SMED30035896

Overview
NameSMED30035896
Smed IDSMED30035896
Length (bp)454
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30035896 (SMED30035896) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035896 (SMED30035896) 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.
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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



SMED30035896

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30035896SMESG000060343.1 dd_Smed_v4_24265_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035896SMESG000060343.1 dd_Smed_v4_24265_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30035896SMESG000060343.1 dd_Smed_v4_24265_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30035896SMESG000060343.1 Contig10038newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035896SMESG000060343.1 Contig10038uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035896SMESG000060343.1 Contig26815newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035896SMESG000060343.1 Contig26815uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035896SMESG000060343.1 Contig8452newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035896SMESG000060343.1 Contig8452uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035896SMESG000060343.1 Contig27296newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035896SMESG000060343.1 Contig27296uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30035896 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.018056:15444..15942 +2191
v31.023887:4518..5016 -2164
v31.018056:8268..8766 +1921
v31.010154:1215..1713 -1885
v31.007567:24395..24893 +1867
Homology
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BLAST of SMED30035896 vs. TrEMBL
Match: I1ZI61 (Hadrian OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 1.161e-10
Identity = 41/139 (29.50%), Postives = 77/139 (55.40%), Query Frame = 3 
Query:   42 DVTEMSKKLIGNNTTF-YMIEEGVNGKIEGLHNVTATFFVSKRRYN--KLFFEFPELYVIPNLPDCNLKFSMKNLTITINLKGFKVRRIKNNLRSFQIIQNDCLKKSLEIQINKLLSTEFSEHVFASLVSTLLQSQIDI 449
            ++TE+ KK++ N     ++    V+  ++GLHN+  T  VS R  N   L   FP+L    +   C +  ++K+L I + + G  VR ++ ++RS +I  NDC  K++E + N+LL    S+   A+ +  L+ ++++I
Sbjct:   25 ELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNI 163
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BLAST of SMED30035896 vs. Planmine SMEST
Match: SMESG000060343.1 (SMESG000060343.1)

HSP 1 Score: 286.189 bits (731), Expect = 1.393e-100
Identity = 139/145 (95.86%), Postives = 143/145 (98.62%), Query Frame = 3 
Query:   18 FNEGHEVVDVTEMSKKLIGNNTTFYMIEEGVNGKIEGLHNVTATFFVSKRRYNKLFFEFPELYVIPNLPDCNLKFSMKNLTITINLKGFKVRRIKNNLRSFQIIQNDCLKKSLEIQINKLLSTEFSEHVFASLVSTLLQSQIDIE 452
            FNEGH+ +D+TEMSKKLIGNNTTFYMIEEGVNGKIEGLHNVTATFFVSKR+YNKLFFEFPELYVIPNLPDCNLK SMKNLTITINLKGFKVRRIKNNLRSFQIIQNDCLKKSLEIQINKLLSTEFSEHVFASLVSTLLQSQIDIE
Sbjct:   17 FNEGHKAIDLTEMSKKLIGNNTTFYMIEEGVNGKIEGLHNVTATFFVSKRKYNKLFFEFPELYVIPNLPDCNLKLSMKNLTITINLKGFKVRRIKNNLRSFQIIQNDCLKKSLEIQINKLLSTEFSEHVFASLVSTLLQSQIDIE 161
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BLAST of SMED30035896 vs. Planmine SMEST
Match: SMESG000060332.1 (SMESG000060332.1)

HSP 1 Score: 247.669 bits (631), Expect = 2.613e-85
Identity = 121/145 (83.45%), Postives = 132/145 (91.03%), Query Frame = 3 
Query:   18 FNEGHEVVDVTEMSKKLIGNNTTFYMIEEGVNGKIEGLHNVTATFFVSKRRYNKLFFEFPELYVIPNLPDCNLKFSMKNLTITINLKGFKVRRIKNNLRSFQIIQNDCLKKSLEIQINKLLSTEFSEHVFASLVSTLLQSQIDIE 452
            FNEGH+VVD+TEMSKKLIGN+  FY+IEEGVNGKIEGLHNVTATFFVS+RRYNKL FEF ELYVIPNLPDCNLK SMKNLTI + LK F    IKNNLRSFQIIQNDCLKKSLEIQINKLLSTE ++++FASLVSTLLQSQ+DIE
Sbjct:   17 FNEGHKVVDLTEMSKKLIGNSIKFYIIEEGVNGKIEGLHNVTATFFVSRRRYNKLVFEFSELYVIPNLPDCNLKLSMKNLTIAVYLKSFNELHIKNNLRSFQIIQNDCLKKSLEIQINKLLSTELAKNLFASLVSTLLQSQVDIE 161
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BLAST of SMED30035896 vs. Planmine SMEST
Match: SMESG000060389.1 (SMESG000060389.1)

HSP 1 Score: 93.2041 bits (230), Expect = 1.368e-24
Identity = 52/129 (40.31%), Postives = 79/129 (61.24%), Query Frame = 3 
Query:    6 VLVVF-----NEGHEVVDVTEMSKKLIGNNTTFYMIEEGVNGKIEGLHNVTATFFVSKRRYNKLFFEFPELYVIPNLPDCNLKFSMKNLTITINLKGFKVRRIKNNLRSFQIIQNDCLKKSLEIQINKL 377
            VL+V+     NEG  VVDVTEM KKL+     F +      G +EGLHN+ AT + +    N+L F FP+L +  +   C +K S++N  ITI L+  K++R++++L S +II+NDC  K+LE + N +
Sbjct:    8 VLIVWAVVDGNEGARVVDVTEMGKKLVPYKILFPIFGTRFYGVVEGLHNMNATLYENPSGLNQLVFIFPKLNISKDFQKCIVKISVRNFAITIELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSI 136
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BLAST of SMED30035896 vs. Planmine SMEST
Match: SMESG000060365.1 (SMESG000060365.1)

HSP 1 Score: 78.5666 bits (192), Expect = 5.043e-19
Identity = 48/129 (37.21%), Postives = 73/129 (56.59%), Query Frame = 3 
Query:    6 VLVVF-----NEGHEVVDVTEMSKKLIGNNTTFYMIEEGVNGKIEGLHNVTATFFVSKRRYNKLFFEFPELYVIPNLPDCNLKFSMKNLTITINLKGFKVRRIKNNLRSFQIIQNDCLKKSLEIQINKL 377
            VL+V+     NEG  VVDVTEM KKL+ +   F + ++   G +E LHN+ AT + +    N             +   C +K S++N  ITI L+  K++R++++L S +IIQNDC  K+LE + N L
Sbjct:    8 VLIVWAVVDGNEGARVVDVTEMGKKLVPHQIVFPIFDKRFYGIVEDLHNMNATLYENPSGLN-------------HFQKCIVKISVRNFVITIELEHSKIQRVRHSLDSCRIIQNDCFIKTLEKKYNSL 123
[Close]
BLAST of SMED30035896 vs. Planmine SMEST
Match: SMESG000043826.1 (SMESG000043826.1)

HSP 1 Score: 66.2402 bits (160), Expect = 3.228e-14
Identity = 41/139 (29.50%), Postives = 77/139 (55.40%), Query Frame = 3 
Query:   42 DVTEMSKKLIGNNTTF-YMIEEGVNGKIEGLHNVTATFFVSKRRYN--KLFFEFPELYVIPNLPDCNLKFSMKNLTITINLKGFKVRRIKNNLRSFQIIQNDCLKKSLEIQINKLLSTEFSEHVFASLVSTLLQSQIDI 449
            ++TE+ KK++ N     ++    V+  ++GLHN+  T  VS R  N   L   FP+L    +   C +  ++K+L I + + G  VR ++ ++RS +I  NDC  K++E + N+LL    S+   A+ +  L+ ++++I
Sbjct:   25 ELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNI 163
The following BLAST results are available for this feature:
BLAST of SMED30035896 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 SMED30035896 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 SMED30035896 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 SMED30035896 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 SMED30035896 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 SMED30035896 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 SMED30035896 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 SMED30035896 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZI611.161e-1029.50Hadrian OS=Schmidtea mediterranea OX=79327 PE=2 SV... [more]
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BLAST of SMED30035896 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 SMED30035896 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 SMED30035896 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 SMED30035896 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 SMED30035896 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 SMED30035896 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000060343.11.393e-10095.86SMESG000060343.1[more]
SMESG000060332.12.613e-8583.45SMESG000060332.1[more]
SMESG000060389.11.368e-2440.31SMESG000060389.1[more]
SMESG000060365.15.043e-1937.21SMESG000060365.1[more]
SMESG000043826.13.228e-1429.50SMESG000043826.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035896 ID=SMED30035896|Name=SMED30035896|organism=Schmidtea mediterranea sexual|type=transcript|length=454bp
TTTCCGTTCTCGTAGTTTTCAATGAAGGTCACGAAGTTGTTGATGTGACG
GAAATGAGTAAAAAACTGATTGGAAATAATACCACATTTTACATGATTGA
AGAAGGTGTGAATGGTAAAATTGAAGGCCTTCATAATGTGACTGCCACCT
TCTTTGTGAGTAAGAGAAGGTATAATAAATTATTCTTCGAATTCCCAGAA
TTATATGTCATACCAAACCTTCCAGATTGCAATTTGAAATTTTCAATGAA
AAACCTAACTATTACTATTAATCTGAAGGGTTTCAAAGTACGTCGCATTA
AAAATAATCTGAGAAGCTTTCAGATTATACAAAATGACTGCTTAAAAAAG
TCTTTGGAGATCCAAATCAACAAACTATTATCAACTGAATTCTCTGAACA
TGTTTTTGCATCACTTGTTTCTACGCTTTTGCAATCTCAAATTGACATTG
AAAC
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protein sequence of SMED30035896-orf-1

>SMED30035896-orf-1 ID=SMED30035896-orf-1|Name=SMED30035896-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=150bp
SVLVVFNEGHEVVDVTEMSKKLIGNNTTFYMIEEGVNGKIEGLHNVTATF
FVSKRRYNKLFFEFPELYVIPNLPDCNLKFSMKNLTITINLKGFKVRRIK
NNLRSFQIIQNDCLKKSLEIQINKLLSTEFSEHVFASLVSTLLQSQIDIE
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ