SMED30021333

Overview
NameSMED30021333
Smed IDSMED30021333
Length (bp)449
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 SMED30021333 (SMED30021333) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021333 (SMED30021333) 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



SMED30021333

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
reproductive organSMED30021333h1SMcG0002010 Contig3718GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30021333h1SMcG0017563 Contig30374uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30021333h1SMcG0017563 Contig30374newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30021333h1SMcG0017563 Contig3718GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021333 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000786:116638..117086 -2218
Homology
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BLAST of SMED30021333 vs. Planmine SMEST
Match: SMESG000057720.1 (SMESG000057720.1)

HSP 1 Score: 241.506 bits (615), Expect = 1.119e-83
Identity = 118/119 (99.16%), Postives = 119/119 (100.00%), Query Frame = 3 
Query:   84 MNYLIAFFSVALSIFCFTVAQPVSTKCSEEFIAGDIPRIPLKNFLYGLNKFKKVLNASEYDSVVCDFNAIKAMKVFYSLKISASDFRISEFYYIEGHLNSMMDKYFSGQNPKRFFFEKE 440
            MNYLIAFFSVALSIFCFTVAQPVSTKCSEEF+AGDIPRIPLKNFLYGLNKFKKVLNASEYDSVVCDFNAIKAMKVFYSLKISASDFRISEFYYIEGHLNSMMDKYFSGQNPKRFFFEKE
Sbjct:    1 MNYLIAFFSVALSIFCFTVAQPVSTKCSEEFMAGDIPRIPLKNFLYGLNKFKKVLNASEYDSVVCDFNAIKAMKVFYSLKISASDFRISEFYYIEGHLNSMMDKYFSGQNPKRFFFEKE 119
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BLAST of SMED30021333 vs. Planmine SMEST
Match: SMESG000057736.1 (SMESG000057736.1)

HSP 1 Score: 60.4622 bits (145), Expect = 2.023e-12
Identity = 31/118 (26.27%), Postives = 55/118 (46.61%), Query Frame = 3 
Query:   84 MNYLIAFFSVALSIFCFTVAQPVSTKCSEEFIAGDIPRIPLKNFLYGLNKFKKVLNASEYDSVVCDFNAIKAMKVFYSLKISASDFRISEFYYIEGHLNSMMDKYFSGQNPKRFFFEK 437
            MN    F S+ +S+  F+  +   + C+E F  GD+P  P+      L+KFK     SEYD +VC  N +K  K      ++ + F   +    +    S++ K + G++ +  +  K
Sbjct:    1 MNRQRTFLSIVISVLLFSKTRSAESGCNENFEDGDVPLYPIDRVRLALSKFKNAFPQSEYDRIVCILNRVKENKELVLKAMTMTSFGKGKVIDTQKLFKSLVKKNYPGESLESLYHSK 118
[Close]
BLAST of SMED30021333 vs. Planmine SMEST
Match: SMESG000005262.1 (SMESG000005262.1)

HSP 1 Score: 55.4546 bits (132), Expect = 1.523e-10
Identity = 29/77 (37.66%), Postives = 41/77 (53.25%), Query Frame = 3 
Query:   84 MNYLIAFFSVALSIFCFTVAQPVSTKCSEEFIAGDIPRIPLKNFLYGLNKFKKVLNASEYDSVVCDFNAIKAMKVFY 314
            M + I F  V ++IF   + Q  +  C ++F  GDIP  P+K+F   +   KK L   +YD +VCD N IK  K  Y
Sbjct:    1 MKHQINFLGVVIAIFISLLLQ-FTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKKNKAKY 76
[Close]
BLAST of SMED30021333 vs. Planmine SMEST
Match: SMESG000005261.1 (SMESG000005261.1)

HSP 1 Score: 55.0694 bits (131), Expect = 2.114e-10
Identity = 29/77 (37.66%), Postives = 41/77 (53.25%), Query Frame = 3 
Query:   84 MNYLIAFFSVALSIFCFTVAQPVSTKCSEEFIAGDIPRIPLKNFLYGLNKFKKVLNASEYDSVVCDFNAIKAMKVFY 314
            M + I F  V ++IF   + Q  +  C ++F  GDIP  P+K+F   +   KK L   +YD +VCD N IK  K  Y
Sbjct:    1 MKHQINFLGVVIAIFISLLLQ-FTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKNNKADY 76
[Close]
BLAST of SMED30021333 vs. Planmine SMEST
Match: SMESG000048416.1 (SMESG000048416.1)

HSP 1 Score: 54.6842 bits (130), Expect = 2.376e-10
Identity = 28/71 (39.44%), Postives = 42/71 (59.15%), Query Frame = 3 
Query:   84 MNYLIAFFSVALSIFCFTVAQPVSTKCSEEFIAGDIPRIPLKNFLYGLNKFKKVLNASEYDSVVCDFNAIK 296
            M Y +A  SVA+ +  F+V +  S  CS++F  GDIP +P K     L  FK V N ++YD ++C +N +K
Sbjct:    1 MGYQMALVSVAI-LTLFSVTRQSSAACSDKFKDGDIPGMPAKKIAKYLTVFKSVYNKADYDKLICIWNEVK 70
The following BLAST results are available for this feature:
BLAST of SMED30021333 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 SMED30021333 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 SMED30021333 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 SMED30021333 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 SMED30021333 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 SMED30021333 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 SMED30021333 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 SMED30021333 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 SMED30021333 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 SMED30021333 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 SMED30021333 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 SMED30021333 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 SMED30021333 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 SMED30021333 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000057720.11.119e-8399.16SMESG000057720.1[more]
SMESG000057736.12.023e-1226.27SMESG000057736.1[more]
SMESG000005262.11.523e-1037.66SMESG000005262.1[more]
SMESG000005261.12.114e-1037.66SMESG000005261.1[more]
SMESG000048416.12.376e-1039.44SMESG000048416.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021333 ID=SMED30021333|Name=SMED30021333|organism=Schmidtea mediterranea sexual|type=transcript|length=449bp
TTATCCTGGAAAATGTACAACTCTAAGTTGTTTCGAAAAATCTCTATATA
ATCTTCAAGGAAATATTAGTTGGGAAAGCTAACATGAACTACCTAATTGC
ATTCTTTTCGGTTGCTCTTTCAATATTCTGCTTTACAGTGGCCCAACCGG
TTTCAACCAAGTGCAGTGAAGAATTCATAGCAGGAGACATTCCACGAATC
CCTTTGAAAAATTTCCTATACGGATTGAACAAATTTAAGAAGGTTTTGAA
TGCTTCCGAATACGACAGCGTTGTATGTGATTTCAACGCAATAAAAGCGA
TGAAAGTATTTTATTCCCTTAAAATATCTGCATCAGACTTTAGGATTTCA
GAGTTCTATTACATTGAAGGCCATTTGAATTCAATGATGGATAAATATTT
CTCAGGCCAAAATCCGAAAAGATTTTTTTTTGAAAAAGAATAAATTAAT
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protein sequence of SMED30021333-orf-1

>SMED30021333-orf-1 ID=SMED30021333-orf-1|Name=SMED30021333-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=120bp
MNYLIAFFSVALSIFCFTVAQPVSTKCSEEFIAGDIPRIPLKNFLYGLNK
FKKVLNASEYDSVVCDFNAIKAMKVFYSLKISASDFRISEFYYIEGHLNS
MMDKYFSGQNPKRFFFEKE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..20
score: 0.886