SMED30005542

Overview
NameSMED30005542
Smed IDSMED30005542
Length (bp)1161
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 SMED30005542 (SMED30005542) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005542 (SMED30005542) 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



SMED30005542

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 cellSMED30005542 SmedASXL_032479SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30005542 SmedASXL_047437SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
pharynxSMED30005542 dd_Smed_v4_23179_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
Alignments
SMED30005542 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007225:7670..9481 -5681
v31.003057:66890..68942 -4886
v31.000110:46990..48054 -3717
Homology
[Close]
BLAST of SMED30005542 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 166.392 bits (420), Expect = 3.586e-51
Identity = 84/136 (61.76%), Postives = 100/136 (73.53%), Query Frame = -3 
Query:  176 SQLARRPNDRGDEIELPSIAIKREPSRNQAQEARQRAEYTAMKMEEMERKYHKKAILGRKRLARVNQDIASGLIPSTDGFTPDYVVSFELDDPRLLQMTAPIQLTYRDQIQSKYPNKRSHRMPGGQERLRRRAQGE 583
            S   RRP DR DE+ELPSIAIKREP RN A+E  QRAEYT+MKMEEMERKYH+KA+L R+RLA++N+DIASG+IPSTD F P Y VSFELDDPRLLQMTAP +L   +++            PG + RL  R  G+
Sbjct:  653 SSWPRRPKDREDEVELPSIAIKREPGRNPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRLLQMTAPTKLVIPEELI----------QPGLRNRLGSRRTGD 778

HSP 2 Score: 54.6842 bits (130), Expect = 3.586e-51
Identity = 23/32 (71.88%), Postives = 28/32 (87.50%), Query Frame = -1 
Query:  571 TAEIRISSAAQYRQALWDQGYTLATYGEASWP 666
            T +I  +SAA+YRQALWD GYTL+TYGE+SWP
Sbjct:  625 TLQISNASAARYRQALWDNGYTLSTYGESSWP 656
[Close]
BLAST of SMED30005542 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 166.007 bits (419), Expect = 5.468e-51
Identity = 84/136 (61.76%), Postives = 100/136 (73.53%), Query Frame = -3 
Query:  176 SQLARRPNDRGDEIELPSIAIKREPSRNQAQEARQRAEYTAMKMEEMERKYHKKAILGRKRLARVNQDIASGLIPSTDGFTPDYVVSFELDDPRLLQMTAPIQLTYRDQIQSKYPNKRSHRMPGGQERLRRRAQGE 583
            S   RRP DR DE+ELPSIAIKREP RN A+E  QRAEYT+MKMEEMERKYH+KA+L R+RLA++N+DIASG+IPSTD F P Y VSFELDDPRLLQMTAP +L   +++            PG + RL  R  G+
Sbjct:  709 SSWPRRPKDREDEVELPSIAIKREPGRNPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRLLQMTAPTKLVIPEELIQ----------PGLRNRLGSRRTGD 834

HSP 2 Score: 54.6842 bits (130), Expect = 5.468e-51
Identity = 23/32 (71.88%), Postives = 28/32 (87.50%), Query Frame = -1 
Query:  571 TAEIRISSAAQYRQALWDQGYTLATYGEASWP 666
            T +I  +SAA+YRQALWD GYTL+TYGE+SWP
Sbjct:  681 TLQISNASAARYRQALWDNGYTLSTYGESSWP 712
[Close]
BLAST of SMED30005542 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 166.007 bits (419), Expect = 5.513e-51
Identity = 84/136 (61.76%), Postives = 100/136 (73.53%), Query Frame = -3 
Query:  176 SQLARRPNDRGDEIELPSIAIKREPSRNQAQEARQRAEYTAMKMEEMERKYHKKAILGRKRLARVNQDIASGLIPSTDGFTPDYVVSFELDDPRLLQMTAPIQLTYRDQIQSKYPNKRSHRMPGGQERLRRRAQGE 583
            S   RRP DR DE+ELPSIAIKREP RN A+E  QRAEYT+MKMEEMERKYH+KA+L R+RLA++N+DIASG+IPSTD F P Y VSFELDDPRLLQMTAP +L   +++            PG + RL  R  G+
Sbjct:  705 SSWPRRPKDREDEVELPSIAIKREPGRNPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRLLQMTAPTKLVIPEELIQ----------PGLRNRLGSRRTGD 830

HSP 2 Score: 54.6842 bits (130), Expect = 5.513e-51
Identity = 23/32 (71.88%), Postives = 28/32 (87.50%), Query Frame = -1 
Query:  571 TAEIRISSAAQYRQALWDQGYTLATYGEASWP 666
            T +I  +SAA+YRQALWD GYTL+TYGE+SWP
Sbjct:  677 TLQISNASAARYRQALWDNGYTLSTYGESSWP 708
[Close]
BLAST of SMED30005542 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 165.236 bits (417), Expect = 7.456e-50
Identity = 85/150 (56.67%), Postives = 103/150 (68.67%), Query Frame = -3 
Query:  137 SQLARRPNDRGDEIELPSIAIKREPSRNQAQEARQRAEYTAMKMEEMERKYHKKAILGRKRLARVNQDIASGLIPSTDGFTPDYVVSFELDDPRLLQMTAPIQLTYRDQ-IQSKYPNKRSHRMPGGQERLRRRAQGETK*MMKSSSNVNA 583
            S   RR   + +EIELPSIAIKREP  N A+EARQRAEY AMKMEE+ERKYH+KA+L R+RLA+VN+DIASG IPSTDGF P+Y VSFELDDPRL+QMTAP ++   ++ +QS   N+   R  G      R  Q   K   + S   N 
Sbjct: 1171 SSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAEYVAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTGDHTYASRHPQWNPKRNNRRSERFNG 1320

HSP 2 Score: 51.2174 bits (121), Expect = 7.456e-50
Identity = 20/32 (62.50%), Postives = 26/32 (81.25%), Query Frame = -1 
Query:  571 TAEIRISSAAQYRQALWDQGYTLATYGEASWP 666
            T +I  +SAA+YRQ LWD GY L+TYG++SWP
Sbjct: 1143 TLQIPSASAARYRQVLWDNGYLLSTYGDSSWP 1174
[Close]
BLAST of SMED30005542 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1)

HSP 1 Score: 160.229 bits (404), Expect = 7.427e-49
Identity = 82/150 (54.67%), Postives = 101/150 (67.33%), Query Frame = -3 
Query:  137 SQLARRPNDRGDEIELPSIAIKREPSRNQAQEARQRAEYTAMKMEEMERKYHKKAILGRKRLARVNQDIASGLIPSTDGFTPDYVVSFELDDPRLLQMTAPIQLTYRDQ-IQSKYPNKRSHRMPGGQERLRRRAQGETK*MMKSSSNVNA 583
            S   RR   + +EIELPSIAIKREP  N A+EARQRA+Y AMKMEE+ERKYH+KA+  R+RLA+VN+DIASG IPSTDGF P+Y VSFELDDPRL QMTAP ++   ++ +QS   N+      G      R  Q  +K   + S   N 
Sbjct: 1681 SSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAKYAAMKMEELERKYHRKAVSARQRLAQVNRDIASGSIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVQSTLRNQLGSHQTGDHTYASRHPQWNSKLNNRRSERFNG 1830

HSP 2 Score: 53.1434 bits (126), Expect = 7.427e-49
Identity = 21/32 (65.62%), Postives = 26/32 (81.25%), Query Frame = -1 
Query:  571 TAEIRISSAAQYRQALWDQGYTLATYGEASWP 666
            T EI  +SAA+YRQ LWD GY L+TYG++SWP
Sbjct: 1653 TLEIPSASAARYRQVLWDNGYLLSTYGDSSWP 1684
The following BLAST results are available for this feature:
BLAST of SMED30005542 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 SMED30005542 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 SMED30005542 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 SMED30005542 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 SMED30005542 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 SMED30005542 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 SMED30005542 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 SMED30005542 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 SMED30005542 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 SMED30005542 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 SMED30005542 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 SMED30005542 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 SMED30005542 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 SMED30005542 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046313.13.586e-5161.76SMESG000046313.1[more]
SMESG000046313.15.468e-5161.76SMESG000046313.1[more]
SMESG000046313.15.513e-5161.76SMESG000046313.1[more]
SMESG000044971.17.456e-5056.67SMESG000044971.1[more]
SMESG000057533.17.427e-4954.67SMESG000057533.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005542 ID=SMED30005542|Name=SMED30005542|organism=Schmidtea mediterranea sexual|type=transcript|length=1161bp
CCTATGTCGGGTTCAGCGGACTGCTGTTAGAAGGCCTCTGTCCGTCTTAT
CCTTCATGTCCCTTAAATATTTCCTCCTTTTACTCGTGTGCGCTAATTAT
TGAAAAGAAAACAAAATATCGGAAACACAATTTTATTGCATTAACATTTG
AACTTGATTTCATCATTTATTTAGTTTCGCCTTGTGCACGTCTTCGTAAG
CGTTCCTGCCCTCCTGGCATGCGATGAGATCGTTTGTTGGGATACTTTGA
TTGGATCTGGTCACGATAGGTCAGCTGTATTGGGGCGGTCATTTGTAGTA
ATCTCGGGTCGTCTAGTTCGAATGAGACCACATAATCTGGAGTAAATCCG
TCGGTGCTTGGAATTAGCCCGCTAGCGATGTCCTGATTCACACGTGCCAA
TCGCTTCCTGCCCAGAATCGCCTTTTTGTGGTACTTCCTTTCCATTTCTT
CCATCTTCATCGCCGTGTATTCTGCTCGTTGACGAGCTTCTTGTGCCTGG
TTTCTACTCGGTTCCCGCTTGATGGCGATGCTGGGCAATTCGATTTCATC
TCCACGATCGTTTGGTCTTCGGGCCAACTGGCTTCTCCGTAGGTGGCCAA
CGTGTATCCTTGGTCCCATAGTGCTTGCCTGTATTGTGCGGCGGAGCTAA
TACGGATCTCTGCGGTCTGAATAGTCAATATAATTAATATTAAATTGTAA
ATTTGTATCTTTAGAATTTATTTATTGGGTGTGGTCCTAAAATCCGTTCT
ATCATCGCCGAACTTGTGGGTGAACATGATTTGTAATTTTACGACAAAAT
GGGAATTTCAAAAAATTAATACCTCGTTGAAGATCAACCGAGTTCTTCAT
AACTGCGTCCTTGGGTGCTAGCCGATTTTGGATACGGTCTCCCAGTCGTT
TCTTAGCGTCGTTTCTACTGTCGGTAGCTGGTAGACGAGAATTAAACATA
ATTGGTAATTATGAATTAGTAGACTTTTCGTTTTATATTTATAGACTCGT
TGTTACGTGAATAATCGAAAACCCCCCCGTTTCTTTATGATTTATTATCA
TTTATTGCAATTCCATTTTTATTTTATTTTTATTACAATGTGAAACTTAT
GTTTCGTATTATCAACAGCTTGAAATTTGTGTTTACGTTGGTTTATTGAT
TCTTTCTCGGT
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protein sequence of SMED30005542-orf-1

>SMED30005542-orf-1 ID=SMED30005542-orf-1|Name=SMED30005542-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=151bp
MGPRIHVGHLRRSQLARRPNDRGDEIELPSIAIKREPSRNQAQEARQRAE
YTAMKMEEMERKYHKKAILGRKRLARVNQDIASGLIPSTDGFTPDYVVSF
ELDDPRLLQMTAPIQLTYRDQIQSKYPNKRSHRMPGGQERLRRRAQGETK
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0002109X1 cell