTLTWEDLASVTTTSTN 1319
            MIELRNAFNHIQNDLIILRQKISEENNGIFNEINSMISFIRQNENYLEKNPFVNELQVTSDSSFSNSGDSDALWKCYKEVLLQIFPTFNSISGLSFQDLSKVQNNEYDLAQNSYLQSKIYFPLQQTLNGSNWSQICNQLNSDNITMISPGTNSVNVADNKNSFRNHIFTQNKISPNVNELFSMHGAGDTIGLHRTKLPPQPEKDIEEIQQTISMQLKLQQHHSKNRYKFQQTHRAWPITPEINVVFQGNSSTNQFPIQNQLFSSNSDPQIFTPNTIVGLHTQYQSQQPNVSQLLNHSLATSNNSFYGFNNAYTNQLTNTQILQANDSEFAQLPSSMFGFLNNSSTNRMVNCSLNSTNSSNSGININVDCPDSPEVTNSQNSYIINNSFASKTCENPSLSKICDPKSNLINYQIKPPTLTWEDLASVTTTSTN
Sbjct:    1 MIELRNAFNHIQNDLIILRQKISEENNGIFNEINSMISFIRQNENYLEKNPFVNELQVTSDSSFSNSGDSDALWKCYKEVLLQIFPTFNSISGLSFQDLSKVQNNEYDLAQNSYLQSKIYFPLQQTLNGSNWSQICNQLNSDNITMISPGTNSVNVADNKNSFRNHIFTQNKISPNVNELFSMHGAGDTIGLHRTKLPPQPEKDIEEIQQTISMQLKLQQHHSKNRYKFQQTHRAWPITPEINVVFQGNSSTNQFPIQNQLFSSNSDPQIFTPNTIVGLHTQYQSQQPNVSQLLNHSLATSNNSFYGFNNAYTNQLTNTQILQANDSEFAQLPSSMFGFLNNSSTNRMVNCSLNSTNSSNSGININVDCPDSPEVTNSQNSYIINNSFASKTCENPSLSKICDPKSNLINYQIKPPTLTWEDLASVTTTSTN 432          
The following BLAST results are available for this feature:
BLAST of SMED30009139 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30009139 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000038387.10.000e+0100.00SMESG000038387.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009139 ID=SMED30009139|Name=SMED30009139|organism=Schmidtea mediterranea sexual|type=transcript|length=1417bp
TATTAAATATGGATTTGAAAGGGATGATCGAATTGCGAAATGCTTTCAAT
CACATACAGAATGATCTAATAATTTTAAGACAAAAAATCTCCGAGGAAAA
CAATGGAATTTTTAATGAAATAAATTCCATGATATCGTTTATTAGACAAA
ATGAAAATTATTTAGAAAAGAATCCATTTGTGAATGAGTTACAAGTGACC
TCGGACAGTTCGTTCTCTAATTCCGGAGACTCGGATGCTCTTTGGAAGTG
TTACAAAGAAGTTTTACTCCAAATTTTTCCAACCTTCAACTCGATCAGTG
GACTGTCTTTTCAAGATCTCTCTAAAGTTCAAAATAACGAATACGATTTG
GCCCAGAATTCCTATTTACAGAGTAAAATATATTTCCCTTTACAACAAAC
TCTAAATGGAAGTAATTGGTCTCAGATTTGTAACCAACTTAACTCTGACA
ACATTACAATGATTTCACCCGGCACAAATTCTGTTAACGTTGCAGATAAC
AAAAATAGCTTTCGAAATCACATCTTTACACAGAATAAAATTAGTCCTAA
TGTAAATGAATTATTCTCCATGCATGGAGCGGGGGATACTATAGGTCTCC
ACCGTACTAAATTGCCGCCGCAGCCAGAAAAAGACATTGAGGAAATTCAG
CAGACCATTTCAATGCAACTGAAACTTCAACAGCATCATTCCAAAAACCG
TTATAAATTTCAACAAACTCACCGAGCATGGCCGATTACGCCAGAAATAA
ATGTCGTGTTCCAAGGCAATAGTTCAACAAATCAATTCCCAATACAAAAT
CAACTATTCTCGTCGAATTCAGACCCTCAAATCTTTACCCCAAATACTAT
AGTTGGCCTTCATACGCAATATCAGTCACAACAACCCAATGTGTCCCAGT
TGCTAAATCATTCACTAGCAACATCAAACAACTCTTTCTATGGTTTTAAC
AATGCTTATACCAATCAACTAACAAACACTCAAATCCTCCAGGCAAACGA
TTCTGAATTCGCCCAATTGCCCTCGAGTATGTTTGGATTTCTGAACAACT
CTTCGACGAACAGAATGGTCAATTGCAGTTTAAATTCAACCAATTCCTCC
AATAGCGGTATAAATATCAATGTCGACTGCCCCGATTCGCCGGAGGTTAC
AAATAGCCAAAATAGCTACATTATCAACAACAGTTTTGCTTCCAAGACCT
GTGAAAATCCAAGCTTATCGAAAATATGTGACCCGAAATCCAATTTAATA
AATTATCAAATCAAACCGCCAACACTAACTTGGGAGGATTTGGCAAGCGT
AACCACCACCTCGACTAATTGAATCTTGTTTTTCCAAGACAGTGATTTCT
AGTTTTTAAGTTTTCTATTTTCAAATTTGATGTAATGTTTAATAACTTAG
TTGCCATTTCAGGGGCG
back to top

protein sequence of SMED30009139-orf-1

>SMED30009139-orf-1 ID=SMED30009139-orf-1|Name=SMED30009139-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=440bp
LNMDLKGMIELRNAFNHIQNDLIILRQKISEENNGIFNEINSMISFIRQN
ENYLEKNPFVNELQVTSDSSFSNSGDSDALWKCYKEVLLQIFPTFNSISG
LSFQDLSKVQNNEYDLAQNSYLQSKIYFPLQQTLNGSNWSQICNQLNSDN
ITMISPGTNSVNVADNKNSFRNHIFTQNKISPNVNELFSMHGAGDTIGLH
RTKLPPQPEKDIEEIQQTISMQLKLQQHHSKNRYKFQQTHRAWPITPEIN
VVFQGNSSTNQFPIQNQLFSSNSDPQIFTPNTIVGLHTQYQSQQPNVSQL
LNHSLATSNNSFYGFNNAYTNQLTNTQILQANDSEFAQLPSSMFGFLNNS
STNRMVNCSLNSTNSSNSGININVDCPDSPEVTNSQNSYIINNSFASKTC
ENPSLSKICDPKSNLINYQIKPPTLTWEDLASVTTTSTN*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003304testis primordium