SMED30005958

Overview
NameSMED30005958
Smed IDSMED30005958
Length (bp)845
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 SMED30005958 (SMED30005958) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005958 (SMED30005958) 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



SMED30005958

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30005958h1SMcG0012153 dd_Smed_v4_10351_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
SMED30005958 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001040:123002..123837 +4171
Homology
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BLAST of SMED30005958 vs. Planmine SMEST
Match: SMESG000007060.1 (SMESG000007060.1)

HSP 1 Score: 463.381 bits (1191), Expect = 4.742e-167
Identity = 255/255 (100.00%), Postives = 255/255 (100.00%), Query Frame = 1 
Query:   28 MGFWFRVLVFVLSSTLNHGDLIYQNKEFQNEYFSTGGYSARFCAKNAKTKDLLLINPPDKNSRFTCYNTVEKCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSKYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDINCLKISVTKRAINCILDLTKLHSNDIIEVNITVKYGKRICNKPQFVGNIFIXXXXXXXXXXXXEWXXXXXXXXXXXXSHLIPFYMRRNNIISKSRIYFENIYETEN 792
            MGFWFRVLVFVLSSTLNHGDLIYQNKEFQNEYFSTGGYSARFCAKNAKTKDLLLINPPDKNSRFTCYNTVEKCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSKYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDINCLKISVTKRAINCILDLTKLHSNDIIEVNITVKYGKRICNKPQFVGNIFIYKLKYSKSSVKYEWIIIILLTLAFALSHLIPFYMRRNNIISKSRIYFENIYETEN
Sbjct:    1 MGFWFRVLVFVLSSTLNHGDLIYQNKEFQNEYFSTGGYSARFCAKNAKTKDLLLINPPDKNSRFTCYNTVEKCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSKYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDINCLKISVTKRAINCILDLTKLHSNDIIEVNITVKYGKRICNKPQFVGNIFIYKLKYSKSSVKYEWIIIILLTLAFALSHLIPFYMRRNNIISKSRIYFENIYETEN 255
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BLAST of SMED30005958 vs. Planmine SMEST
Match: SMESG000033282.1 (SMESG000033282.1)

HSP 1 Score: 66.2402 bits (160), Expect = 6.204e-12
Identity = 55/174 (31.61%), Postives = 85/174 (48.85%), Query Frame = 1 
Query:  118 EYFSTGGYSARFCAKNAKTKDLLLINPPDKNS-RFTCYNTVEKCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSKYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDIN--CLKISVTKRAINCILDL-TKLHSNDIIEVNITVKYGKRICNKPQFVGNIFI 627
            EYF+ GGY + FC    KT D ++++  +  +   +C      C+ GN + C LPCNF   +   N  + +L    +P F+++ L  Y     L IG  S+  S+    +E    N SD+N  C +I  T  +I C+L L        I+ V+I + YG   CN+ Q +G I I
Sbjct:   26 EYFNRGGYISLFCIN--KTDDNIILHKQNSYAVNISCNKMKIVCKSGNFYKCNLPCNFNLTALENNKKIFRLQRFEAPIFAISELEYYQNRSNLTIG-VSNKVSISSIRLENYHFNFSDVNVLCRQIWNTDSSIICLLHLKMTCVYYKILNVSILISYGNSSCNERQNLGFILI 196
[Close]
BLAST of SMED30005958 vs. Planmine SMEST
Match: SMESG000033282.1 (SMESG000033282.1)

HSP 1 Score: 66.2402 bits (160), Expect = 6.250e-12
Identity = 55/174 (31.61%), Postives = 85/174 (48.85%), Query Frame = 1 
Query:  118 EYFSTGGYSARFCAKNAKTKDLLLINPPDKNS-RFTCYNTVEKCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSKYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDIN--CLKISVTKRAINCILDL-TKLHSNDIIEVNITVKYGKRICNKPQFVGNIFI 627
            EYF+ GGY + FC    KT D ++++  +  +   +C      C+ GN + C LPCNF   +   N  + +L    +P F+++ L  Y     L IG S+   S+    +E    N SD+N  C +I  T  +I C+L L        I+ V+I + YG   CN+ Q +G I I
Sbjct:   26 EYFNRGGYISLFCIN--KTDDNIILHKQNSYAVNISCNKMKIVCKSGNFYKCNLPCNFNLTALENNKKIFRLQRFEAPIFAISELEYYQNRSNLTIGVSNKV-SISSIRLENYHFNFSDVNVLCRQIWNTDSSIICLLHLKMTCVYYKILNVSILISYGNSSCNERQNLGFILI 196
[Close]
BLAST of SMED30005958 vs. Planmine SMEST
Match: SMESG000033322.1 (SMESG000033322.1)

HSP 1 Score: 61.6178 bits (148), Expect = 2.145e-10
Identity = 45/167 (26.95%), Postives = 81/167 (48.50%), Query Frame = 1 
Query:  133 GGYSARFCAKNAKTKDLLLINPPDKNSRFTCYNTVE---KCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLS-KYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDINCLKISVTKRAINCILDLTKLHSNDIIEVNITVKYGKRICNKPQFVGNI 621
            GGY+AR C  +      + +     +  F+C  + E   +C+  ++++C +PCNF   +      + KL  +  PKF L   + KY  N  L I S +    L    + I F+ N  ++C +  +   +I C LD  ++  +  ++++I + YG+ ICN   F+G I
Sbjct:   31 GGYTARICLNHHPEN--VSVKTTMGDYVFSCRKSNETGTECKNKSVYSCPIPCNFSESAVKIGMKVYKLSHLSKPKFELAEKNLKYNSNGNLTIKSDASLPLLAADQINIDFSAN--VSCSRKYIQNYSIICRLDAQRIPIDQALDISINISYGE-ICNSKHFLGKI 192
[Close]
BLAST of SMED30005958 vs. Planmine SMEST
Match: SMESG000033300.1 (SMESG000033300.1)

HSP 1 Score: 59.6918 bits (143), Expect = 6.270e-10
Identity = 48/167 (28.74%), Postives = 81/167 (48.50%), Query Frame = 1 
Query:  139 YSARFCAKNAKTKDLLLINPPDKNSRFTCYNTVE---KCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSK-YGENDILKIGSSSDTFSLFDWDVEIKFNNNSDINCLKISVTKRAINCILDLTKLHSNDIIEVNITVKYGKRICNKPQFVGNIFI 627
            Y+AR C  N   +++ +   P  +  F+C  T E   +C+  ++++C +PCN    +    + + KL     PKF L    K Y  N  L I S +    L    + I F+ N   +CL+  +   +I C LD  ++  +  ++++I + YG+ ICN  QF  NI I
Sbjct:   33 YTARICL-NHHPENVSVNKTPMGDYVFSCRKTNETGTECKNKSVYSCPIPCNLSLQTVKIGTKIYKLSYSPKPKFELAEKDKKYNSNGDLTIKSDASLPLLAADQINIDFSAN--FSCLRKYIQNYSIICRLDAQRIPIDQALDISINISYGE-ICNSKQFTINITI 195
The following BLAST results are available for this feature:
BLAST of SMED30005958 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 SMED30005958 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 SMED30005958 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 SMED30005958 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 SMED30005958 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 SMED30005958 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 SMED30005958 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 SMED30005958 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 SMED30005958 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 SMED30005958 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 SMED30005958 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 SMED30005958 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 SMED30005958 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 SMED30005958 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000007060.14.742e-167100.00SMESG000007060.1[more]
SMESG000033282.16.204e-1231.61SMESG000033282.1[more]
SMESG000033282.16.250e-1231.61SMESG000033282.1[more]
SMESG000033322.12.145e-1026.95SMESG000033322.1[more]
SMESG000033300.16.270e-1028.74SMESG000033300.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005958 ID=SMED30005958|Name=SMED30005958|organism=Schmidtea mediterranea sexual|type=transcript|length=845bp
CGGGATTATTTTTCATTTTTATTATTCATGGGTTTTTGGTTCAGAGTTTT
AGTATTTGTACTTTCATCAACACTAAATCATGGTGATCTTATATATCAAA
ACAAAGAATTTCAGAATGAATATTTTTCAACTGGTGGATATTCAGCGAGA
TTTTGCGCAAAAAATGCGAAAACTAAAGATCTACTTCTCATTAATCCACC
GGATAAAAATTCTCGTTTCACTTGTTATAATACTGTAGAAAAATGTCAAA
AAGGAAACATATTTAATTGTTTTCTCCCATGCAACTTTAGGCGTTTTTCT
TTTATAAAGAATTCTTATTTGGGAAAACTTGTCAGCATTGGTTCTCCAAA
GTTTTCTCTGAATCCATTAAGCAAATATGGTGAAAATGACATTTTAAAGA
TTGGATCCAGTAGCGACACGTTCTCTCTATTCGATTGGGATGTTGAAATA
AAGTTCAACAACAATTCAGATATAAATTGCCTGAAGATCTCTGTGACCAA
GCGAGCGATAAATTGCATTTTAGATTTGACAAAGTTGCATTCCAATGATA
TTATTGAAGTAAATATTACAGTGAAATACGGGAAAAGAATTTGCAATAAA
CCTCAATTTGTAGGAAATATATTTATTTATAAATTGAAATACTCCAAGAG
CTCTGTTAAATATGAATGGATAATTATCATTTTATTAACTTTGGCTTTTG
CGTTGAGCCATTTGATCCCGTTCTACATGAGGAGAAATAATATTATTTCA
AAATCAAGGATTTATTTTGAAAATATTTACGAAACTGAAAATGTTTATTA
AGTACTTTTTGTAATAAAATAAATAATTTTTAATTTCAAAAAAAA
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protein sequence of SMED30005958-orf-1

>SMED30005958-orf-1 ID=SMED30005958-orf-1|Name=SMED30005958-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=267bp
RDYFSFLLFMGFWFRVLVFVLSSTLNHGDLIYQNKEFQNEYFSTGGYSAR
FCAKNAKTKDLLLINPPDKNSRFTCYNTVEKCQKGNIFNCFLPCNFRRFS
FIKNSYLGKLVSIGSPKFSLNPLSKYGENDILKIGSSSDTFSLFDWDVEI
KFNNNSDINCLKISVTKRAINCILDLTKLHSNDIIEVNITVKYGKRICNK
PQFVGNIFIYKLKYSKSSVKYEWIIIILLTLAFALSHLIPFYMRRNNIIS
KSRIYFENIYETENVY*
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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..25
score: 0.797
NoneNo IPR availableTMHMMTMhelixcoord: 218..240