SMED30009865

Overview
NameSMED30009865
Smed IDSMED30009865
Length (bp)2092
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



SMED30009865

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
posterior region of the whole animalSMED30009865 dd_Smed_v4_3082_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30009865SMESG000061329.1 Contig2867newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30009865SMESG000061329.1 Contig2867uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30009865 dd_Smed_v4_3082_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30009865 dd_Smed_v4_3082_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30009865 dd_Smed_v4_3082_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30009865 vs. TrEMBL
Match: K2EG17 (Uncharacterized protein OS=uncultured bacterium OX=77133 GN=ACD_20C00008G0002 PE=4 SV=1)

HSP 1 Score: 127.487 bits (319), Expect = 8.731e-30
Identity = 82/171 (47.95%), Postives = 107/171 (62.57%), Query Frame = -3 
Query:  468 LAFHPYPQVISKLFNVYEFGPPVYFTTPSTCSWIDHKVSRLSPLTKSPYXXXXXXXXXXLKT*PRQ*STTRRLIMQKARRHNIMLLRPLVGVRFQVLFHSSDSKYFSPFPYGTSSLSVSEEYLALPDGAGDFMQNFSGSALLRVPLTCYNLCLQGYHLMLLFFPENSA*YN 980
            + FHPYPQVI K+F+   F PP+ FT  S CSWIDH VS L P TK+PY D LSLRLR  +    + S +     +  R H   +L PLVG RFQVL HS +   FSPFP+GT SLSV++EYLAL DG   F ++FSG  +L   L  + + ++G+H +   FP+ S  Y+
Sbjct:    1 MVFHPYPQVIQKVFSPNWFEPPLGFTRASLCSWIDHSVSGLLPRTKAPYSDSLSLRLRHFRLNLARKSNSLTHYAKGTRSHP-KVLPPLVGNRFQVLLHSPNRGSFSPFPHGTGSLSVAKEYLALEDGPPRFPRDFSGLVVLGYRLRHFQVRVRGFHTLWRAFPDASPAYS 170
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BLAST of SMED30009865 vs. TrEMBL
Match: A0A0A7RQ73 (Uncharacterized protein OS=Thermotoga sp. TBYP3.1.4.1 OX=1587550 PE=4 SV=1)

HSP 1 Score: 100.908 bits (250), Expect = 1.890e-26
Identity = 63/125 (50.40%), Postives = 72/125 (57.60%), Query Frame = -3 
Query:  660 KAVPKNISGRTSYLSV*LAFHPYPQVISKLFNVYEFGPPVYFTTPSTCSWIDHKVSRLSPLTKSPYXXXXXXXXXXLK-T*PRQ*STTRRLIMQKARRHNIMLLRPLVGVRFQVLFHSSDSKYFS 1031
            +A P+ ISGRTSY  V LAFH YPQVI  LF V+ FGPPV F  PS C  + H  S L P+T+ P           +  T P   + TR LI QKARRH    LR LVG RFQVLFHS     F+
Sbjct:   10 EAAPQCISGRTSYHRVRLAFHSYPQVIRGLFTVHRFGPPVGFNPPSPCPGVAHPASGLPPVTERPVRTRFRCGYAFIGLTSPP--TATRGLINQKARRHPKWGLRLLVGTRFQVLFHSPSGVLFT 132

HSP 2 Score: 49.2914 bits (116), Expect = 1.890e-26
Identity = 60/184 (32.61%), Postives = 74/184 (40.22%), Query Frame = -2 
Query:  172 VLFTFPLRY*FTIGF*GVFSLTRWCW*LHAEFLRFRITQ--GTAHLL*FV-----LTGLSPYVAFLSRKFSLI*LIKCGPITSQ*HAIAIWAVPLSL-----------ATT*GITVLFYFPPGT*MFQFSGLAFVLLQILDLQSSGLPHSEICGYNACFQLTAAYRSLPRPSSPLRTKASAIRP 669
            VLFTFP RY  TIG   VFSL  W   L   F   R T+  G      F      L+G    V  L   F     ++   +     A   W  P +L           +   G + L  FP GT MF F        + +   ++ +      G NAC +L  AYRSLPRPSSP   KAS   P
Sbjct:  129 VLFTFPSRYWCTIGRRVVFSLGGWSPQLPTGFHVSRGTREHGPGSPSPFAYGAVTLSGPPSQVVRLEEGFVTPRRVRG--LARPCPATPAWQRPRALTPRWFGLLPVRSPLLGESRLISFPRGTEMFHFPRYRTAFRRRVASTATQVSPFGNPGINACLRLPRAYRSLPRPSSPPAAKASTACP 310
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BLAST of SMED30009865 vs. TrEMBL
Match: A0A132GPZ6 (Uncharacterized protein OS=bacterium P201 OX=1768112 GN=AUK64_2547 PE=4 SV=1)

HSP 1 Score: 118.242 bits (295), Expect = 1.317e-25
Identity = 93/228 (40.79%), Postives = 116/228 (50.88%), Query Frame = -3 
Query:  156 TTRRLIMQKARRHNIMLL----RPLVGVRFQVLFHSSDSKYFSPFPYGTSSLSVSEEYLALPDGAGDFMQNFSGSALLRVPLTCYNLCLQGYHLMLLFFPENS------A*YNSLNAAL*PRNSTLLRFGLFPFRSPLLRESLYCFIFLRVLRCFSSPG*LLYCYKYLIFNQV-----------GCPIRKSAGIMLVFSLPQLIAVYHVLLRLSEPRHPPYALSCFKN 776
             TRR IMQKARRH+  +     R +V     + ++      FSPFP+GT SLSVS EYLALPDG G F Q++S  ALLR+P     + ++  H + L FPE+S        ++   A   P      RFGL P RSPLL ESL           FSSPG     +++  F  V           G    + AG   + S P LIA  HVL RL EPRHPP ALS F+ 
Sbjct:   81 ATRRFIMQKARRHHEKMAPTACRRMVSGTLSLPYYGC----FSPFPHGTRSLSVSREYLALPDGPGGFAQDYSCPALLRIPKGPIPVHIRDSHPLWLNFPEHSIPGQGTKSWSYYPACALPHK----RFGLLPGRSPLLGESLL----------FSSPG-GTKMFQFPPFASVTQLRIAALQTAGLSHSEIAGSRDICSYPALIAACHVLHRLREPRHPPCALSYFRQ 289
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BLAST of SMED30009865 vs. TrEMBL
Match: A0A1B2Z6N4 (Uncharacterized protein OS=uncultured bacterium OX=77133 PE=4 SV=1)

HSP 1 Score: 109.768 bits (273), Expect = 1.476e-24
Identity = 66/131 (50.38%), Postives = 79/131 (60.31%), Query Frame = -3 
Query:  597 LAFHPYPQVISKLFNVYEFGPPVYFTTPSTCSWIDHKVSRLSPLTKSPYXXXXXXXXXXLKT*PRQ*STTRRLIMQKARRHNI---MLLRPLVGVRFQVLFHSSDSKYFSPFPYGTSSLSVSEEYLALPDG 980
            +AFHPYPQVI +LFNV  FGPP++    STC W+DH VSRL  LT      L       LK        TRRLIMQKARRH +      + +V   F + +    S +FSPFP+GT SLSVS+EYLAL DG
Sbjct:    1 MAFHPYPQVIPRLFNVNGFGPPLWVNKASTCPWVDHTVSRLLLLTMVALFRLAFATDPHLKCLTLLVKVTRRLIMQKARRHPLRAPTACKRMVSGSFSLPY----SGFFSPFPHGTGSLSVSQEYLALTDG 127
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BLAST of SMED30009865 vs. TrEMBL
Match: A5KL06 (Uncharacterized protein OS=[Ruminococcus] torques ATCC 27756 OX=411460 GN=RUMTOR_00910 PE=4 SV=1)

HSP 1 Score: 113.62 bits (283), Expect = 1.782e-24
Identity = 93/237 (39.24%), Postives = 121/237 (51.05%), Query Frame = -3 
Query:  330 IYKAVPKNISGRTSYLSV*LAFHPYPQVISKLFNVYEFGPPVYFTTPSTCSWIDHKVSRLSPLTKSPYXXX-XXXXXXXLKT*PRQ*STTRRLIMQKARRHNIMLLRPLVGVRFQVLFHSSDSKYFSPFPYGTSSLSVSEEYLALPDGAGDFMQNFSGSALLRVPLTCYNLCLQGYHLMLLFFPENSA*YNSLNAAL*PRNSTLLRFGLFPFRSPLLRESLYCFIFLRVLRCFSSPG 1037
            +Y+A PK IS RTSYL V L F PYP +I  LFN   FGPP+ FT  ST +WIDH VS L  LT + +     S       T P   S TRR ++QK    +   +  L  + FQVLF S     F PFP    +LS ++EYLAL  G+    Q  +   LL +P       L+ +H +   FP+  A          PR++ +  + L PF          CF+FLR+LRCFSSPG
Sbjct:    1 MYEASPKAISRRTSYLRVRLEFLPYPHLIPTLFNGCGFGPPLPFTATSTWTWIDHPVSGLLRLTFALFRLGFPSAPHLQCLTSPA--SVTRRTVLQKYAGSSYKDVPQLENIWFQVLFQSPPGGLF-PFPSQYYALSGTKEYLALRGGSPHISQGSTCLDLLWIPPCQLAFRLRDFHPLWSAFPKLFAKLVESIPRSEPRDARIPVWVL-PFSLAATHRITCCFLFLRLLRCFSSPG 233
The following BLAST results are available for this feature:
BLAST of SMED30009865 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 SMED30009865 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 SMED30009865 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 SMED30009865 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 SMED30009865 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 SMED30009865 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 SMED30009865 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 SMED30009865 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
K2EG178.731e-3047.95Uncharacterized protein OS=uncultured bacterium OX... [more]
A0A0A7RQ731.890e-2650.40Uncharacterized protein OS=Thermotoga sp. TBYP3.1.... [more]
A0A132GPZ61.317e-2540.79Uncharacterized protein OS=bacterium P201 OX=17681... [more]
A0A1B2Z6N41.476e-2450.38Uncharacterized protein OS=uncultured bacterium OX... [more]
A5KL061.782e-2439.24Uncharacterized protein OS=[Ruminococcus] torques ... [more]
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BLAST of SMED30009865 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 SMED30009865 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 SMED30009865 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 SMED30009865 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 SMED30009865 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 SMED30009865 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009865 ID=SMED30009865|Name=SMED30009865|organism=Schmidtea mediterranea sexual|type=transcript|length=2092bp
CTTTGACATTTTGGTAATAAATTAAACAAAGTTGTTATATACAACGGAGT
AATCTTTTAAAATAAATTATAGTATACTATTTAATTTAATATTATATAGT
ATGAAATTATAGATGTAAATCTTATAATTAAAACCCTAGTTGAATAACTA
CAAAAATTTTTAAAGCAACTAAGGGCGTATGGCGGATGCCTTGGTTCTGA
GAGGCGAAGAAGGACGTGGTAAACTGCGATAAGCTGCGGTAAGCTGAAAA
CAAGCATTATACCCGCAGATTTCCGAATGGGGCAACCCACTTGATTGAAG
ATCAAGTATTTGTAGCAATACAAAAGCTAACCCGGAGAACTGAAACATCT
AAGTACCCGGAGGAAAATAAAACAATACAGTGATTCCCTAAGTAGTGGCG
AGCGAAAGGGGAACAGCCCAAATCGCAATAGCGTGCTATTGCGAGGTTAT
AGGGCCGCATTTAATGAGTTATATCAAGCTGAATTTTCTGGAAAGAAAAG
CAACATAAGGTGATAGCCCTGTAAGCACAAATTATAACAAGTGAGCGGTA
CCCTGAGTAATGCGGAACCGGAGAAATTCTGCATGAAGTCACCAGCACCA
TCTGGTAAGGCTAAATACTCCTCAGAAACCGATAGTGAACTAGTACCGTA
AGGGAAAGGTGAAAAGTACTTCGAATCAGAAGAGTGAAATAGTACCTGAA
ACCGTACGCCTACAAGCGGTCGGAGCAACATTATGTTGTGACGGCGTGCC
TTTTGCATAATGAGCCTACGAGTTGTACTTCACTGGCGAGGTTAAGTTTT
TAAGCAACGAAGCCGTAGCGAAAGCAAGTCCAAATAGGGCGATTTAGTCA
GTGGAGACAGACGCGAAACTTTGTGATCTATCCATGAGCAGGTTGAAGGT
GTAGTAAAATATACTGGAGGACCGAACTCATAAACGTTGAAAAGTTTTGA
GATGACTTGTGGATAGGGGTGAAAGGCCAATCAAACTGAGAGATAGCTCG
TTCTCCCCGAAATGTTTTTAGGAACAGCCTTGTATATTGAGGTGTGATAG
AGGTAGAGCTACTGATTGGGTGAGGGGGTGTCAAAGCCAGCCAAGCCCTA
ACAAACTCCGAATGCTATCACATATCTACAGGAGTGAGGCTGTGGGCGAT
AAGGTCCATGGCCAAAAGGGAAATAACCCAGACTAACAGTTAAGGTCCCT
AAGCGTATGTTAAGTTGATCAAACGAAGTTAGAATCCTATAACACCCAGG
ATGTTGGCTTGGAAGCAGCCATTCATTTAAAGAGTGCGTAACAGCTCACT
GGTCGAGGATTCTTGCACGGAAAATAATCGGGCATCAAACATACCACCGA
AACTTTAGACTCATACTATGTATGAGTGGTAGGGGAGCATTCTAAACTGC
ATCGAAGGTGTTGGGTGACCAATGCTGGAGCGTTTAGAAAAGAAAATGTA
GGCATAAGTAACGATAAATGTAGTGAAAAACTATATCGCCGCAAGTCCAA
GGTTTCCTGATCAACGTTAATCGAATCAGGGTTAGTCGGGTCCTTAGGAA
TACCCGAAAGGGGAATCTGATGGCAAATTGATTAATATTTCAATACTTGC
TTTAACTTCGATGGGGTGACGGAGTAGTGAAAGGTTCGCGAACAGACGTA
ATAGTTCGTTAAAGCGTGTAGTTATATTTGTTGTAGGTAAATCCGCAATG
AATGATGAACGTGATAGTACCACAAGTCTTCGGATGAGTGGATAGTAACC
CTAAACAAACTTCCAAGAAAAACCTCTAAGTTATGGTTAAAGCAACCCGT
ACCGTAAACCGACACAGGTGGACGAGATGAATATTCTAAGGCGCTCGGGT
GAGCCGTGGAGAAGGAACTAGGCAAATTAACGCTGTAACTTCGGGATAAA
GCGTACCGCAGTGATGCGGTCTCAGTAAAATGGTTCAACCAACTGTTTAA
CAAAAACATAGGGCTCTGCAAAATCGCAAGATGAAGTATAGGGCCTGATA
CCTGCCCGGTGCTGGAAGGTTAAGGAAGGGGGTTCGGCGCAAGCCAAAGC
TCTTGACTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000142posterior region of the whole animal
PLANA:0002056medial muscle cell