SMED30016476

Overview
NameSMED30016476
Smed IDSMED30016476
Length (bp)1844
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 SMED30016476 (SMED30016476) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016476 (SMED30016476) 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



SMED30016476

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
epidermisSMED30016476 dd_Smed_v4_14672_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30016476 dd_Smed_v4_14672_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated epidermisSMED30016476 dd_Smed_v4_14672_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
SMED30016476 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009748:4172..6007 -8997
v31.012727:9957..12055 +8900
Homology
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BLAST of SMED30016476 vs. Planmine SMEST
Match: SMESG000042162.1 (SMESG000042162.1)

HSP 1 Score: 86.6557 bits (213), Expect = 1.404e-30
Identity = 54/76 (71.05%), Postives = 63/76 (82.89%), Query Frame = 2 
Query:  185 GEQAEVTDLPPAYEEFEFPDIDPDVVYAPSMTFHPPPPSIYIDLEEEENDPSXXXXXXXXXXXXXXXIAVLSGRAP 412
            G+Q ++T+ PPAY E EFP  DPDVVYAPS+T +PPPPSIYIDLE EEN+P N N+TLE L+L PEEIAVLSGR P
Sbjct:  209 GDQTDMTNSPPAYTEVEFPAYDPDVVYAPSLTIYPPPPSIYIDLEAEENEPPNFNHTLERLNLAPEEIAVLSGRVP 284

HSP 2 Score: 66.2402 bits (160), Expect = 1.404e-30
Identity = 31/45 (68.89%), Postives = 37/45 (82.22%), Query Frame = 1 
Query:  406 STHSAVEPSTSTQEDPSQVTSTHNHRQPKRRCLPVDIDMED*TTI 540
            + HSA+EP+TSTQE+PSQ+T T  HR PK RCLPVDID ED +TI
Sbjct:  286 TIHSAIEPATSTQEEPSQLTPTSTHRYPKLRCLPVDIDTEDRSTI 330
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BLAST of SMED30016476 vs. Planmine SMEST
Match: SMESG000061044.1 (SMESG000061044.1)

HSP 1 Score: 75.485 bits (184), Expect = 7.098e-30
Identity = 34/42 (80.95%), Postives = 38/42 (90.48%), Query Frame = 1 
Query:  403 TSTHSAVEPSTSTQEDPSQVTSTHNHRQPKRRCLPVDIDMED 528
            ++THSAVEPSTSTQEDPSQ  +T NHRQPKRRCLP+DID ED
Sbjct:  226 SNTHSAVEPSTSTQEDPSQAIATTNHRQPKRRCLPIDIDQED 267

HSP 2 Score: 75.0998 bits (183), Expect = 7.098e-30
Identity = 105/135 (77.78%), Postives = 117/135 (86.67%), Query Frame = 2 
Query:    2 INIIPAXXXXXXXXXXXXXXXXXSGTIETRTGTQXXXXXXXXXXXXXXXXXXXXXXXXXXTGEQAEVTDLPPAYEEFEFPDIDPDVVYAPSMTFHPPPPSIYIDLEEEENDPSXXXXXXXXXXXXXXXIAVLSGR 406
            INIIPAQ+LPLNQV QQ NGPPPSGTIETR+G QRR+PN N RRRERRRAEANLLRANGRTGEQAEV   PPAY EFEFP++DPDVVYAP+MT +PPPP IYIDLE +E +P  L  TLE L+LTP+EIAVLSG+
Sbjct:   89 INIIPAQHLPLNQVSQQSNGPPPSGTIETRSGIQRRRPNLNHRRRERRRAEANLLRANGRTGEQAEVNYPPPAYTEFEFPELDPDVVYAPAMTVYPPPPPIYIDLEADEPEPPRLKLTLERLNLTPDEIAVLSGQ 223
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BLAST of SMED30016476 vs. Planmine SMEST
Match: SMESG000020775.1 (SMESG000020775.1)

HSP 1 Score: 100.138 bits (248), Expect = 1.375e-26
Identity = 59/78 (75.64%), Postives = 68/78 (87.18%), Query Frame = 2 
Query:  182 TGEQAEVTDLPPAYEEFEFPDIDPDVVYAPSMTFHPPPPSIYIDLEEEENDPSXXXXXXXXXXXXXXXIAVLSGRAPT 415
            TG   EV DLPPAYEEFEFPD+DPDVVYAP++TF+PPPPSIYIDLEE+EN+   LN++LE LDL P+EIAVLSGR PT
Sbjct:  148 TGGTVEVNDLPPAYEEFEFPDLDPDVVYAPAVTFYPPPPSIYIDLEEDENEAPILNHSLEQLDLAPDEIAVLSGRVPT 225

HSP 2 Score: 39.2762 bits (90), Expect = 1.375e-26
Identity = 19/30 (63.33%), Postives = 21/30 (70.00%), Query Frame = 1 
Query:  424 EPSTSTQEDPSQVTSTHNHRQPKRRCLPVD 513
            EP TSTQE  +   S+  H QPKRRCLPVD
Sbjct:  232 EPETSTQEGQNPTISSPLHLQPKRRCLPVD 261
[Close]
BLAST of SMED30016476 vs. Planmine SMEST
Match: SMESG000038618.1 (SMESG000038618.1)

HSP 1 Score: 71.633 bits (174), Expect = 1.153e-25
Identity = 85/138 (61.59%), Postives = 105/138 (76.09%), Query Frame = 2 
Query:    2 INIIPAXXXXXXXXXXXXXXXXXSGTIETRTGTQXXXXXXXXXXXXXXXXXXXXXXXXXXTGEQAEVTDLPPAYEEFEFPDIDPDVVYAPSMTFHPPPPSIYIDLEEEENDPSXXXXXXXXXXXXXXXIAVLSGRAPT 415
            INIIPAQ+LP+N      NG P SGT E ++G QRR+PNRNRRRRERRRA+ANLL+ N RTGE  EV D P AY EFEFP++DP++VYAPS   +P PP IYIDLE +E +  N+N  LE L LTP++IA+LSG+ P+
Sbjct:  108 INIIPAQHLPINPGSLPSNGSPLSGTTENQSGVQRRRPNRNRRRRERRRAQANLLQVNERTGEPVEVNDPPFAYTEFEFPEMDPEIVYAPSSIIYPLPPPIYIDLEADEPETPNVNLILERLRLTPDKIALLSGQVPS 245

HSP 2 Score: 65.0846 bits (157), Expect = 1.153e-25
Identity = 29/42 (69.05%), Postives = 34/42 (80.95%), Query Frame = 1 
Query:  403 TSTHSAVEPSTSTQEDPSQVTSTHNHRQPKRRCLPVDIDMED 528
            ++ +SA+EPSTS QEDPS   S  NHRQPKRR LPVDID+ED
Sbjct:  245 SNAYSAIEPSTSMQEDPSPTVSISNHRQPKRRYLPVDIDLED 286
[Close]
BLAST of SMED30016476 vs. Planmine SMEST
Match: SMESG000010369.1 (SMESG000010369.1)

HSP 1 Score: 65.0846 bits (157), Expect = 1.013e-22
Identity = 46/78 (58.97%), Postives = 59/78 (75.64%), Query Frame = 2 
Query:  182 TGEQAEVTDLPPAYEEFEFPDIDPDVVYAPSM-TFHPPPPSIYIDLEEEENDPSXXXXXXXXXXXXXXXIAVLSGRAP 412
            TG QAE+ D PPAYEE EFP++DPDVVYAP++ +FH  P +I+I+   E+  P NLN  LE LDL+P +IA+LS RAP
Sbjct:   48 TGGQAEIADSPPAYEEIEFPELDPDVVYAPTLPSFH-QPTTIHINRNVEDGTPPNLNRALERLDLSPGKIAILSRRAP 124

HSP 2 Score: 61.6178 bits (148), Expect = 1.013e-22
Identity = 30/47 (63.83%), Postives = 35/47 (74.47%), Query Frame = 1 
Query:  388 SRSEWTSTHSAVEPSTSTQEDPSQVTSTHNHRQPKRRCLPVDIDMED 528
            SR    ST SAVEP+T++QE PS+ T   +HR PKRRCLPVDID ED
Sbjct:  120 SRRAPLSTPSAVEPATTSQEGPSRATPAPDHRYPKRRCLPVDIDAED 166
The following BLAST results are available for this feature:
BLAST of SMED30016476 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 SMED30016476 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 SMED30016476 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 SMED30016476 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 SMED30016476 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 SMED30016476 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 SMED30016476 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 SMED30016476 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 SMED30016476 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 SMED30016476 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 SMED30016476 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 SMED30016476 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 SMED30016476 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 SMED30016476 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000042162.11.404e-3071.05SMESG000042162.1[more]
SMESG000061044.17.098e-3080.95SMESG000061044.1[more]
SMESG000020775.11.375e-2675.64SMESG000020775.1[more]
SMESG000038618.11.153e-2561.59SMESG000038618.1[more]
SMESG000010369.11.013e-2258.97SMESG000010369.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016476 ID=SMED30016476|Name=SMED30016476|organism=Schmidtea mediterranea sexual|type=transcript|length=1844bp
GATCAACATTATCCCAGCCCAATATCTCCCCCTCAACCAAGTACCTCAGC
AGCCAAATGGACCTCCCCCGAGTGGGACAATCGAAACTAGAACCGGAACA
CAGAGGCGAAAGCCAAATCGAAACCGCCGTCGTCGCGAAAGACGCCGAGC
CGAAGCAAATCTCCTACGAGCGAATGGGAGGACGGGAGAACAAGCTGAAG
TGACTGACCTGCCCCCCGCCTACGAAGAATTTGAGTTTCCCGACATAGAT
CCGGACGTAGTGTACGCACCGTCGATGACGTTCCACCCACCACCTCCCTC
AATATACATCGATTTGGAGGAGGAAGAGAATGATCCATCCAATCTGAATA
ACACTTTGGAGCTATTAGATCTCACTCCGGAAGAGATAGCCGTTCTGAGT
GGACGAGCACCCACTCCGCGGTAGAACCGTCAACCTCGACTCAGGAAGAT
CCGAGTCAAGTCACCTCAACTCATAACCATCGTCAGCCAAAACGTCGATG
CCTACCGGTCGACATTGATATGGAAGATTGAACCACAATCCTGGATTTAA
ACCTTAATCGACATGTTTTTGAGTGTTATTTATCTCCTAATTCTTCTGTA
CTATTCTTATGATTATGTTTCTCTTCAATATCGTACTATTGTATTATTTT
ATTTGCAGTATTAGAAATTGTATTTACGAATTATAGTATTCAACTTTTCG
CATTTGTTTTCTTTTCTTCTTAGCGCAACTAATAATCAATATCATAATAA
ACCGATTGTTGTTTACGCATAGTACCAACATGGTTTCGACCATGGGTGCG
TATCAGTAAGTGATGATTGTGGGGTTGTGCGCGGATAAATCAACCCTAGA
TTATAAATGGGATAGCTGTTAACCAGGAGTGCAAGTTTTTCACGGATTAA
GTTTCCCCATACACCAACAATTAGTTTTTTTAATTATTTATTATATTTTA
CACTTAAATCAAAGGAATATTACTCGTTCTGTAAATTAATATGGAAAATG
CTTGCTAAAACTAATAAATTAAGATTTTTTAAAGGTTATAATGCAAATGT
TAACAATAAATAAAAGTCGTTGGACAAATTATTGAATGGAATAACTCAAT
ATTTTACAATATATAGAGACATTGAATGGATGCTAATAAAATTGTCAATA
AAATCTATTGGTTTTAGATTGTAATTTATTTCTTGGTGGATCAAATGGGA
TATAAATATGTAGAATCTCTTAGTTACCGTATGTATATATTTTATTACAA
TTTGACCAACATCTTTTATAGTCAAACTATTATAAAGCTCGCTTTACTGT
CTTAAATGTATACAACTGATGATTAATACTTTTTTATCTTAGGAGAGATG
TTCACTGTCCCACCATTACAAACGTTTACAATGTTTACATCCGATTGTCA
TACTAGTTACAGTATTTCTAATTGCATAATATAGAACAAAGAGTATTGCA
AGTTTATATAATATTGTTGATATTGATCACATGCATACTTACTTCATTTC
ATTGCACAAACATTCCCTCGTCATTCCTCAAACAAAGTCACAGTGACCTG
ATTATATAATTAGTTTATGATAATTATTATTATATCACCTTACATAATCC
TCCAGTTAAAAATTAAATCCATTAGACATTTCGAATAATTACGTTTCTTT
GTTGATTCTTTTGTCGCTAAGGTCAATATGACTTTAAAAATGTCATCAAG
AGATCACAGAACCAGAAATATTGGTAACAAATGTTTTTGAATTATCCATT
CTCATATTCACAAACAATATTACCCAGTTTCAGGTGATAGCTAACGAATT
ATTTTTTTATATTTCCTTTAAAAATGAAAACTGAAGATCGGAAG
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protein sequence of SMED30016476-orf-1

>SMED30016476-orf-1 ID=SMED30016476-orf-1|Name=SMED30016476-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=141bp
INIIPAQYLPLNQVPQQPNGPPPSGTIETRTGTQRRKPNRNRRRRERRRA
EANLLRANGRTGEQAEVTDLPPAYEEFEFPDIDPDVVYAPSMTFHPPPPS
IYIDLEEEENDPSNLNNTLELLDLTPEEIAVLSGRAPTPR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002063non-ciliated epidermis
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 7..73