SMED30025536

Overview
NameSMED30025536
Smed IDSMED30025536
Length (bp)1655
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 SMED30025536 (SMED30025536) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30025536 (SMED30025536) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30025536

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
X1 cellSMED30025536 SmedASXL_062809SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30025536 SmedASXL_062809SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
epidermisSMED30025536 dd_Smed_v4_14193_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
[Close]
BLAST of SMED30025536 vs. TrEMBL
Match: V4BIY8 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_165460 PE=4 SV=1)

HSP 1 Score: 85.1149 bits (209), Expect = 6.930e-16
Identity = 41/96 (42.71%), Postives = 61/96 (63.54%), Query Frame = -1 
Query: 1023 KYRGEMHVPGYNFCGPGTRTDLRLDDNKKPVQTSLPVNAIDELCVAHDIYYSSKSRLVRYQSDLRLIKALETMDTNNLSKQDRVVRRLIIYVFRLK 1310
            KY GE H+PG+N+ GPGTR DLRLD+N KP     PVN +D   + HDI Y +K    R+++D ++I  LE +   N + ++R+ R LI+ + + K
Sbjct:   30 KYPGEKHLPGHNYTGPGTRLDLRLDENDKPKPGEEPVNRVDAAALKHDILYRNKDIQFRHEADKQMIIELENIP--NPTFKERMERALIVKLLKAK 123
[Close]
BLAST of SMED30025536 vs. TrEMBL
Match: V3ZXK7 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_155209 PE=4 SV=1)

HSP 1 Score: 83.9593 bits (206), Expect = 1.724e-15
Identity = 42/96 (43.75%), Postives = 57/96 (59.38%), Query Frame = -1 
Query: 1023 KYRGEMHVPGYNFCGPGTRTDLRLDDNKKPVQTSLPVNAIDELCVAHDIYYSSKSRLVRYQSDLRLIKALETMDTNNLSKQDRVVRRLIIYVFRLK 1310
            KY GE H+PG+N+ GPGTR DLRLD N KP Q   PVN +D   + HDI Y +K  + R+++D ++I  LE +         R+ R LII +   K
Sbjct:   31 KYPGEKHLPGHNYTGPGTRLDLRLDQNDKPKQGEEPVNRVDAAALKHDILYRNKDIISRHEADKQMIIELENI--------PRIQRALIIKLLTAK 118
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BLAST of SMED30025536 vs. TrEMBL
Match: V4AAM0 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_172863 PE=4 SV=1)

HSP 1 Score: 84.7297 bits (208), Expect = 3.555e-15
Identity = 41/96 (42.71%), Postives = 60/96 (62.50%), Query Frame = -1 
Query: 1023 KYRGEMHVPGYNFCGPGTRTDLRLDDNKKPVQTSLPVNAIDELCVAHDIYYSSKSRLVRYQSDLRLIKALETMDTNNLSKQDRVVRRLIIYVFRLK 1310
            KY GE H+PG+N+ GPGTR DLRLD+N  P     PVN +D   + HDI Y +K    R+Q+D ++I  LE +   N + ++++ R LII + + K
Sbjct:   32 KYPGEKHLPGHNYTGPGTRLDLRLDENDNPKPGEEPVNRVDAAALKHDILYRNKDITFRHQADKQMIDELENIP--NPTFKEKLQRALIIKLLKAK 125
[Close]
BLAST of SMED30025536 vs. TrEMBL
Match: V3ZPR9 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_155882 PE=4 SV=1)

HSP 1 Score: 84.3445 bits (207), Expect = 6.227e-15
Identity = 41/96 (42.71%), Postives = 60/96 (62.50%), Query Frame = -1 
Query: 1023 KYRGEMHVPGYNFCGPGTRTDLRLDDNKKPVQTSLPVNAIDELCVAHDIYYSSKSRLVRYQSDLRLIKALETMDTNNLSKQDRVVRRLIIYVFRLK 1310
            KY GE H+PG+N+ GPGTR DLRLD N KP     PVN +D   + HDI Y +K    R+++D ++I  LE +   N + ++++ R LII + + K
Sbjct:  109 KYSGEKHLPGHNYTGPGTRLDLRLDQNDKPKPGEEPVNRVDAAALKHDILYRNKDLKFRHEADKQMIIELENIP--NPTFKEKMQRALIIKLLKTK 202
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BLAST of SMED30025536 vs. TrEMBL
Match: V4A7J7 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_162196 PE=4 SV=1)

HSP 1 Score: 86.6557 bits (213), Expect = 1.838e-14
Identity = 43/100 (43.00%), Postives = 62/100 (62.00%), Query Frame = -1 
Query: 1011 KYRGEMHVPGYNFCGPGTRTDLRLDDNKKPVQTSLPVNAIDELCVAHDIYYSSKSRLVRYQSDLRLIKALETMDTNNLSKQDRVVRRLIIYVFRLKSNFE 1310
            KY GE H+PG+N+ GPGTR DLRLD+N KP     PVN +D   + HDI Y +K    R+++D ++I  LE +   N + ++R+ R LII + + K   E
Sbjct:   30 KYPGEKHLPGHNYTGPGTRLDLRLDENDKPKPGEEPVNRVDAAALKHDILYRNKDINFRHEADKQMIIELENIP--NPTFKERMERALIIKLLKAKMKLE 127
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BLAST of SMED30025536 vs. Ensembl Nematostella
Match: EDO44700 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RUZ8])

HSP 1 Score: 50.8322 bits (120), Expect = 4.888e-7
Identity = 33/91 (36.26%), Postives = 52/91 (57.14%), Query Frame = -1 
Query: 1047 GEMHV--P---GYNFCGPGTRTDLRLDDNKKPVQTSLPVNAIDELCVAHDIYYS-SKSRLVRYQSDLRLIKALETMDTNNLSKQDRVVRRL 1301
            GE+H+  P    YN+CGPGTR   RL+ +   +  S P+N +D LC  HDI YS SK    ++ +D  L++A+  +   N+  +   +RR+
Sbjct:   19 GEIHLRTPTGLSYNYCGPGTRLRQRLNSSNPGI--SNPINILDALCQKHDIAYSKSKDLDDKHVADDNLLEAISNIP-KNMQHKKTPLRRV 106
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BLAST of SMED30025536 vs. Planmine SMEST
Match: SMESG000012349.1 (SMESG000012349.1)

HSP 1 Score: 174.096 bits (440), Expect = 3.629e-52
Identity = 77/99 (77.78%), Postives = 92/99 (92.93%), Query Frame = -1 
Query:  999 MHVPGYNFCGPGTRTDLRLDDNKKPVQTSLPVNAIDELCVAHDIYYSSKSRLVRYQSDLRLIKALETMDTNNLSKQDRVVRRLIIYVFRLKSNFEVMAG 1295
            MHVPGYNFCGPGTRTDLRLD NKKPV TSLP+N+IDELCVAHDI Y +++RLVRY+SDL+LIKAL+ M T N+SKQD++VR+LIIYVF+LK+NFEV+AG
Sbjct:    1 MHVPGYNFCGPGTRTDLRLDKNKKPVPTSLPINSIDELCVAHDIEYGNQNRLVRYKSDLKLIKALQDMATENMSKQDKLVRKLIIYVFKLKTNFEVLAG 99
[Close]
BLAST of SMED30025536 vs. Planmine SMEST
Match: SMESG000000949.1 (SMESG000000949.1)

HSP 1 Score: 120.939 bits (302), Expect = 4.792e-32
Identity = 58/104 (55.77%), Postives = 75/104 (72.12%), Query Frame = -1 
Query:  999 KYRGEMHVPGYNFCGPGTRTDLRLDDNKKPVQTSLPVNAIDELCVAHDIYYSSKSRLVRYQSDLRLIKALETMDTNNLSKQDRVVRRLIIYVFRLKSNFEVMAG 1310
            K +GEMH+PGYNF GPGTRTDLRLD++KKPV  S P+N IDE C+ HDI Y+SK + VRY SD +LI  ++ +   + + ++ VV  LIIYVF LK+ FE   G
Sbjct:    3 KLKGEMHIPGYNFWGPGTRTDLRLDEHKKPVSWSKPINKIDEQCLTHDIAYNSKDKRVRYDSDRQLI--MDILYLRHKTPEEEVVGNLIIYVFELKNIFEKKLG 104
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BLAST of SMED30025536 vs. Planmine SMEST
Match: SMESG000003420.1 (SMESG000003420.1)

HSP 1 Score: 64.6994 bits (156), Expect = 1.235e-12
Identity = 30/70 (42.86%), Postives = 43/70 (61.43%), Query Frame = -1 
Query: 1101 KYRGEMHVPGYNFCGPGTRTDLRLDDNKKPVQTSLPVNAIDELCVAHDIYYSSKSRLVRYQSDLRLIKAL 1310
            KY GE H+P +N+ GP TR D+RLD N  P     P+N +DE  + HDI Y +++   R + D+ LI+ L
Sbjct:   34 KYTGEHHLPKFNYLGPRTRLDIRLDSNDIPKPGEEPINRVDEDALRHDIAYRNENLRNRQKPDIDLIEDL 103
[Close]
BLAST of SMED30025536 vs. Planmine SMEST
Match: SMESG000057616.1 (SMESG000057616.1)

HSP 1 Score: 63.929 bits (154), Expect = 3.427e-11
Identity = 29/35 (82.86%), Postives = 31/35 (88.57%), Query Frame = -2 
Query: 1550 STDGYAPPYNTSFNLDDSRLNARSTAIDVVVPRRV 1654
            STDGYAPPYNTSFNLDD RLN  S A+DVVVPRR+
Sbjct:   97 STDGYAPPYNTSFNLDDRRLNTNSKAVDVVVPRRI 131
[Close]
BLAST of SMED30025536 vs. Planmine SMEST
Match: SMESG000079932.1 (SMESG000079932.1)

HSP 1 Score: 62.7734 bits (151), Expect = 5.086e-11
Identity = 28/35 (80.00%), Postives = 33/35 (94.29%), Query Frame = -2 
Query: 1550 STDGYAPPYNTSFNLDDSRLNARSTAIDVVVPRRV 1654
            STDGYAPPYNTS+NLDD RLN RSTAI+VVVP+++
Sbjct:   87 STDGYAPPYNTSYNLDDERLNIRSTAINVVVPQKI 121
The following BLAST results are available for this feature:
BLAST of SMED30025536 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 SMED30025536 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 SMED30025536 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 SMED30025536 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 SMED30025536 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 SMED30025536 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 SMED30025536 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 SMED30025536 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
V4BIY86.930e-1642.71Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
V3ZXK71.724e-1543.75Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
V4AAM03.555e-1542.71Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
V3ZPR96.227e-1542.71Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
V4A7J71.838e-1443.00Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
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BLAST of SMED30025536 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 SMED30025536 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 SMED30025536 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 SMED30025536 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO447004.888e-736.26Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30025536 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 SMED30025536 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000012349.13.629e-5277.78SMESG000012349.1[more]
SMESG000000949.14.792e-3255.77SMESG000000949.1[more]
SMESG000003420.11.235e-1242.86SMESG000003420.1[more]
SMESG000057616.13.427e-1182.86SMESG000057616.1[more]
SMESG000079932.15.086e-1180.00SMESG000079932.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025536 ID=SMED30025536|Name=SMED30025536|organism=Schmidtea mediterranea sexual|type=transcript|length=1655bp
CCCCAATGCCTTTCATATTGATTAATTAATCCCAAGAAATTCTGATTTTT
AAAATTTTTGCTATTTCCTACTAATTGTTCATATAATCCAACATTATCAT
CTAATAATCTCTTCATTTCATCATCATTTTTTATCAAATCATATATACCA
TCACCAATCTCATTACTCTCTTTATCTTGATGCAATGTTTTTTCCAACAA
CTTTATACCGTTATATATTGATATTTCAGCAATTTCTTTATCAAATAAAT
TAATTAAATCTTTAAAATCCTTTTGCCTGTTTGGCTGATATATTTCTTCA
AAATCTTTCTCTTTAAATAATCTGAAATCATCTAGTTTTAAATCATTAAG
GAACATATTTCTGACGTCTACATAACCGTCGTGGTTTGAAAGTTCATTAA
ATGCCTTTAATACATAATCACTTGTGTATGGTTTTAAATGATCTTTAACT
AACAATTCCAAAGGTTCTGCATAGAAGCTTCTGATATAAGCACTTAGGTA
GAATCCAATTGTAAAACCAGCTACTGCAGCTAAATCATTAATATTATGTT
TGACACCTCCGATTTTCTTCATAAATCCTTTCATACCAGGTCTTAATATA
TTACGAACTGTATAATTTAATATATTATTTTTGAATGTCTGGTTTAATTT
TAATGGCTTAAATAAATCACTACTTAGAGATTTTAATGAATTTGACAATA
ATAATTGTTGATAAGGAGTAGATTTAAAATTTACTTTTGCTTTAACTTGT
CTTAAAACTCCCTGTACTTTCCCAAATGTTGTAGTGGCAAAAACATTAAA
TAACTGTGCTGTTGCGTTGATGGCATTAAGCCTGTCTCTTTCTGCTAAGC
CAGCGTGCTGTTGATTTTCGAAATGAGCTTTCATGTACAACCTTAAATCT
TGTGCGACTTTTATGTTTTCAGAAAAACGCTTAATTAATTCGATGTCTGT
TATATTTAATTTGATATCTTTGTTATCATTGTTAATATTTTTTATTAACC
CCGCCATTACTTCAAAATTAGATTTTAATCTGAAAACATAGATTATTAAT
CTTCTCACCACTCGATCTTGTTTAGACAGGTTATTTGTGTCCATTGTTTC
TAACGCTTTTATCAGACGTAAATCGGATTGATATCTGACAAGCCTAGACT
TGCTGCTGTAGTAAATGTCATGAGCTACGCAGAGTTCATCGATGGCATTT
ACAGGTAAACTTGTTTGGACTGGTTTTTTATTGTCATCTAATCTGAGATC
AGTTCGTGTGCCTGGCCCACAGAAGTTGTAGCCAGGTACATGCATCTCGC
CTCTATATTTAATCGGTGCCATCTAGAAATAAAATCATTATGCTTTCATT
CGTACAAAGAGATAGTTATTACGAAGAACAATTTAAGAACGCGGAAAATC
TTAAAAATTACTTGGTATCGCCACTAACAAGCTATATTGATTTTCGATTG
AACAACTTCTTTATAATCAGAAATAATATCGAGACGTGTGAGCCAGTTTA
TTATTTGGCAGGCCTCTTCTCAGCTTATAAATCGCAATTAGATAAATTCA
ACCCGCCGTGGGACCACCACATCGATGGCCGTGGATCTCGCATTCAATCT
GCTGTCATCGAGGTTAAAAGATGTGTTGTACGGAGGAGCGTATCCGTCCG
TACTG
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protein sequence of SMED30025536-orf-1

>SMED30025536-orf-1 ID=SMED30025536-orf-1|Name=SMED30025536-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
MLSFVQRDSYYEEQFKNAENLKNYLVSPLTSYIDFRLNNFFIIRNNIETC
EPVYYLAGLFSAYKSQLDKFNPPWDHHIDGRGSRIQSAVIEVKRCVVRRS
VSVRT
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protein sequence of SMED30025536-orf-2

>SMED30025536-orf-2 ID=SMED30025536-orf-2|Name=SMED30025536-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=440bp
MAPIKYRGEMHVPGYNFCGPGTRTDLRLDDNKKPVQTSLPVNAIDELCVA
HDIYYSSKSRLVRYQSDLRLIKALETMDTNNLSKQDRVVRRLIIYVFRLK
SNFEVMAGLIKNINNDNKDIKLNITDIELIKRFSENIKVAQDLRLYMKAH
FENQQHAGLAERDRLNAINATAQLFNVFATTTFGKVQGVLRQVKAKVNFK
STPYQQLLLSNSLKSLSSDLFKPLKLNQTFKNNILNYTVRNILRPGMKGF
MKKIGGVKHNINDLAAVAGFTIGFYLSAYIRSFYAEPLELLVKDHLKPYT
SDYVLKAFNELSNHDGYVDVRNMFLNDLKLDDFRLFKEKDFEEIYQPNRQ
KDFKDLINLFDKEIAEISIYNGIKLLEKTLHQDKESNEIGDGIYDLIKND
DEMKRLLDDNVGLYEQLVGNSKNFKNQNFLGLINQYERHW
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell