SMED30012397

Overview
NameSMED30012397
Smed IDSMED30012397
Length (bp)911
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

 



 

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




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30012397 (SMED30012397) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012397 (SMED30012397) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30012397

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30012397SMESG000048320.1 SmedASXL_077520SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30012397SMESG000078691.1 SMESG000070088.1 SMESG000066677.1 SMESG000051450.1 SMESG000049178.1 SMESG000048320.1 SMESG000047889.1 SMESG000042542.1 SMESG000033144.1 SMESG000022579.1 SMESG000010579.1 SMESG000010549.1 SMESG000010548.1 SMESG000010546.1 SMESG000010469.1 SMESG000010468.1 SMESG000010222.1 SMESG000010218.1 SMESG000009697.1 Contig19174newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30012397SMESG000078691.1 SMESG000070088.1 SMESG000066677.1 SMESG000051450.1 SMESG000049178.1 SMESG000048320.1 SMESG000047889.1 SMESG000042542.1 SMESG000033144.1 SMESG000022579.1 SMESG000010579.1 SMESG000010549.1 SMESG000010548.1 SMESG000010546.1 SMESG000010469.1 SMESG000010468.1 SMESG000010222.1 SMESG000010218.1 SMESG000009697.1 Contig19174uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30012397 vs. Planmine SMEST
Match: SMESG000069193.1 (SMESG000069193.1)

HSP 1 Score: 311.997 bits (798), Expect = 6.637e-106
Identity = 183/289 (63.32%), Postives = 204/289 (70.59%), Query Frame = -3
Query:    1 LGHTGAMIELPAHIVEQWRQAWDRVYRERYPDVPEDDQQADISPEEFMRQFRKPSDEPNPSQDIXXXXXXXXXXXXXXXXQVEAAEVRATEYLDNVKDDLANGRLASNYPPSLRPIRNLKRPVFVIPGYSPEEGIKRFLTDE*FLQQTAINDLYILSFDVILV*I*KTFCLFSYYCCSLRFVYLFCV*IHXXXXXXXXXXXXXXLEMDPMQLFQNELTQARQTNRKLHDQLVQLVRETQ*IKATWVEPSKVKRLYQKLAVAQKGWAEETQLVQSQKTQIKGLEVALSAC 867
            L  +GA++ELPAHIVEQWRQAW+RVYRER PD+PEDD+Q DISPEEFMRQFRK S+EPNPSQDILAQAQELLE L QHQR VEAA  RAT++L NV+DDLA G LAS+YPPS RPIRN KRPVFVIPGYSPEEGIKRFL DE   Q + +         +IL                                           EMDP++L Q ELT ARQ N+KLHDQLVQ+VRE Q IKATW+EP +VK LYQKLA AQKGWAEE QLVQ  KTQI+GLEVALSAC
Sbjct:   35 LRQSGAIVELPAHIVEQWRQAWNRVYRERCPDMPEDDRQEDISPEEFMRQFRKLSNEPNPSQDILAQAQELLEGLRQHQRHVEAAVERATKHLANVQDDLAAGCLASSYPPSPRPIRNTKRPVFVIPGYSPEEGIKRFLADEPSSQNSPL---------IIL-------------------------------------------EMDPVKLLQTELTHARQANKKLHDQLVQIVREIQQIKATWIEPKRVKPLYQKLATAQKGWAEEKQLVQGLKTQIRGLEVALSAC 271          
BLAST of SMED30012397 vs. Planmine SMEST
Match: SMESG000069193.1 (SMESG000069193.1)

HSP 1 Score: 307.76 bits (787), Expect = 2.469e-104
Identity = 182/289 (62.98%), Postives = 201/289 (69.55%), Query Frame = -3
Query:    1 LGHTGAMIELPAHIVEQWRQAWDRVYRERYPDVPEDDQQADISPEEFMRQFRKPSDEPNPSQDIXXXXXXXXXXXXXXXXQVEAAEVRATEYLDNVKDDLANGRLASNYPPSLRPIRNLKRPVFVIPGYSPEEGIKRFLTDE*FLQQTAINDLYILSFDVILV*I*KTFCLFSYYCCSLRFVYLFCV*IHXXXXXXXXXXXXXXLEMDPMQLFQNELTQARQTNRKLHDQLVQLVRETQ*IKATWVEPSKVKRLYQKLAVAQKGWAEETQLVQSQKTQIKGLEVALSAC 867
            L  +GA++ELPAHIVEQWRQAW+RVYRER PD+PEDD+Q DISPEEFMRQFRK S+EPNPSQDILAQAQELLE L QHQR VEAA  RAT++L NV+DDLA G LAS+YPPS RPIRN KRPVFVIPGYSPEEGIKRFL DE   Q +    L IL  D                                                 P++L Q ELT ARQ N+KLHDQLVQ+VRE Q IKATW+EP +VK LYQKLA AQKGWAEE QLVQ  KTQI+GLEVALSAC
Sbjct:   23 LRQSGAIVELPAHIVEQWRQAWNRVYRERCPDMPEDDRQEDISPEEFMRQFRKLSNEPNPSQDILAQAQELLEGLRQHQRHVEAAVERATKHLANVQDDLAAGCLASSYPPSPRPIRNTKRPVFVIPGYSPEEGIKRFLADEPSSQNSP---LIILEMD-------------------------------------------------PVKLLQTELTHARQANKKLHDQLVQIVREIQQIKATWIEPKRVKPLYQKLATAQKGWAEEKQLVQGLKTQIRGLEVALSAC 259          
BLAST of SMED30012397 vs. Planmine SMEST
Match: SMESG000080120.1 (SMESG000080120.1)

HSP 1 Score: 300.442 bits (768), Expect = 2.342e-101
Identity = 176/287 (61.32%), Postives = 197/287 (68.64%), Query Frame = -3
Query:    1 HTGAMIELPAHIVEQWRQAWDRVYRERYPDVPEDDQQADISPEEFMRQFRKPSDEPNPSQDIXXXXXXXXXXXXXXXXQVEAAEVRATEYLDNVKDDLANGRLASNYPPSLRPIRNLKRPVFVIPGYSPEEGIKRFLTDE*FLQQTAINDLYILSFDVILV*I*KTFCLFSYYCCSLRFVYLFCV*IHXXXXXXXXXXXXXXLEMDPMQLFQNELTQARQTNRKLHDQLVQLVRETQ*IKATWVEPSKVKRLYQKLAVAQKGWAEETQLVQSQKTQIKGLEVALSAC 861
             TGA++ELP HIVEQWRQAW+RVY ER PD+PEDD+Q DIS E+FMRQFRK S+EPNPSQDILAQAQELLE LL HQR VE A  R T YL NV+DDL  GRLAS+YPPS RP RN KRPVFVIPGYSPEEGIKRFLTD+   + + +         +IL                                           EMDP++L Q ELTQARQ N+KLHDQLVQ+VRETQ IKATW+E  +VK LYQKLA AQ GWAEE QLVQ  KTQI+GLEVALSAC
Sbjct:   26 QTGAIVELPTHIVEQWRQAWNRVYLERCPDMPEDDRQEDISREDFMRQFRKLSNEPNPSQDILAQAQELLECLLHHQRHVEVAVERVTRYLANVQDDLTTGRLASSYPPSPRPTRNTKRPVFVIPGYSPEEGIKRFLTDDNHHRNSTL---------IIL-------------------------------------------EMDPVKLLQTELTQARQANKKLHDQLVQIVRETQQIKATWIESKRVKPLYQKLAAAQNGWAEEKQLVQRLKTQIRGLEVALSAC 260          
BLAST of SMED30012397 vs. Planmine SMEST
Match: SMESG000015751.1 (SMESG000015751.1)

HSP 1 Score: 298.516 bits (763), Expect = 4.770e-100
Identity = 177/290 (61.03%), Postives = 199/290 (68.62%), Query Frame = -3
Query:    1 HLGHTGAMIELPAHIVEQWRQAWDRVYRERYPDVPEDDQQADISPEEFMRQFRKPSDEPNPSQDIXXXXXXXXXXXXXXXXQVEAAEVRATEYLDNVKDDLANGRLASNYPPSLRPIRNLKRPVFVIPGYSPEEGIKRFLTDE*FLQQTAINDLYILSFDVILV*I*KTFCLFSYYCCSLRFVYLFCV*IHXXXXXXXXXXXXXXLEMDPMQLFQNELTQARQTNRKLHDQLVQLVRETQ*IKATWVEPSKVKRLYQKLAVAQKGWAEETQLVQSQKTQIKGLEVALSAC 870
            ++G TGA++ELPAHIVEQWRQAW+RVYRER  ++PEDD+Q DISPE+FMRQFRK S+EPNPSQDILAQAQELLE LL HQR VEAA  RAT YL NV+DDLA G LASNYPPS RP RN KRPVFVIPGYSPEE IKRFLTD+   + +    L IL  D                                                 P++L Q ELT ARQ N+KLHDQLVQ+VRETQ IKATW+EP +VK LY K+A AQK WAEE QLVQ  KTQI+GLEVALSAC
Sbjct:   61 NVGQTGAIVELPAHIVEQWRQAWNRVYRERCHNMPEDDRQEDISPEDFMRQFRKLSNEPNPSQDILAQAQELLEGLLHHQRHVEAAVERATRYLANVQDDLAAGCLASNYPPSPRPTRNTKRPVFVIPGYSPEERIKRFLTDDNHHRNST---LIILEMD-------------------------------------------------PVKLLQTELTHARQANKKLHDQLVQIVRETQQIKATWIEPKRVKPLYHKMAAAQKEWAEEMQLVQGLKTQIRGLEVALSAC 298          
BLAST of SMED30012397 vs. Planmine SMEST
Match: SMESG000022579.1 (SMESG000022579.1)

HSP 1 Score: 229.565 bits (584), Expect = 3.554e-75
Identity = 126/140 (90.00%), Postives = 133/140 (95.00%), Query Frame = -3
Query:  442 HTGAMIELPAHIVEQWRQAWDRVYRERYPDVPEDDQQADISPEEFMRQFRKPSDEPNPSQDIXXXXXXXXXXXXXXXXQVEAAEVRATEYLDNVKDDLANGRLASNYPPSLRPIRNLKRPVFVIPGYSPEEGIKRFLTDE 861
            H GAMIELPAHIVEQWRQAWDRVYRERYPD+PEDDQQ D+SPEEFMR+FRKPSDEPNPSQDILAQAQ++LEDLLQ+QRQVEAA  RATEYLDNVKDDLANGRLASNYPPS RPIRNLKRPVFVIPGYSPEEGIKRF  D+
Sbjct:   71 HAGAMIELPAHIVEQWRQAWDRVYRERYPDMPEDDQQVDVSPEEFMRRFRKPSDEPNPSQDILAQAQKILEDLLQYQRQVEAAVERATEYLDNVKDDLANGRLASNYPPSPRPIRNLKRPVFVIPGYSPEEGIKRFFADD 210          
The following BLAST results are available for this feature:
BLAST of SMED30012397 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012397 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000069193.16.637e-10663.32SMESG000069193.1[more]
SMESG000069193.12.469e-10462.98SMESG000069193.1[more]
SMESG000080120.12.342e-10161.32SMESG000080120.1[more]
SMESG000015751.14.770e-10061.03SMESG000015751.1[more]
SMESG000022579.13.554e-7590.00SMESG000022579.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012397 ID=SMED30012397|Name=SMED30012397|organism=Schmidtea mediterranea sexual|type=transcript|length=911bp
ACAGGCGGATAACGCTACCTCTAATCCCTTGATTTGGGTCTTTTGGCTCT
GTACTAACTGCGTTTCTTCTGCCCACCCCTTCTGGGCCACAGCTAGCTTT
TGGTACAGTCGTTTGACCTTCGAGGGCTCTACCCATGTTGCTTTGATCTA
CTGGGTTTCCCTGACCAGTTGAACGAGTTGGTCGTGTAGTTTCCTGTTAG
TTTGCCTTGCCTGAGTTAACTCGTTTTGGAATAGTTGCATGGGGTCCATT
TCTAGAATAATGGCGATTGAAATTCATGATGACTGTTACAATAATGAGTG
TATTTAAACACAAAACAGATATACGAAACGAAGACTACAACAATAATAAG
AGAAGAGACAAAAAGTTTTCTAAATCTATACTAATATTACATCAAATGAT
AAAATGTACAAATCATTAATTGCCGTTTGTTGCAAAAATCATTCGTCCGT
GAGAAATCGTTTAATCCCTTCTTCTGGAGAATAACCCGGGATCACAAATA
CGGGTCGCTTGAGATTTCGGATTGGCCTCAGGGAAGGTGGGTAATTGCTG
GCCAGACGTCCGTTTGCCAGGTCATCTTTGACATTATCCAGATATTCCGT
GGCTCGCACCTCAGCGGCCTCGACTTGGCGCTGATGTTGTAAAAGGTCTT
CTAGGAGCTCTTGGGCCTGAGCGAGTATATCTTGCGATGGGTTGGGTTCA
TCCGACGGCTTCCGGAATTGCCGCATGAATTCTTCCGGCGATATGTCTGC
TTGTTGGTCGTCCTCAGGCACGTCAGGGTATCGTTCTCGGTACACCCGAT
CCCATGCCTGCCTCCATTGTTCCACGATATGAGCCGGAAGTTCGATCATA
GCTCCCGTATGTCCTAAATGAAGACAAAAATTAGTGCCTTCCTCGGCATT
TCTCTAGGCAG
back to top

protein sequence of SMED30012397-orf-1

>SMED30012397-orf-1 ID=SMED30012397-orf-1|Name=SMED30012397-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=137bp
MIELPAHIVEQWRQAWDRVYRERYPDVPEDDQQADISPEEFMRQFRKPSD
EPNPSQDILAQAQELLEDLLQHQRQVEAAEVRATEYLDNVKDDLANGRLA
SNYPPSLRPIRNLKRPVFVIPGYSPEEGIKRFLTDE*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head