SMED30008029

Overview
NameSMED30008029
Smed IDSMED30008029
Length (bp)2607
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell 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 SMED30008029 (SMED30008029) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008029 (SMED30008029) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30008029 (SMED30008029) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008029 (SMED30008029) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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

 

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Anatomical Expression

PAGE et. al., 2020




SMED30008029

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30008029 dd_Smed_v4_1314_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30008029 Contig18057newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30008029 Contig18057uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
epidermisSMED30008029 dd_Smed_v4_1314_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
SMED30008029 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007403:9844..12569 -12616
v31.038831:302..2654 -10827
Homology
BLAST of SMED30008029 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1)

HSP 1 Score: 162.925 bits (411), Expect = 3.841e-44
Identity = 78/131 (59.54%), Postives = 102/131 (77.86%), Query Frame = 1
Query: 1336 QTTLKVSSRFESRYLQALLDRGYTLSTYGSKEWPYRN-ARQDEDMEIPILAIKRELGRNSDREIRHPVEVAQQQFEYMERKFRWKANMQRRQLARINADIVSGRIPSSDGYTPEYGVSFNLNNPALLKTEA 1725
            +TTL + S+F  RY QAL D  Y+LSTYG+ EWP R+  R DED+E+P LAIKRE GRN+ R+IRH  EVA QQF+++ERK+RWKA++QR++L RIN DI SGRI SSDGY P+Y ++F+  +PALL+  A
Sbjct:   64 RTTLIIPSKFAGRYRQALWDGVYSLSTYGTSEWPNRSRIRHDEDVELPSLAIKREPGRNTARKIRHEAEVALQQFDHLERKYRWKASLQRKRLMRINKDIASGRISSSDGYLPDYNIAFDPEDPALLELSA 194          
BLAST of SMED30008029 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1)

HSP 1 Score: 162.925 bits (411), Expect = 4.002e-44
Identity = 78/131 (59.54%), Postives = 102/131 (77.86%), Query Frame = 1
Query: 1336 QTTLKVSSRFESRYLQALLDRGYTLSTYGSKEWPYRN-ARQDEDMEIPILAIKRELGRNSDREIRHPVEVAQQQFEYMERKFRWKANMQRRQLARINADIVSGRIPSSDGYTPEYGVSFNLNNPALLKTEA 1725
            +TTL + S+F  RY QAL D  Y+LSTYG+ EWP R+  R DED+E+P LAIKRE GRN+ R+IRH  EVA QQF+++ERK+RWKA++QR++L RIN DI SGRI SSDGY P+Y ++F+  +PALL+  A
Sbjct:   66 RTTLIIPSKFAGRYRQALWDGVYSLSTYGTSEWPNRSRIRHDEDVELPSLAIKREPGRNTARKIRHEAEVALQQFDHLERKYRWKASLQRKRLMRINKDIASGRISSSDGYLPDYNIAFDPEDPALLELSA 196          
BLAST of SMED30008029 vs. Planmine SMEST
Match: SMESG000037536.1 (SMESG000037536.1)

HSP 1 Score: 152.525 bits (384), Expect = 1.245e-43
Identity = 77/78 (98.72%), Postives = 78/78 (100.00%), Query Frame = 1
Query:   34 MQSEQAQNNRMKELDVDPNEKIKSVKDKLESLLKVQSRFIELSFSAEALDNEKTVKECDIEEGDTIIMIAKVVGGIEK 267
            MQSEQAQN+RMKELDVDPNEKIKSVKDKLESLLKVQSRFIELSFSAEALDNEKTVKECDIEEGDTIIMIAKVVGGIEK
Sbjct:    1 MQSEQAQNSRMKELDVDPNEKIKSVKDKLESLLKVQSRFIELSFSAEALDNEKTVKECDIEEGDTIIMIAKVVGGIEK 78          
BLAST of SMED30008029 vs. Planmine SMEST
Match: SMESG000059844.1 (SMESG000059844.1)

HSP 1 Score: 158.303 bits (399), Expect = 1.303e-43
Identity = 78/128 (60.94%), Postives = 94/128 (73.44%), Query Frame = 1
Query: 1336 QTTLKVSSRFESRYLQALLDRGYTLSTYGSKEWPYRNA-RQDEDMEIPILAIKRELGRNSDREIRHPVEVAQQQFEYMERKFRWKANMQRRQLARINADIVSGRIPSSDGYTPEYGVSFNLNNPALLK 1716
            Q TL + S+F  RY QAL D  Y+LST+G+ EWPYRN  R DEDME+  LAIKRE GRN  REIRH  EVA QQF ++ERK+ WKA++Q R+L +IN DI  GRIPSSDGY  EY V+FN  +PA L+
Sbjct:   54 QNTLTIPSKFAGRYRQALWDPRYSLSTHGTSEWPYRNKNRHDEDMELLSLAIKREPGRNPAREIRHEAEVALQQFVHLERKYHWKASLQLRRLVKINKDIAGGRIPSSDGYLLEYNVTFNPEDPAFLE 181          

HSP 2 Score: 38.891 bits (89), Expect = 1.303e-43
Identity = 16/42 (38.10%), Postives = 27/42 (64.29%), Query Frame = 3
Query: 1692 PQ*PSSAKNRSSIHQKLPRRIIQHDLLEGLKSRVNDDHTYSR 1817
            P+ P+  +  + +H  LP+R++Q D+LE L  R  ++H YSR
Sbjct:  174 PEDPAFLELNTPVHLALPKRLLQPDILEALTDRTYEEHAYSR 215          

HSP 3 Score: 75.0998 bits (183), Expect = 7.654e-14
Identity = 40/69 (57.97%), Postives = 46/69 (66.67%), Query Frame = 1
Query: 2278 VKPSRVKKIYQRLTVAQWGWKEEKVLNQPQQTQILGLEVALSASQVWSVVTYSLVFAPAQLAYRVQGGP 2484
             KPS+VK+I QRLT AQ  W+EEK LNQ Q+ QI GLEVA       S VTY LVFAP Q+ Y+ Q  P
Sbjct:  273 TKPSQVKRICQRLTEAQREWQEEKALNQAQKVQISGLEVARKEG---SAVTYPLVFAPTQVTYQEQDCP 338          
BLAST of SMED30008029 vs. Planmine SMEST
Match: SMESG000003895.1 (SMESG000003895.1)

HSP 1 Score: 144.05 bits (362), Expect = 1.314e-37
Identity = 67/127 (52.76%), Postives = 94/127 (74.02%), Query Frame = 1
Query: 1342 TLKVSSRFESRYLQALLDRGYTLSTYGSKEWPYRNARQDEDMEIPILAIKRELGRNSDREIRHPVEVAQQQFEYMERKFRWKANMQRRQLARINADIVSGRIPSSDGYTPEYGVSFNLNNPALLKTE 1722
             L+V+++F +RY QAL DR Y+L+T G+ EWP R+  +D + E+P +AIKRE GRN  R+IR   +    + E +++KFRW+ANM RR+LARINADI SG   S+DG+ P+YGVSF+L++PAL K E
Sbjct:  145 CLRVTAQFAARYRQALWDRQYSLATCGNDEWPCRSISRDNETELPSVAIKREPGRNPSRQIRQKAKFTLYRLENLKKKFRWRANMARRKLARINADIASGLKLSTDGFAPDYGVSFDLHDPALPKIE 271          
The following BLAST results are available for this feature:
BLAST of SMED30008029 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 SMED30008029 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 SMED30008029 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 SMED30008029 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 SMED30008029 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 SMED30008029 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 SMED30008029 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 SMED30008029 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 SMED30008029 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 SMED30008029 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 SMED30008029 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 SMED30008029 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 SMED30008029 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 SMED30008029 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000010307.13.841e-4459.54SMESG000010307.1[more]
SMESG000010307.14.002e-4459.54SMESG000010307.1[more]
SMESG000037536.11.245e-4398.72SMESG000037536.1[more]
SMESG000059844.11.303e-4360.94SMESG000059844.1[more]
SMESG000003895.11.314e-3752.76SMESG000003895.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008029 ID=SMED30008029|Name=SMED30008029|organism=Schmidtea mediterranea sexual|type=transcript|length=2607bp
TTTTTTACAGTTATGAAAATTTTTGTGTCCATAATGCAAAGTGAGCAAGC
TCAAAATAATAGAATGAAAGAATTAGACGTAGATCCTAATGAAAAGATAA
AATCAGTAAAAGATAAATTAGAAAGTTTATTGAAAGTCCAGTCCAGGTTT
ATTGAGCTTTCTTTTTCAGCTGAAGCTTTGGATAATGAAAAAACAGTCAA
GGAGTGCGATATAGAAGAAGGTGATACAATAATTATGATTGCAAAGGTGG
TTGGAGGAATAGAGAAATAGAGTTATAAATGATATGACCGTGATATTTTA
TATTCTATAAACAATTATTATTTATTCATTTTTTATGAATTTTCATTTTA
CAATAAATTCATATTTGACAAATTGAGGTTACTGGTTGATTATTTTATTA
ACGGGGAAGAGTTATATTTGTTAGCACGCCGAAATGTAATAGAACATATT
TTGTGCTGCAGTTTTATCGGAAACTTGAATGAAGTAATTGATAGTTTTAA
CGCGGTCTGCTAAAACCATCCATTATTTGTTTTTAACTGCTAAATAATAT
TGTATACTAAATGTGTTTTATTTGATTACTTTAATTTATTGCAATCTTAG
AAAGGTGTTAAGGATAATCCCTCAACCAGTACTGAATACAAATGAAAAAA
TCAACCCCTACACTATCAAAATGATTATATAATAATTTAATGAAGCCAAC
AAAATCAATTTATTAATTAAAATGCTTGCCGAAATTATCATAAATTCAAA
AAATAAATTAACCCTTCAACCAAAAATTAAATCGAGTGTAAATAAAACTC
AACCTGAAATCATATTGGAAAAAATGTTGAATAATGACAAACAATAATTT
AGGAGAAGCCGAAGAGAAATCCGGCATTATAAGGCAGATGGCCGAGGTTT
CGTCAACGTAGACATTGCTGGCCATGTCCTCGAAAAAATTCACGCTCGAT
TTATCCATAAGTTGACTTGCAGACAAACGAATAAATCTAAAAGAAAAACA
AGATTAATTACCAAGCACTAATTATATTCACTTACCTAAATAATGGTTAA
CACTGCTAAACCATACTAAAATATTCTCTGAAAATTTTCGGTGTTTAGTA
AACACACCCCCGTCAACTCACTCGTGAATGATATAAATTCACTACTATAT
CACAATCCGGTCAAATATATTGCAAGATGTCAGATACATGTAGCATGAAT
AATAAAATCCTTAATGGAACGATTCCAAAACGAAACAAAGTTGACCGACC
TTCGATGGAAGTCGATCCAGAGTATAGCCACCTGGACCACGGACGAAAAG
TAAGCTCATCCGAGGTCGAGTGGTCCGATGATTCCCAAACGACGCTGAAA
GTTTCAAGCCGGTTCGAAAGTCGATATCTCCAAGCCCTCTTGGATCGCGG
CTATACGCTATCCACCTACGGTAGCAAGGAGTGGCCTTATCGAAACGCGC
GCCAGGATGAGGATATGGAGATTCCAATTCTTGCTATAAAGCGAGAACTG
GGTCGAAATTCGGATAGAGAAATCCGGCACCCAGTAGAAGTCGCACAGCA
GCAGTTTGAATATATGGAGCGGAAATTTCGCTGGAAAGCCAACATGCAGA
GAAGACAGCTGGCTCGGATTAATGCCGATATAGTAAGTGGCCGAATTCCC
AGCTCTGACGGGTATACCCCAGAGTATGGCGTATCGTTCAACCTCAATAA
CCCAGCTCTGCTAAAAACCGAAGCTCAATACATCAGAAATTACCAAGACG
CATAATCCAGCACGACCTATTAGAAGGTTTGAAAAGTCGAGTGAATGATG
ATCACACTTATTCCCGACAATTATCGTATTAAAGTACTTAAATGTTCTTA
GATTATAAGAGTTGCTATTAATTAAATGAGTTTTTTGGTGTAGTACAACA
AAGTTAGTAGAGATTAGTAAAGTAATTATTTAGTTATTTTATGATAATAA
ATTACAAAAATTTGACTAAAGTTTGATACATATCAAGGTGAAATAAATGT
AGTAAATGAATTAATCGTATGATAAAGTAAAATATGATTTTGGCCGCAGA
TATTTTAATGAGAAGCAAAAAGGAATATTTTTATGAAATATTTCTAATTC
ACCTCGTAACGCGAAAACATTGATCATATAACGTTTTAATATATTTTGTT
TAAATTTAGCGATGGAAGCGATCCAATCAATTGGCAAGGAATTGAAGCAG
CTGCGCTGTGAGAATGCTGATCTTCAACAGCAACGGCTACAACTAAGCCG
AGAACTACAACGGATTAGAGCCACTTGGTCAAACCATCGCGGGTGAAGAA
AATATATCAGCGCCTTACCGTGGCCCAATGGGGGTGGAAGGAGGAGAAAG
TACTAAATCAGCCCCAGCAAACCCAGATCCTAGGGCTTGAGGTCGCCTTA
TCAGCTAGCCAGGTGTGGAGTGTGGTCACGTACTCCCTGGTATTTGCCCC
AGCACAACTCGCATACCGAGTCCAAGGCGGTCCCGATAAACTGAAGAAAC
AATCGCAGCCTCATTCAAGGCCAGGTAAAGCCTAAAGAGAGCGTAGGCGA
CTCCAACAAATAAAATCTAAAAAATGAAGCAGTGTGTAATATTGCAATAA
ATGTTTA
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protein sequence of SMED30008029-orf-1

>SMED30008029-orf-1 ID=SMED30008029-orf-1|Name=SMED30008029-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=193bp
MSDTCSMNNKILNGTIPKRNKVDRPSMEVDPEYSHLDHGRKVSSSEVEWS
DDSQTTLKVSSRFESRYLQALLDRGYTLSTYGSKEWPYRNARQDEDMEIP
ILAIKRELGRNSDREIRHPVEVAQQQFEYMERKFRWKANMQRRQLARINA
DIVSGRIPSSDGYTPEYGVSFNLNNPALLKTEAQYIRNYQDA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR000626Ubiquitin-like_dom
IPR029071Ubiquitin-like_domsf
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding