SMED30017442

Overview
NameSMED30017442
Smed IDSMED30017442
Length (bp)1041
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



SMED30017442

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
reproductive organSMED30017442SMESG000033545.1 Contig43369newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30017442SMESG000033545.1 Contig43369uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30017442 vs. Planmine SMEST
Match: SMESG000002835.1 (SMESG000002835.1)

HSP 1 Score: 217.624 bits (553), Expect = 5.784e-63
Identity = 149/214 (69.63%), Postives = 169/214 (78.97%), Query Frame = 1 
Query:  106 AYTETELRMKVPGSVRTEQIDIFPAHHLPRTEDQAPTVMNTLISNTGVPRSSPMETTESEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTEGVDNLDDLPPPYQEFENSGMDPDIRYAPRILFSSPPASIHINLVDEENEAHPLMQALSDLELDFDEIAILTGTVPNIGPGGEIAGPSSRRDEDPRGHPPSYRPPKRRRLPTDMDAEED 747
            A+++TELR+ VPG++R EQ+DI PAHHLP  EDQ+    +   S+  + +  P  T E+ AN + PTAR RPNRNKRRRDRRRQEEARLR TQ  EGV  LDDLPPPYQEFE+S  DPDI YAPRILFSSPPASIHINLVDEENE   L+++LSDLELD +EIA L   VPNIGP GEIAGPSSRRDED RG PP YRPPKRR LPTDMDAEE+
Sbjct: 1329 AFSDTELRIWVPGNIRAEQLDIVPAHHLPNIEDQSNPTTSAFPSSANLTQLPPPGTVETRANSSTPTARHRPNRNKRRRDRRRQEEARLRETQPMEGVGQLDDLPPPYQEFESSEFDPDICYAPRILFSSPPASIHINLVDEENEPPQLIRSLSDLELDLEEIATLMWEVPNIGPRGEIAGPSSRRDEDSRGDPPPYRPPKRRCLPTDMDAEEN 1542
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BLAST of SMED30017442 vs. Planmine SMEST
Match: SMESG000015007.1 (SMESG000015007.1)

HSP 1 Score: 191.43 bits (485), Expect = 1.309e-58
Identity = 119/249 (47.79%), Postives = 160/249 (64.26%), Query Frame = 1 
Query:    1 LRQKIARITQARDELIVESRAQRLLIREQSTALHQAYTETELRMKVPGSVRTEQIDIFPAHHLPRTEDQAPTVMNTLISNTGVPRSSPMETTESEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTEGVDNLDDLPPPYQEFENSGMDPDIRYAPRILFSSPPASIHINLVDEENEAHPLMQALSDLELDFDEIAILTGTVPNIGPGGEIAGPSSRRDEDPRGHPPSYRPPKRRRLPTDMDAEED 747
            L Q+IAR+T+AR+ELI ESR+QRLLI+EQ+TAL QA+T+ EL+  VPGSVR  Q++I PAHHLP T+   PT   + + +   P+   ME+                  ++R    RR+ + R R T+  EG   +DDLPP YQEFE  G+DPDI YAP + F S  + IHINLVDE+++   +++ L  L LD ++IA+LTG  P +    EIAGPS+R D +    PP YRP KRR LPTDMDAE++
Sbjct:   59 LLQEIARLTEAREELIAESRSQRLLIKEQATALRQAFTDVELQTHVPGSVRAHQLNIIPAHHLPITK-LPPTPTASTLPSMESPQIPVMES-------------PAHPAHRRPNRNRRRSDRRRRETEPIEGPCRVDDLPPHYQEFEIPGLDPDILYAPNVTFPSRASLIHINLVDEDSDPPQVVRVLDRLGLDLEDIAVLTGDTPMVSHSIEIAGPSTRVDGNCHASPPPYRPAKRRYLPTDMDAEDE 293
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BLAST of SMED30017442 vs. Planmine SMEST
Match: SMESG000064895.1 (SMESG000064895.1)

HSP 1 Score: 186.808 bits (473), Expect = 2.189e-56
Identity = 135/229 (58.95%), Postives = 160/229 (69.87%), Query Frame = 1 
Query:    1 LRQKIARITQARDELIVESRAQRLLIREQSTALHQAYTETELRMKVPGSVRTEQIDIFPAHHLPRTEDQAPTVMNTLISNTGVPRSSPMETTESEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTEGVDNLDDLPPPYQEFENSGMDPDIRYAPRILFSSPPASIHINLVDEENEAHPLMQALSDLELDFDEIAILTGTVPNIGPGGEIAGPSSRRDEDPRGHP 687
            LRQKI R TQARDELI+ESR+Q+LLIREQS AL QA+T+ ELR  V  SVR  Q+ I PAHHLP  ED   + ++   S    P S      E   N    TAR RPNRN+RRRDRRRQEE R R T+A E    +DDLPPPY+EFE   +DPDI YAP+++FSSPP SIHINLVDEE E   +++AL  L LD  EIAILTG VPN+GP GEIAGPS++ ++D R  P
Sbjct:   57 LRQKIFRFTQARDELIIESRSQQLLIREQSMALRQAFTDVELRTHVLESVRAGQLGIIPAHHLPNIEDLPASTVHISSSVVNPPSSLNPPLAEITTNSAISTARHRPNRNRRRRDRRRQEEERFRETRAAEDTYRIDDLPPPYREFEIPELDPDILYAPQVMFSSPPESIHINLVDEEIEPPRVIRALDRLGLDTGEIAILTGEVPNVGPQGEIAGPSTQSNDDYRVDP 285
[Close]
BLAST of SMED30017442 vs. Planmine SMEST
Match: SMESG000002835.1 (SMESG000002835.1)

HSP 1 Score: 192.2 bits (487), Expect = 3.222e-54
Identity = 138/195 (70.77%), Postives = 152/195 (77.95%), Query Frame = 1 
Query:  163 IDIFPAHHLPRTEDQAPTVMNTLISNTGVPRSSPMETTESEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTEGVDNLDDLPPPYQEFENSGMDPDIRYAPRILFSSPPASIHINLVDEENEAHPLMQALSDLELDFDEIAILTGTVPNIGPGGEIAGPSSRRDEDPRGHPPSYRPPKRRRLPTDMDAEED 747
            +DI PAHHLP  EDQ+    +   S+  + +  P  T E+ AN + PTAR RPNRNKRRRDRRRQEEARLR TQ  EGV  LDDLPPPYQEFE+S  DPDI YAPRILFSSPPASIHINLVDEENE   L+++LSDLELD +EIA L   VPNIGP GEIAGPSSRRDED RG PP YRPPKRR LPTDMDAEE+
Sbjct: 1329 LDIVPAHHLPNIEDQSNPTTSAFPSSANLTQLPPPGTVETRANSSTPTARHRPNRNKRRRDRRRQEEARLRETQPMEGVGQLDDLPPPYQEFESSEFDPDICYAPRILFSSPPASIHINLVDEENEPPQLIRSLSDLELDLEEIATLMWEVPNIGPRGEIAGPSSRRDEDSRGDPPPYRPPKRRCLPTDMDAEEN 1523
[Close]
BLAST of SMED30017442 vs. Planmine SMEST
Match: SMESG000009535.1 (SMESG000009535.1)

HSP 1 Score: 181.415 bits (459), Expect = 1.325e-52
Identity = 118/253 (46.64%), Postives = 154/253 (60.87%), Query Frame = 1 
Query:    1 LRQKIARITQARDELIVESRAQRLLIREQSTALHQAYTETELRMKVPGSVRTEQIDIFPAHHLPRTEDQAPT--VMNTLISNTGVPRSSPMETTESEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTEGVDNLD------DLPPPYQEFENSGMDPDIRYAPRILFSSPPASIHINLVDEENEAHPLMQALSDLELDFDEIAILTGTVPNIGPGGEIAGPSSRRDEDPRGHPPSYRPPKRRRLPTDMD 735
            LRQKI R+T+ARDEL+ ESR QRLLIREQSTAL +A+T+ ELR  VPG+VR  Q++I PAHH+P      P+  V N   S    P ++P+    S+    A          +R    RR+ + R R  + ++GV+  +      D PPPY+EFE   +DPDI YAP ++F SP  SIHINLVDE+    P+ Q L  L L  +EIAIL G VP I    E+AGPS+R +E+    PP YRP KR+  PTD+D
Sbjct:   91 LRQKIERLTRARDELVTESRIQRLLIREQSTALRRAFTDIELRTLVPGNVRASQLEIIPAHHIP-VMGILPSLPVSNPSTSEARAPAATPVV---SQPPTGAVETPTISTTRRRPNRNRRRRDRRRREEELSQGVETSELSRQTGDPPPPYEEFEFPDLDPDICYAPNVVFRSPVPSIHINLVDEDPNPFPVTQVLDGLGLGTEEIAILMGEVPQIVSSQEVAGPSTRGEENRPTSPPPYRPMKRKYFPTDID 339
The following BLAST results are available for this feature:
BLAST of SMED30017442 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 SMED30017442 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 SMED30017442 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 SMED30017442 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 SMED30017442 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 SMED30017442 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 SMED30017442 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 SMED30017442 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 SMED30017442 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 SMED30017442 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 SMED30017442 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 SMED30017442 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 SMED30017442 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 SMED30017442 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000002835.15.784e-6369.63SMESG000002835.1[more]
SMESG000015007.11.309e-5847.79SMESG000015007.1[more]
SMESG000064895.12.189e-5658.95SMESG000064895.1[more]
SMESG000002835.13.222e-5470.77SMESG000002835.1[more]
SMESG000009535.11.325e-5246.64SMESG000009535.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017442 ID=SMED30017442|Name=SMED30017442|organism=Schmidtea mediterranea sexual|type=transcript|length=1041bp
CTCAGGCAAAAGATTGCCCGTATTACTCAAGCGCGCGACGAACTCATCGT
CGAGTCGCGCGCTCAGAGACTGTTAATCCGTGAACAATCTACAGCCCTAC
ACCAGGCTTACACTGAAACGGAACTCCGGATGAAGGTCCCGGGGAGTGTT
CGGACTGAGCAAATCGATATCTTCCCTGCTCATCACCTCCCCCGTACCGA
GGACCAAGCCCCGACGGTAATGAACACTCTGATCTCGAATACGGGAGTTC
CCCGATCATCACCCATGGAGACTACAGAAAGCGAGGCAAACCTTAATGCC
CCTACGGCCCGTCGTCGGCCGAATCGAAATAAGCGACGCCGAGATCGTCG
TAGACAAGAAGAGGCCCGTCTCCGGAGAACTCAAGCGACGGAAGGGGTAG
ACAATTTGGATGATCTGCCACCCCCTTACCAGGAGTTCGAAAACTCGGGG
ATGGACCCCGATATTCGATATGCTCCACGAATCTTATTTTCCTCGCCCCC
AGCTTCTATACATATCAACCTGGTGGACGAAGAAAATGAAGCTCACCCAT
TAATGCAGGCATTAAGCGATCTTGAATTAGATTTCGACGAGATCGCTATT
CTCACGGGAACGGTCCCCAACATTGGCCCCGGGGGCGAAATAGCTGGACC
ATCCTCGCGGAGGGATGAGGATCCTCGAGGCCATCCCCCATCGTATCGAC
CACCGAAACGGAGACGCCTCCCGACAGATATGGACGCGGAAGAAGACTGA
ACCGCCAAAACCCTAAGTCTATTTGTAGTTGCTCGTATGCTGACAAATGC
GCGAACTGTTCATTTTTCGTTTGCTTAAATTTTCCTTTTTAATAAATGTT
GTTGAATTCATGTCTCTTCTTATTAAGCGAAAGCGGGAGCATCGGGGATG
AAGGTTACGGGCACGCGGGGACAATTTTTTTTGGTTTCCATTGCGGAAAG
GAATGTAATATCGCGGAATAAAGGGTTTTACTGTGCTTGAAAGAAGAGCG
TAAGTCCTCCTATCGGCAGCTATGAACCGGGAAAGACGAAT
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protein sequence of SMED30017442-orf-1

>SMED30017442-orf-1 ID=SMED30017442-orf-1|Name=SMED30017442-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=250bp
LRQKIARITQARDELIVESRAQRLLIREQSTALHQAYTETELRMKVPGSV
RTEQIDIFPAHHLPRTEDQAPTVMNTLISNTGVPRSSPMETTESEANLNA
PTARRRPNRNKRRRDRRRQEEARLRRTQATEGVDNLDDLPPPYQEFENSG
MDPDIRYAPRILFSSPPASIHINLVDEENEAHPLMQALSDLELDFDEIAI
LTGTVPNIGPGGEIAGPSSRRDEDPRGHPPSYRPPKRRRLPTDMDAEED*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ