SMED30026542

Overview
NameSMED30026542
Smed IDSMED30026542
Length (bp)508
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 SMED30026542 (SMED30026542) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026542 (SMED30026542) 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.
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




SMED30026542

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testisSMED30026542SMESG000060332.1 GDAG01038768.1SmedSxl_ww_GDAG01.fsa_ntPMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
vitelline glandSMED30026542SMESG000060332.1 GDAG01038768.1SmedSxl_ww_GDAG01.fsa_ntPMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
reproductive organSMED30026542SMESG000060332.1 Contig5452newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30026542SMESG000060332.1 Contig5452uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30026542SMESG000060332.1 Contig27211newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30026542SMESG000060332.1 Contig27211uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30026542SMESG000035214.1 Contig5452newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30026542SMESG000035214.1 Contig5452uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30026542 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.018056:8258..8807 +2455
v31.010154:1174..1723 -2392
v31.007567:24385..24934 +2347
v31.023887:4477..5026 -2176
Homology
BLAST of SMED30026542 vs. TrEMBL
Match: I1ZI61 (Hadrian OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 8.795e-8
Identity = 47/164 (28.66%), Postives = 84/164 (51.22%), Query Frame = 1
Query:    1 LSIISVLVVFNEGHKVV-DLTEMSKKLIGNSIKF-YIIEEGVNGKIEGLHNVTATFFVSRR---------RYNKLVFEFSELYVIPNLPDCNLKLSMKNLTIAVYLKSFNELHIKNNLRSFQIIQNDCLKKSLEIQINKLLSTELAKNLFASLVSTLLQSQVDI 459
            L +I   V+   G K   +LTE+ KK++ N I   ++    V+  ++GLHN+  T  VS R         R+ KLVF + ++        C +  ++K+L I V +       ++ ++RS +I  NDC  K++E + N+LL    +K   A+ +  L+ ++V+I
Sbjct:    7 LLLIVAFVLLAHGEKTSKELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVV-------CKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNI 163          
BLAST of SMED30026542 vs. Planmine SMEST
Match: SMESG000060332.1 (SMESG000060332.1)

HSP 1 Score: 306.605 bits (784), Expect = 3.061e-108
Identity = 155/156 (99.36%), Postives = 155/156 (99.36%), Query Frame = 1
Query:    1 LSIISVLVVFNEGHKVVDLTEMSKKLIGNSIKFYIIEEGVNGKIEGLHNVTATFFVSRRRYNKLVFEFSELYVIPNLPDCNLKLSMKNLTIAVYLKSFNELHIKNNLRSFQIIQNDCLKKSLEIQINKLLSTELAKNLFASLVSTLLQSQVDIETI 468
            L IISVLVVFNEGHKVVDLTEMSKKLIGNSIKFYIIEEGVNGKIEGLHNVTATFFVSRRRYNKLVFEFSELYVIPNLPDCNLKLSMKNLTIAVYLKSFNELHIKNNLRSFQIIQNDCLKKSLEIQINKLLSTELAKNLFASLVSTLLQSQVDIETI
Sbjct:    8 LLIISVLVVFNEGHKVVDLTEMSKKLIGNSIKFYIIEEGVNGKIEGLHNVTATFFVSRRRYNKLVFEFSELYVIPNLPDCNLKLSMKNLTIAVYLKSFNELHIKNNLRSFQIIQNDCLKKSLEIQINKLLSTELAKNLFASLVSTLLQSQVDIETI 163          
BLAST of SMED30026542 vs. Planmine SMEST
Match: SMESG000060343.1 (SMESG000060343.1)

HSP 1 Score: 252.292 bits (643), Expect = 9.066e-87
Identity = 123/147 (83.67%), Postives = 134/147 (91.16%), Query Frame = 1
Query:   28 FNEGHKVVDLTEMSKKLIGNSIKFYIIEEGVNGKIEGLHNVTATFFVSRRRYNKLVFEFSELYVIPNLPDCNLKLSMKNLTIAVYLKSFNELHIKNNLRSFQIIQNDCLKKSLEIQINKLLSTELAKNLFASLVSTLLQSQVDIETI 468
            FNEGHK +DLTEMSKKLIGN+  FY+IEEGVNGKIEGLHNVTATFFVS+R+YNKL FEF ELYVIPNLPDCNLKLSMKNLTI + LK F    IKNNLRSFQIIQNDCLKKSLEIQINKLLSTE ++++FASLVSTLLQSQ+DIETI
Sbjct:   17 FNEGHKAIDLTEMSKKLIGNNTTFYMIEEGVNGKIEGLHNVTATFFVSKRKYNKLFFEFPELYVIPNLPDCNLKLSMKNLTITINLKGFKVRRIKNNLRSFQIIQNDCLKKSLEIQINKLLSTEFSEHVFASLVSTLLQSQIDIETI 163          
BLAST of SMED30026542 vs. Planmine SMEST
Match: SMESG000060389.1 (SMESG000060389.1)

HSP 1 Score: 91.2781 bits (225), Expect = 1.452e-23
Identity = 56/159 (35.22%), Postives = 90/159 (56.60%), Query Frame = 1
Query:    7 IISVLVVF-----NEGHKVVDLTEMSKKLIGNSIKFYIIEEGVNGKIEGLHNVTATFFVSRRRYNKLVFEFSELYVIPNLPDCNLKLSMKNLTIAVYLKSFNELHIKNNLRSFQIIQNDCLKKSLEIQINKLLSTELAKNLFASLVSTLLQSQVDIETI 468
            II VL+V+     NEG +VVD+TEM KKL+   I F I      G +EGLHN+ AT + +    N+LVF F +L +  +   C +K+S++N  I + L+      ++++L S +II+NDC  K+LE + N +      K   A  +  ++   V+++TI
Sbjct:    5 IILVLIVWAVVDGNEGARVVDVTEMGKKLVPYKILFPIFGTRFYGVVEGLHNMNATLYENPSGLNQLVFIFPKLNISKDFQKCIVKISVRNFAITIELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSIFLENPTKTFIAESLLNVISMNVNVDTI 163          
BLAST of SMED30026542 vs. Planmine SMEST
Match: SMESG000060365.1 (SMESG000060365.1)

HSP 1 Score: 80.1073 bits (196), Expect = 2.198e-19
Identity = 54/159 (33.96%), Postives = 85/159 (53.46%), Query Frame = 1
Query:    7 IISVLVVF-----NEGHKVVDLTEMSKKLIGNSIKFYIIEEGVNGKIEGLHNVTATFFVSRRRYNKLVFEFSELYVIPNLPDCNLKLSMKNLTIAVYLKSFNELHIKNNLRSFQIIQNDCLKKSLEIQINKLLSTELAKNLFASLVSTLLQSQVDIETI 468
            II VL+V+     NEG +VVD+TEM KKL+ + I F I ++   G +E LHN+ AT + +    N             +   C +K+S++N  I + L+      ++++L S +IIQNDC  K+LE + N L     AK   A  +  ++   V+I+TI
Sbjct:    5 IILVLIVWAVVDGNEGARVVDVTEMGKKLVPHQIVFPIFDKRFYGIVEDLHNMNATLYENPSGLN-------------HFQKCIVKISVRNFVITIELEHSKIQRVRHSLDSCRIIQNDCFIKTLEKKYNSLFLENPAKTFIAESLLNVISKNVNIDTI 150          
BLAST of SMED30026542 vs. Planmine SMEST
Match: SMESG000043826.1 (SMESG000043826.1)

HSP 1 Score: 59.3066 bits (142), Expect = 2.446e-11
Identity = 47/164 (28.66%), Postives = 84/164 (51.22%), Query Frame = 1
Query:    1 LSIISVLVVFNEGHKVV-DLTEMSKKLIGNSIKF-YIIEEGVNGKIEGLHNVTATFFVSRR---------RYNKLVFEFSELYVIPNLPDCNLKLSMKNLTIAVYLKSFNELHIKNNLRSFQIIQNDCLKKSLEIQINKLLSTELAKNLFASLVSTLLQSQVDI 459
            L +I   V+   G K   +LTE+ KK++ N I   ++    V+  ++GLHN+  T  VS R         R+ KLVF + ++        C +  ++K+L I V +       ++ ++RS +I  NDC  K++E + N+LL    +K   A+ +  L+ ++V+I
Sbjct:    7 LLLIVAFVLLAHGEKTSKELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVV-------CKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNI 163          
The following BLAST results are available for this feature:
BLAST of SMED30026542 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 SMED30026542 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 SMED30026542 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 SMED30026542 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 SMED30026542 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 SMED30026542 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 SMED30026542 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 SMED30026542 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZI618.795e-828.66Hadrian OS=Schmidtea mediterranea OX=79327 PE=2 SV... [more]
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BLAST of SMED30026542 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 SMED30026542 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 SMED30026542 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 SMED30026542 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 SMED30026542 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 SMED30026542 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000060332.13.061e-10899.36SMESG000060332.1[more]
SMESG000060343.19.066e-8783.67SMESG000060343.1[more]
SMESG000060389.11.452e-2335.22SMESG000060389.1[more]
SMESG000060365.12.198e-1933.96SMESG000060365.1[more]
SMESG000043826.12.446e-1128.66SMESG000043826.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026542 ID=SMED30026542|Name=SMED30026542|organism=Schmidtea mediterranea sexual|type=transcript|length=508bp
TTATCAATAATTTCCGTTCTTGTAGTTTTCAATGAAGGTCACAAAGTTGT
TGATTTGACGGAAATGAGTAAAAAACTGATTGGAAATAGTATTAAATTTT
ACATAATCGAAGAAGGTGTGAATGGTAAAATTGAAGGCCTTCATAATGTG
ACTGCCACCTTCTTTGTGAGTCGGAGAAGGTATAATAAATTAGTCTTCGA
ATTCTCGGAATTATATGTCATACCAAACCTTCCAGATTGCAATTTGAAAT
TGTCAATGAAAAACCTAACTATTGCAGTTTATCTTAAGAGTTTCAATGAA
CTTCACATTAAAAATAATCTGAGAAGCTTTCAGATTATACAAAATGATTG
TTTAAAAAAGTCTTTGGAGATCCAAATCAACAAACTATTATCAACTGAAT
TAGCCAAAAATCTTTTTGCATCACTTGTTTCTACGCTTTTGCAATCTCAA
GTTGACATAGAAACGATAAAAAACAAGCTAAATAAATATATAAATTGATA
AAAAAAAA
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protein sequence of SMED30026542-orf-1

>SMED30026542-orf-1 ID=SMED30026542-orf-1|Name=SMED30026542-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=166bp
LSIISVLVVFNEGHKVVDLTEMSKKLIGNSIKFYIIEEGVNGKIEGLHNV
TATFFVSRRRYNKLVFEFSELYVIPNLPDCNLKLSMKNLTIAVYLKSFNE
LHIKNNLRSFQIIQNDCLKKSLEIQINKLLSTELAKNLFASLVSTLLQSQ
VDIETIKNKLNKYIN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0000231vitelline gland
PLANA:0002089reproductive organ