SMED30001775

Overview
NameSMED30001775
Smed IDSMED30001775
Length (bp)968
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




SMED30001775

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 primordiumSMED30001775SMESG000049051.1 PL06004A2F07_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001775 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006179:3757..18308 -4722
Homology
BLAST of SMED30001775 vs. Planmine SMEST
Match: SMESG000049051.1 (SMESG000049051.1)

HSP 1 Score: 293.508 bits (750), Expect = 7.387e-101
Identity = 142/142 (100.00%), Postives = 142/142 (100.00%), Query Frame = 3
Query:   15 MKEIVFGFFGLLFLAECQMVNKMFSLDFNNYLDQFTDAWCWTYDNDDCNDFNITKHMKCKSCAFYGYRHRKFGDITMNPMCLRDYNFNYYNITGRNITDRYKYIKTYLELRLCNKVEYCSLTNKNFLKNTVKNRLKWFCKNY 440
            MKEIVFGFFGLLFLAECQMVNKMFSLDFNNYLDQFTDAWCWTYDNDDCNDFNITKHMKCKSCAFYGYRHRKFGDITMNPMCLRDYNFNYYNITGRNITDRYKYIKTYLELRLCNKVEYCSLTNKNFLKNTVKNRLKWFCKNY
Sbjct:    1 MKEIVFGFFGLLFLAECQMVNKMFSLDFNNYLDQFTDAWCWTYDNDDCNDFNITKHMKCKSCAFYGYRHRKFGDITMNPMCLRDYNFNYYNITGRNITDRYKYIKTYLELRLCNKVEYCSLTNKNFLKNTVKNRLKWFCKNY 142          
BLAST of SMED30001775 vs. Planmine SMEST
Match: SMESG000052821.1 (SMESG000052821.1)

HSP 1 Score: 93.9745 bits (232), Expect = 3.922e-22
Identity = 72/228 (31.58%), Postives = 116/228 (50.88%), Query Frame = 3
Query:   99 NNYLDQFTDAWCWTYDNDDCNDFNITKHMKCKSCAFYGYRHRKFGDITMN-PMCLRDYNFNYYNITGRNITDRYKYIKTYLELRLCNKVEYCSLTNKNFLKNTVKNRLKWFCKNYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXFSGKTTTISDKICMGYNQNKTAGEWFPCVECEVSPIFHDKDIPWLQCRKSRMEVVQTFYLFCYQRFVNKQVLVYARCCFSNDC 779
            NNYL     A C  ++N+ C DFNIT +  C++CA+     ++  D   + PMC+ DY FNY  ITG +IT+      TY  + LC     C   N+ F++N++  R K  C ++TTT   TTT    TTTK                 T       C GY+ NK+   +  C  C ++ +   ++  WL C + +++  Q ++LFC Q F++++ L++ +CC+ + C
Sbjct:   18 NNYLSPPNSAECNEFNNNLCTDFNITYYNGCRNCAYSFIPTKQLADYVYDLPMCIADYQFNYRGITGIDITNGTLRENTYYVV-LCPIAISCYRANQFFMRNSMDKRRKPNCLSFTTTKPPTTTGTIKTTTK--------------RTTTKKKPGFRCYGYHSNKSVVLYQQCTGCVITTVIDKEEKRWLDCIRPKVDPSQVYHLFCNQYFLDQETLIFVKCCYFDLC 230          
BLAST of SMED30001775 vs. Planmine SMEST
Match: SMESG000052821.1 (SMESG000052821.1)

HSP 1 Score: 93.9745 bits (232), Expect = 1.104e-21
Identity = 74/228 (32.46%), Postives = 118/228 (51.75%), Query Frame = 3
Query:   99 NNYLDQFTDAWCWTYDNDDCNDFNITKHMKCKSCAFYGYRHRKFGDITMN-PMCLRDYNFNYYNITGRNITDRYKYIKTYLELRLCNKVEYCSLTNKNFLKNTVKNRLKWFCKNYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXFSGKTTTISDKICMGYNQNKTAGEWFPCVECEVSPIFHDKDIPWLQCRKSRMEVVQTFYLFCYQRFVNKQVLVYARCCFSNDC 779
            NNYL     A C  ++N+ C DFNIT +  C++CA+     ++  D   + PMC+ DY FNY  ITG +IT+      TY  + LC     C   N+ F++N++  R K  C ++TTT   TTT    TTTK  TT  K                  C GY+ NK+   +  C  C ++ +   ++  WL C + +++  Q ++LFC Q F++++ L++ +CC+ + C
Sbjct:  101 NNYLSPPNSAECNEFNNNLCTDFNITYYNGCRNCAYSFIPTKQLADYVYDLPMCIADYQFNYRGITGIDITNGTLRENTYY-VVLCPIAISCYRANQFFMRNSMDKRRKPNCLSFTTTKPPTTTGTIKTTTKRTTTKKKPGFR--------------CYGYHSNKSVVLYQQCTGCVITTVIDKEEKRWLDCIRPKVDPSQVYHLFCNQYFLDQETLIFVKCCYFDLC 313          
The following BLAST results are available for this feature:
BLAST of SMED30001775 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 SMED30001775 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 SMED30001775 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 SMED30001775 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 SMED30001775 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 SMED30001775 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 SMED30001775 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 SMED30001775 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 SMED30001775 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 SMED30001775 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 SMED30001775 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 SMED30001775 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 SMED30001775 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 SMED30001775 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000049051.17.387e-101100.00SMESG000049051.1[more]
SMESG000052821.13.922e-2231.58SMESG000052821.1[more]
SMESG000052821.11.104e-2132.46SMESG000052821.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001775 ID=SMED30001775|Name=SMED30001775|organism=Schmidtea mediterranea sexual|type=transcript|length=968bp
TTTCTTTTATCTAAATGAAAGAAATAGTTTTTGGATTTTTCGGACTTCTC
TTTTTGGCAGAATGCCAAATGGTGAACAAGATGTTCAGCCTGGACTTTAA
TAATTATCTCGACCAGTTTACGGATGCTTGGTGTTGGACATATGACAATG
ACGATTGTAACGATTTCAACATTACCAAACATATGAAATGTAAAAGCTGT
GCTTTTTATGGATATCGTCATCGCAAATTCGGGGACATCACAATGAATCC
GATGTGTCTTCGAGATTACAATTTCAACTATTACAACATCACAGGGAGGA
ACATAACCGACAGATATAAATACATAAAGACATACTTGGAGCTTCGGCTT
TGCAACAAAGTTGAATATTGTTCCCTTACGAATAAGAACTTTTTAAAAAA
TACTGTCAAAAATCGTCTTAAATGGTTCTGTAAAAATTATACCACTACGA
CTAAGGCCACAACTACGACTAAGAGAACGACTACAACTAAAATGGTCACT
ACTACTACGAAAAAACAGCCCAGTACAACATTTTCCGGCAAGACCACAAC
GATTTCGGACAAAATTTGTATGGGATATAATCAGAATAAAACAGCAGGAG
AATGGTTTCCATGTGTGGAATGTGAAGTCAGTCCCATCTTCCATGACAAA
GACATACCCTGGCTTCAATGCAGAAAATCGAGAATGGAGGTCGTTCAAAC
CTTTTATTTGTTTTGCTATCAGCGATTTGTAAATAAGCAAGTTCTTGTTT
ATGCTAGGTGCTGCTTTTCAAATGACTGTAAAGAAATTAGTGGGAATTCA
ATTATTTTTTCAAAAACGAATTTTTATTTTTTAAATTATCTTTTAATTAT
ATTTTTTAATTTGTTTATTACCTAAAAATAACTTTTTGTGGAATTTGAGC
TATTTTTAGATTTGACTCAACTTTTTGTTTCATCTTGAAAAATGTTGTTA
GATACTTCAACTATCGCA
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protein sequence of SMED30001775-orf-1

>SMED30001775-orf-1 ID=SMED30001775-orf-1|Name=SMED30001775-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=287bp
MKEIVFGFFGLLFLAECQMVNKMFSLDFNNYLDQFTDAWCWTYDNDDCND
FNITKHMKCKSCAFYGYRHRKFGDITMNPMCLRDYNFNYYNITGRNITDR
YKYIKTYLELRLCNKVEYCSLTNKNFLKNTVKNRLKWFCKNYTTTTKATT
TTKRTTTTKMVTTTTKKQPSTTFSGKTTTISDKICMGYNQNKTAGEWFPC
VECEVSPIFHDKDIPWLQCRKSRMEVVQTFYLFCYQRFVNKQVLVYARCC
FSNDCKEISGNSIIFSKTNFYFLNYLLIIFFNLFIT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003304testis primordium