SMED30033528

Overview
NameSMED30033528
Smed IDSMED30033528
Length (bp)735
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




SMED30033528

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30033528h1SMcG0005913 Contig41036newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033528h1SMcG0005913 Contig41036uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033528h1SMcG0005913 Contig1057uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033528h1SMcG0005913 Contig1057newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30033528h1SMcG0005913 dd_Smed_v4_6804_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30033528h1SMcG0005913 dd_Smed_v4_6804_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30033528h1SMcG0005913 dd_Smed_v4_6804_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30033528h1SMcG0005913 dd_Smed_v4_6804_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30033528h1SMcG0005913 dd_Smed_v4_6804_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033528h1SMcG0013150 Contig1057uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033528h1SMcG0013150 Contig1057newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
zeta neoblastSMED30033528h1SMcG0005913 dd_Smed_v4_6804_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
SMED30033528 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005648:4248..4976 +3542
Homology
BLAST of SMED30033528 vs. TrEMBL
Match: A0A3S1BHR1 (Integrase catalytic domain-containing protein OS=Elysia chlorotica OX=188477 GN=EGW08_008294 PE=4 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 5.121e-11
Identity = 36/101 (35.64%), Postives = 50/101 (49.50%), Query Frame = 3
Query:   96 TYRPEGSGLEERNHRTIKRIITRSCCDPLKAVFFFYYITTHSGLDSNTVPSKVHIGTEWRNP*LILPDTVSESCDNHVHSHYTIGRYIFAKSLNAKCNTQW 398
             +R  G+G+ ERNHRTIK I  R    P+KAV F+Y ++  SG    T+P +      WR+     PD           S ++IG  ++ K    KC TQW
Sbjct:  226 AHRASGNGIVERNHRTIKAISERGRVSPMKAV-FWYNMSPRSGQKEATIPQRSVHSYSWRH-----PDVEPHIEPQESRSSFSIGDEVWVKPAAVKCTTQW 320          

HSP 2 Score: 33.113 bits (74), Expect = 5.121e-11
Identity = 15/22 (68.18%), Postives = 17/22 (77.27%), Query Frame = 2
Query:  407 INSSTNVEVDGLPRHVNHMRTV 472
            INS  NVEVDG+PRHV  +R V
Sbjct:  328 INSKNNVEVDGVPRHVLDLRPV 349          
BLAST of SMED30033528 vs. TrEMBL
Match: A0A3S1AH33 (Integrase catalytic domain-containing protein OS=Elysia chlorotica OX=188477 GN=EGW08_000310 PE=4 SV=1)

HSP 1 Score: 63.1586 bits (152), Expect = 7.822e-10
Identity = 36/101 (35.64%), Postives = 50/101 (49.50%), Query Frame = 3
Query:   96 TYRPEGSGLEERNHRTIKRIITRSCCDPLKAVFFFYYITTHSGLDSNTVPSKVHIGTEWRNP*LILPDTVSESCDNHVHSHYTIGRYIFAKSLNAKCNTQW 398
             +R  G+G+ ERNHRTIK I  R    P+KAV F+Y ++  SG    T+P +      WR+     PD           S ++IG  ++ K    KC TQW
Sbjct:  105 AHRASGNGIVERNHRTIKAISERGRVSPMKAV-FWYNMSPRSGQKEATIPQRSVHSYSWRH-----PDVEPHIEPQESRSSFSIGDEVWVKPAAVKCTTQW 199          

HSP 2 Score: 28.8758 bits (63), Expect = 7.822e-10
Identity = 13/22 (59.09%), Postives = 16/22 (72.73%), Query Frame = 2
Query:  407 INSSTNVEVDGLPRHVNHMRTV 472
            INS  NVEV+G+PR V  +R V
Sbjct:  207 INSKNNVEVNGVPRRVLDLRQV 228          
BLAST of SMED30033528 vs. TrEMBL
Match: A0A085LLS4 (Uncharacterized protein OS=Trichuris suis OX=68888 GN=M513_13205 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 4.574e-9
Identity = 35/114 (30.70%), Postives = 55/114 (48.25%), Query Frame = 3
Query:   72 NSRIK*CYTYRPEGSGLEERNHRTIKRIITRSCCDPLKAVFFFYYITTHSGLDSNTVPSKVHIGTEWRNP*LILPDTVSESCDNHVHSHYTIGRYIFAKSLNAKCNTQWTHVSI 413
            N R++    + P G+G+ ER HRT+K I+ R  C   +AV   Y IT     ++ T P+        R     L    + + D H  S Y +G +++ K   A+CNTQ+   S+
Sbjct: 1067 NVRVRFRCAHNPSGNGIVERCHRTVKVIVARKECSVPEAV-HLYNITPRDDCNAETAPANTLYAYRIR-----LRGIDARAPDGHPQSQYKVGDHVWVKPPGARCNTQYHRASV 1174          

HSP 2 Score: 30.0314 bits (66), Expect = 4.574e-9
Identity = 13/22 (59.09%), Postives = 16/22 (72.73%), Query Frame = 2
Query:  401 TCINSSTNVEVDGLPRHVNHMR 466
            T I S   VEV+G+PRHV H+R
Sbjct: 1175 TGIVSDNAVEVNGIPRHVRHVR 1196          
BLAST of SMED30033528 vs. TrEMBL
Match: A0A085MRT3 (Integrase catalytic domain-containing protein OS=Trichuris suis OX=68888 GN=M514_27900 PE=4 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 5.446e-7
Identity = 34/114 (29.82%), Postives = 54/114 (47.37%), Query Frame = 3
Query:   72 NSRIK*CYTYRPEGSGLEERNHRTIKRIITRSCCDPLKAVFFFYYITTHSGLDSNTVPSKVHIGTEWRNP*LILPDTVSESCDNHVHSHYTIGRYIFAKSLNAKCNTQWTHVSI 413
            N R++    + P G+ + ER HRT+K I+ R  C   +AV   Y IT     ++ T P+        R     L    + + D H  S Y +G +++ K   A+CNTQ+   S+
Sbjct:  130 NVRVRFRCAHNPSGNDIVERCHRTVKVIVARKECSVPEAVHL-YNITPRDDCNAETAPANTLYAYRIR-----LRGIDARAPDGHPQSQYKVGDHVWVKPPGARCNTQYHRASV 237          

HSP 2 Score: 28.4906 bits (62), Expect = 5.446e-7
Identity = 13/22 (59.09%), Postives = 16/22 (72.73%), Query Frame = 2
Query:  401 TCINSSTNVEVDGLPRHVNHMR 466
            T I S   VEV+G+PRHV H+R
Sbjct:  238 TGIVSDNAVEVNGIPRHVRHVR 259          
BLAST of SMED30033528 vs. Planmine SMEST
Match: SMESG000007937.1 (SMESG000007937.1)

HSP 1 Score: 148.288 bits (373), Expect = 1.189e-46
Identity = 73/107 (68.22%), Postives = 84/107 (78.50%), Query Frame = 3
Query:   96 TYRPEGSGLEERNHRTIKRIITRSCCDPLKAVFFFYYITTHSGLDSNTVPSKVHIGTEWRNP*LILPDTVSESCDNHVHSHYTIGRYIFAKSLNAKCNTQWTHVSIL 416
             YRPE +G+ ERNH TIKRI+ RS CDP KA  F Y IT HSGLDSNTVPS +H GTEWR+P L L DT SESCD++VHSHYT+G ++F K  NAKCNTQWT VSI+
Sbjct:   80 AYRPERNGITERNHSTIKRIVARSGCDPFKA-GFIYNITPHSGLDSNTVPSMLHFGTEWRSPKLFLADTASESCDDYVHSHYTVGSHVFVKPPNAKCNTQWT-VSIV 184          

HSP 2 Score: 56.6102 bits (135), Expect = 1.189e-46
Identity = 26/38 (68.42%), Postives = 34/38 (89.47%), Query Frame = 2
Query:  392 SMDTCINSSTNVEVDGLPRHVNHMRTVTNFLDKLETIS 505
            S+ T INSSTN EVDG+PR V+H+RTVTN++DK+ET+S
Sbjct:  182 SIVTGINSSTNKEVDGMPRKVSHLRTVTNYMDKVETVS 219          
BLAST of SMED30033528 vs. Planmine SMEST
Match: SMESG000002973.1 (SMESG000002973.1)

HSP 1 Score: 54.299 bits (129), Expect = 3.056e-12
Identity = 25/60 (41.67%), Postives = 32/60 (53.33%), Query Frame = 3
Query:  219 SGLDSNTVPSKVHIGTEWRNP*LILPDTVSESCDNHVHSHYTIGRYIFAKSLNAKCNTQW 398
            +GLD  TVPSK+H G +WR P  +L DT+   C       Y +G  +F K   AK N  W
Sbjct:  684 AGLDDETVPSKLHSGWKWRIPKFLLGDTILYRCKGRKAGLYEVGSQVFVKPPRAKSNAPW 743          

HSP 2 Score: 35.039 bits (79), Expect = 3.056e-12
Identity = 12/24 (50.00%), Postives = 19/24 (79.17%), Query Frame = 2
Query:  401 TCINSSTNVEVDGLPRHVNHMRTV 472
            T INS  N++VD +PRH++H+R +
Sbjct:  749 TGINSPNNIDVDDIPRHISHLRLI 772          
BLAST of SMED30033528 vs. Planmine SMEST
Match: SMESG000039779.1 (SMESG000039779.1)

HSP 1 Score: 58.151 bits (139), Expect = 3.867e-11
Identity = 25/58 (43.10%), Postives = 34/58 (58.62%), Query Frame = 3
Query:  225 LDSNTVPSKVHIGTEWRNP*LILPDTVSESCDNHVHSHYTIGRYIFAKSLNAKCNTQW 398
            LD  TV SK+H G +WRNP  +L DT+ + C +     Y +G  +F K  +AKCN  W
Sbjct:   18 LDDKTVTSKLHSGRKWRNPKFLLVDTIPDRCKDRKAGLYEVGSQMFVKPPSAKCNVPW 75          
BLAST of SMED30033528 vs. Planmine SMEST
Match: SMESG000040019.1 (SMESG000040019.1)

HSP 1 Score: 50.0618 bits (118), Expect = 2.088e-7
Identity = 28/61 (45.90%), Postives = 37/61 (60.66%), Query Frame = 3
Query:   72 NSRIK*CYTYRPEGSGLEERNHRTIKRIITRSCCDPLKAVFFFYYITTHSGLDSNTVPSKV 254
            N ++K   T +   S    +NHRT+KRI+ RS C+P KAV      + HS LDSN VPSK+
Sbjct:  129 NKKVKLLQTRKEWNS---RKNHRTMKRIVARSGCNPFKAV------SPHSILDSNIVPSKI 180          
The following BLAST results are available for this feature:
BLAST of SMED30033528 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 SMED30033528 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 SMED30033528 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 SMED30033528 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 SMED30033528 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 SMED30033528 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 SMED30033528 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 SMED30033528 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A3S1BHR15.121e-1135.64Integrase catalytic domain-containing protein OS=E... [more]
A0A3S1AH337.822e-1035.64Integrase catalytic domain-containing protein OS=E... [more]
A0A085LLS44.574e-930.70Uncharacterized protein OS=Trichuris suis OX=68888... [more]
A0A085MRT35.446e-729.82Integrase catalytic domain-containing protein OS=T... [more]
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BLAST of SMED30033528 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 SMED30033528 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 SMED30033528 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 SMED30033528 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 SMED30033528 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 SMED30033528 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000007937.11.189e-4668.22SMESG000007937.1[more]
SMESG000002973.13.056e-1241.67SMESG000002973.1[more]
SMESG000039779.13.867e-1143.10SMESG000039779.1[more]
SMESG000040019.12.088e-745.90SMESG000040019.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033528 ID=SMED30033528|Name=SMED30033528|organism=Schmidtea mediterranea sexual|type=transcript|length=735bp
ATAAAATGCATCACTCAAAATACTTCGACTACTTCAATAGAATAATTTAA
CATGGAACAACAGATATGTGAAACAGCAGGATAAAATAGTGTTACACTTA
TAGACCAGAGGGGAGTGGATTAGAAGAAAGAAACCACAGAACCATAAAGC
GAATAATAACGAGGTCATGCTGCGACCCTCTTAAGGCTGTTTTCTTCTTC
TATTACATTACGACACATTCAGGTTTAGACAGTAACACCGTCCCATCAAA
GGTACACATCGGTACAGAATGGAGAAACCCGTAATTAATTCTTCCAGATA
CCGTATCCGAGAGTTGCGATAACCATGTTCATAGTCACTATACCATTGGC
AGGTATATATTTGCCAAATCACTTAACGCAAAATGCAACACTCAATGGAC
ACATGTATCAATTCTTCGACCAATGTGGAAGTTGATGGATTGCCCAGACA
TGTTAATCACATGAGAACAGTTACCAATTTTCTGGACAAACTAGAAACTA
TAAGCTGAATCGATCCAGATCATTCTGATGTAGAAAATTTGTCGATTTCA
AGATCTAGAAGAGAGCGAAGACCTCCAGAACGATTGATAGACTATGAGAT
TGATCCTAAGATCACGGGGCGTGCAATGAGTATGACACTATTGCATAATA
GTGTTGAACTGCAAGACGTAAATCACTTCTTTGTAAACTTTACAAATACT
ATTGATCATAGCAACAATCTATAATATTTTTTTTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 4..23