SMED30033320

Overview
NameSMED30033320
Smed IDSMED30033320
Length (bp)442
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




SMED30033320

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 primordiumSMED30033320 Contig1497_WUSTLGPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30033320 vs. Planmine SMEST
Match: SMESG000004514.1 (SMESG000004514.1)

HSP 1 Score: 56.9954 bits (136), Expect = 6.101e-11
Identity = 37/54 (68.52%), Postives = 43/54 (79.63%), Query Frame = 3
Query:  186 GIAIIREPVWNPVREARQRVESXXXXXXXXXXXXQHRRRMTRMELNKINREIAA 347
            GIAI REP  NP RE RQ+VE  LL L EE+R LQHRRRM ++EL+KINR+IAA
Sbjct:   73 GIAIKREPGRNPARETRQKVEFYLLLLVEEERRLQHRRRMPQVELDKINRDIAA 126          
BLAST of SMED30033320 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 38.5058 bits (88), Expect = 7.514e-9
Identity = 22/53 (41.51%), Postives = 31/53 (58.49%), Query Frame = 3
Query:  189 IAIIREPVWNPVREARQRVESXXXXXXXXXXXXQHRRRMTRMELNKINREIAA 347
            IAI REP  NP RE  QR E   +++ E +R    +  + R  L +INR+IA+
Sbjct:  723 IAIKREPGRNPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIAS 775          

HSP 2 Score: 30.4166 bits (67), Expect = 7.514e-9
Identity = 14/28 (50.00%), Postives = 19/28 (67.86%), Query Frame = 2
Query:  350 DPILRTLTAPT*VMISDELIHPSMMERL 433
            DP L  +TAPT ++I +ELI P +  RL
Sbjct:  796 DPRLLQMTAPTKLVIPEELIQPGLRNRL 823          

HSP 3 Score: 26.1794 bits (56), Expect = 7.514e-9
Identity = 12/34 (35.29%), Postives = 18/34 (52.94%), Query Frame = 1
Query:   49 QQILRFSKMATAQGR*IFWDYGCTVFTPETATWP 150
            Q  L+ S  + A+ R   WD G T+ T   ++WP
Sbjct:  675 QITLQISNASAARYRQALWDNGYTLSTYGESSWP 708          
BLAST of SMED30033320 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 35.4242 bits (80), Expect = 2.279e-8
Identity = 22/54 (40.74%), Postives = 31/54 (57.41%), Query Frame = 3
Query:  186 GIAIIREPVWNPVREARQRVESXXXXXXXXXXXXQHRRRMTRMELNKINREIAA 347
             IAI REP  NP RE  QR E   +++ E +R    +  + R  L +INR+IA+
Sbjct:  670 SIAIKREPGRNPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIAS 723          

HSP 2 Score: 31.5722 bits (70), Expect = 2.279e-8
Identity = 14/28 (50.00%), Postives = 19/28 (67.86%), Query Frame = 2
Query:  350 DPILRTLTAPT*VMISDELIHPSMMERL 433
            DP L  +TAPT ++I +ELI P +  RL
Sbjct:  744 DPRLLQMTAPTKLVIPEELIQPGLRNRL 771          

HSP 3 Score: 26.5646 bits (57), Expect = 2.279e-8
Identity = 15/50 (30.00%), Postives = 23/50 (46.00%), Query Frame = 1
Query:    1 SILYIGPSSSGIPVQGQQILRFSKMATAQGR*IFWDYGCTVFTPETATWP 150
            S+L+      G     Q  L+ S  + A+ R   WD G T+ T   ++WP
Sbjct:  607 SVLHRRDPHGGWRDDSQITLQISNASAARYRQALWDNGYTLSTYGESSWP 656          
BLAST of SMED30033320 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 35.4242 bits (80), Expect = 4.472e-8
Identity = 22/54 (40.74%), Postives = 31/54 (57.41%), Query Frame = 3
Query:  186 GIAIIREPVWNPVREARQRVESXXXXXXXXXXXXQHRRRMTRMELNKINREIAA 347
             IAI REP  NP RE  QR E   +++ E +R    +  + R  L +INR+IA+
Sbjct:  726 SIAIKREPGRNPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIAS 779          

HSP 2 Score: 30.8018 bits (68), Expect = 4.472e-8
Identity = 14/28 (50.00%), Postives = 19/28 (67.86%), Query Frame = 2
Query:  350 DPILRTLTAPT*VMISDELIHPSMMERL 433
            DP L  +TAPT ++I +ELI P +  RL
Sbjct:  800 DPRLLQMTAPTKLVIPEELIQPGLRNRL 827          

HSP 3 Score: 26.5646 bits (57), Expect = 4.472e-8
Identity = 12/34 (35.29%), Postives = 18/34 (52.94%), Query Frame = 1
Query:   49 QQILRFSKMATAQGR*IFWDYGCTVFTPETATWP 150
            Q  L+ S  + A+ R   WD G T+ T   ++WP
Sbjct:  679 QITLQISNASAARYRQALWDNGYTLSTYGESSWP 712          
BLAST of SMED30033320 vs. Planmine SMEST
Match: SMESG000025928.1 (SMESG000025928.1)

HSP 1 Score: 49.6766 bits (117), Expect = 1.152e-7
Identity = 26/67 (38.81%), Postives = 37/67 (55.22%), Query Frame = 1
Query:   40 VQGQQILRFSKMATAQGR*IFWDYGCTVFTPETATWPTLLDTIGDMDFSASPS*ESLSGTQSEKPAR 240
            +QG+++++F     AQGR + W+YG TV   E  TW    D++       SPS  +L G   EKPAR
Sbjct:    1 MQGRRMIQFDDRTAAQGRQLLWNYGYTVAASEPVTWAGRFDSMEVRISLDSPSRGNLDGILPEKPAR 67          
The following BLAST results are available for this feature:
BLAST of SMED30033320 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 SMED30033320 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 SMED30033320 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 SMED30033320 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 SMED30033320 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 SMED30033320 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 SMED30033320 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 SMED30033320 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 SMED30033320 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 SMED30033320 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 SMED30033320 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 SMED30033320 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 SMED30033320 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 SMED30033320 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000004514.16.101e-1168.52SMESG000004514.1[more]
SMESG000046313.17.514e-941.51SMESG000046313.1[more]
SMESG000046313.12.279e-840.74SMESG000046313.1[more]
SMESG000046313.14.472e-840.74SMESG000046313.1[more]
SMESG000025928.11.152e-738.81SMESG000025928.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033320 ID=SMED30033320|Name=SMED30033320|organism=Schmidtea mediterranea sexual|type=transcript|length=442bp
AGTATACTATATATAGGACCATCTTCTTCAGGTATACCGGTGCAAGGTCA
ACAAATACTTCGGTTCAGCAAAATGGCGACAGCACAAGGTCGCTAGATCT
TCTGGGATTATGGGTGCACCGTCTTCACACCGGAAACTGCCACTTGGCCA
ACTCTACTAGATACGATCGGAGACATGGATTTCTCGGCATCGCCATCATA
AGAGAGCCTGTCTGGAACCCAGTCAGAGAAGCCCGCCAGAGAGTAGAGTC
TTTATTACTCCGTCTGAATGAGGAAGATAGAAATTTGCAACATCGACGAC
GAATGACCCGAATGGAGCTGAACAAGATCAACCGTGAGATAGCGGCAGTG
ACCCTATTCTGAGGACTTTGACTGCCCCAACATAAGTGATGATATCAGAT
GAACTGATCCACCCAAGTATGATGGAACGGCTAGAATTGCTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003304testis primordium