SMED30004172

Overview
NameSMED30004172
Smed IDSMED30004172
Length (bp)1277
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 SMED30004172 (SMED30004172) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004172 (SMED30004172) 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



SMED30004172

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30004172h1SMcG0013788 SmedASXL_016975SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30004172h1SMcG0013788 SmedASXL_004140SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30004172h1SMcG0013788 dd_Smed_v4_13697_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30004172h1SMcG0013788 dd_Smed_v4_13697_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30004172h1SMcG0013788 dd_Smed_v4_13697_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30004172h1SMcG0013788 dd_Smed_v4_13697_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30004172h1SMcG0013788 dd_Smed_v4_13697_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30004172h1SMcG0013788 dd_Smed_v6_13697_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30004172h1SMcG0013788 OX_Smed_1.0.07767ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
body wall musculatureSMED30004172h1SMcG0013788 dd_Smed_v4_13697_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30004172 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.015885:13981..15108 +3696
Homology
[Close]
BLAST of SMED30004172 vs. TrEMBL
Match: A0A419PDX9 (LAM_G_DOMAIN domain-containing protein OS=Clonorchis sinensis OX=79923 GN=CSKR_345s PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 7.539e-6
Identity = 51/175 (29.14%), Postives = 84/175 (48.00%), Query Frame = 2 
Query:  179 MKFEIKFGKTSGLIFYAEDSLTNTFSSLKLLDRGRVRLDMGIF-----SSKNQSDIIPDYISCYIDLSDNVPLIHNLSTGWCHVEIQISQQKLT-----LII---EKSKNTQTFPNHYYKKFQLHKNP---IGKYLYFAGLPQKMKQDATKRVQFSSAVESYNKGEIKHLQTWNC 655
            M FE +  + +GL+ Y+ED+ T  F S+ LL   R+++++ +      +S++ + ++ D+ + +    + V   H L   W    + +S  +       LII   EK    Q  P   Y     HK P    G+ LY   +P  M+ DATKR  FSSA++    G I++LQ   C
Sbjct:   54 MSFEFQTTQPTGLLVYSEDNSTGRFLSITLLPMHRLKVELELRLPQYRTSRDHTTMVLDFATSH--WKEPVEKGHQL---WHFFNMTMSSGQTGNILSGLIIHLDEKRFVHQFTPALIYSAPLSHKTPKVYFGEPLYIGQIPDHMRSDATKRSLFSSAMQPTYNGLIQNLQLGEC 223
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BLAST of SMED30004172 vs. Planmine SMEST
Match: SMESG000058569.1 (SMESG000058569.1)

HSP 1 Score: 426.787 bits (1096), Expect = 5.876e-136
Identity = 204/208 (98.08%), Postives = 206/208 (99.04%), Query Frame = 2 
Query:  104 HIFLQNFSSLVLTPSIEICDYSATIMKFEIKFGKTSGLIFYAEDSLTNTFSSLKLLDRGRVRLDMGIFSSKNQSDIIPDYISCYIDLSDNVPLIHNLSTGWCHVEIQISQQKLTLIIEKSKNTQTFPNHYYKKFQLHKNPIGKYLYFAGLPQKMKQDATKRVQFSSAVESYNKGEIKHLQTWNCHNKTFSKPSVVNGEFYNNFETGNP 727
            ++ L NFSSLVLTPSIEICDYSATIMKFEIKFGKTSGLIFYAEDSLTNTFSSLKLLDRGRVRLDMGIFSSKNQSDIIPDYISCYIDLSDNVPLIHNLSTGWCHVEIQISQQKLTLIIEKSKNTQTFPNHYYKKFQLHKNPIGKYLYFAGLPQKMKQDATKRVQFSSAVESYNKGEIKHLQTWNCHNKTFSKPSVVNGEFYNNFETGNP
Sbjct:  178 YLSLGNFSSLVLTPSIEICDYSATIMKFEIKFGKTSGLIFYAEDSLTNTFSSLKLLDRGRVRLDMGIFSSKNQSDIIPDYISCYIDLSDNVPLIHNLSTGWCHVEIQISQQKLTLIIEKSKNTQTFPNHYYKKFQLHKNPIGKYLYFAGLPQKMKQDATKRVQFSSAVESYNKGEIKHLQTWNCHNKTFSKPSVVNGEFYNNFETGNP 385
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BLAST of SMED30004172 vs. Planmine SMEST
Match: SMESG000058569.1 (SMESG000058569.1)

HSP 1 Score: 426.017 bits (1094), Expect = 7.020e-136
Identity = 204/208 (98.08%), Postives = 206/208 (99.04%), Query Frame = 2 
Query:  104 HIFLQNFSSLVLTPSIEICDYSATIMKFEIKFGKTSGLIFYAEDSLTNTFSSLKLLDRGRVRLDMGIFSSKNQSDIIPDYISCYIDLSDNVPLIHNLSTGWCHVEIQISQQKLTLIIEKSKNTQTFPNHYYKKFQLHKNPIGKYLYFAGLPQKMKQDATKRVQFSSAVESYNKGEIKHLQTWNCHNKTFSKPSVVNGEFYNNFETGNP 727
            ++ L NFSSLVLTPSIEICDYSATIMKFEIKFGKTSGLIFYAEDSLTNTFSSLKLLDRGRVRLDMGIFSSKNQSDIIPDYISCYIDLSDNVPLIHNLSTGWCHVEIQISQQKLTLIIEKSKNTQTFPNHYYKKFQLHKNPIGKYLYFAGLPQKMKQDATKRVQFSSAVESYNKGEIKHLQTWNCHNKTFSKPSVVNGEFYNNFETGNP
Sbjct:  147 YLSLGNFSSLVLTPSIEICDYSATIMKFEIKFGKTSGLIFYAEDSLTNTFSSLKLLDRGRVRLDMGIFSSKNQSDIIPDYISCYIDLSDNVPLIHNLSTGWCHVEIQISQQKLTLIIEKSKNTQTFPNHYYKKFQLHKNPIGKYLYFAGLPQKMKQDATKRVQFSSAVESYNKGEIKHLQTWNCHNKTFSKPSVVNGEFYNNFETGNP 354
[Close]
BLAST of SMED30004172 vs. Planmine SMEST
Match: SMESG000066308.1 (SMESG000066308.1)

HSP 1 Score: 102.834 bits (255), Expect = 3.453e-23
Identity = 67/179 (37.43%), Postives = 93/179 (51.96%), Query Frame = 2 
Query:  134 VLTPSIEICDYSATIMKFEIKFGKTSGLIFYAEDSLTNTFSSLKLLDRGRVRLDMGIF---------SSKNQSDIIPDYISCYIDLSDNVPLIHNLSTGWCHVEIQISQQKLTLIIEKSKNTQTFPNHYYKKFQLHKNPIGKYLYFAGLPQKMKQDATKRVQFSSAVESYNKGEIKHLQ 643
            V  PSI +   S+  + F+IK     GLIFYAED  TN+F SLKLL   +VRLD+G+F         S   +    PDY++C IDLS    LIH     W  + I   ++ + L   +       P   Y  F+     +G  ++F GLP+K+KQDA+ RV FSSA+E    G I  ++
Sbjct:   29 VYHPSINVNTNSS--LSFQIKIDTLMGLIFYAEDIKTNSFVSLKLLSSAKVRLDVGLFYHDSTRENISMSKEYPTAPDYLTCIIDLSKIDGLIHE----WHTIMINFHKKSIILQFNQFSEKVNIPIG-YNSFKRFDGFLGDTMFFGGLPEKLKQDASHRVFFSSAIEPSFSGRISAVR 200
[Close]
BLAST of SMED30004172 vs. Planmine SMEST
Match: SMESG000066308.1 (SMESG000066308.1)

HSP 1 Score: 102.834 bits (255), Expect = 3.530e-23
Identity = 67/179 (37.43%), Postives = 93/179 (51.96%), Query Frame = 2 
Query:  134 VLTPSIEICDYSATIMKFEIKFGKTSGLIFYAEDSLTNTFSSLKLLDRGRVRLDMGIF---------SSKNQSDIIPDYISCYIDLSDNVPLIHNLSTGWCHVEIQISQQKLTLIIEKSKNTQTFPNHYYKKFQLHKNPIGKYLYFAGLPQKMKQDATKRVQFSSAVESYNKGEIKHLQ 643
            V  PSI +   S+  + F+IK     GLIFYAED  TN+F SLKLL   +VRLD+G+F         S   +    PDY++C IDLS    LIH     W  + I   ++ + L   +       P   Y  F+     +G  ++F GLP+K+KQDA+ RV FSSA+E    G I  ++
Sbjct:   34 VYHPSINVNTNSS--LSFQIKIDTLMGLIFYAEDIKTNSFVSLKLLSSAKVRLDVGLFYHDSTRENISMSKEYPTAPDYLTCIIDLSKIDGLIHE----WHTIMINFHKKSIILQFNQFSEKVNIPIG-YNSFKRFDGFLGDTMFFGGLPEKLKQDASHRVFFSSAIEPSFSGRISAVR 205
[Close]
BLAST of SMED30004172 vs. Planmine SMEST
Match: SMESG000066308.1 (SMESG000066308.1)

HSP 1 Score: 102.834 bits (255), Expect = 3.668e-23
Identity = 67/179 (37.43%), Postives = 93/179 (51.96%), Query Frame = 2 
Query:  134 VLTPSIEICDYSATIMKFEIKFGKTSGLIFYAEDSLTNTFSSLKLLDRGRVRLDMGIF---------SSKNQSDIIPDYISCYIDLSDNVPLIHNLSTGWCHVEIQISQQKLTLIIEKSKNTQTFPNHYYKKFQLHKNPIGKYLYFAGLPQKMKQDATKRVQFSSAVESYNKGEIKHLQ 643
            V  PSI +   S+  + F+IK     GLIFYAED  TN+F SLKLL   +VRLD+G+F         S   +    PDY++C IDLS    LIH     W  + I   ++ + L   +       P   Y  F+     +G  ++F GLP+K+KQDA+ RV FSSA+E    G I  ++
Sbjct:   34 VYHPSINVNTNSS--LSFQIKIDTLMGLIFYAEDIKTNSFVSLKLLSSAKVRLDVGLFYHDSTRENISMSKEYPTAPDYLTCIIDLSKIDGLIHE----WHTIMINFHKKSIILQFNQFSEKVNIPIG-YNSFKRFDGFLGDTMFFGGLPEKLKQDASHRVFFSSAIEPSFSGRISAVR 205
The following BLAST results are available for this feature:
BLAST of SMED30004172 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 SMED30004172 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 SMED30004172 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 SMED30004172 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 SMED30004172 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 SMED30004172 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 SMED30004172 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 SMED30004172 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A419PDX97.539e-629.14LAM_G_DOMAIN domain-containing protein OS=Clonorch... [more]
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BLAST of SMED30004172 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 SMED30004172 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 SMED30004172 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 SMED30004172 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 SMED30004172 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 SMED30004172 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000058569.15.876e-13698.08SMESG000058569.1[more]
SMESG000058569.17.020e-13698.08SMESG000058569.1[more]
SMESG000066308.13.453e-2337.43SMESG000066308.1[more]
SMESG000066308.13.530e-2337.43SMESG000066308.1[more]
SMESG000066308.13.668e-2337.43SMESG000066308.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004172 ID=SMED30004172|Name=SMED30004172|organism=Schmidtea mediterranea sexual|type=transcript|length=1277bp
GGCAATTAAAAATAAAATGCATTCAAAAAAAATATTCGGAACAATAATTT
TTTGTATCACACAAATTTGCATTTGTGAATTCAATAAAAAAGATTTTTCC
GATCATATTTTCCTACAGAATTTTTCTTCTCTCGTTTTGACGCCATCTAT
TGAAATTTGTGATTATTCTGCAACAATTATGAAATTCGAAATCAAATTTG
GGAAAACCTCAGGATTAATTTTCTACGCAGAAGACTCTTTGACAAACACT
TTCTCGTCATTGAAATTACTCGACCGTGGACGAGTTCGATTAGACATGGG
AATATTTTCTTCAAAAAATCAATCTGACATAATTCCAGATTACATTTCTT
GCTACATAGACTTGTCGGATAATGTGCCACTAATTCACAATTTATCGACC
GGTTGGTGCCATGTTGAAATTCAGATCAGTCAGCAAAAACTGACACTAAT
TATCGAAAAATCTAAAAACACTCAAACATTCCCAAATCATTATTATAAAA
AATTCCAACTCCATAAAAACCCAATTGGGAAATATCTGTATTTTGCTGGG
CTGCCTCAAAAAATGAAACAAGACGCTACGAAACGCGTTCAATTTTCTTC
GGCTGTCGAATCCTACAACAAAGGAGAAATCAAACATTTACAAACCTGGA
ATTGCCACAATAAAACATTTTCTAAACCTTCTGTCGTAAACGGTGAATTT
TACAACAACTTTGAAACCGGAAATCCAGGTTTCATTTTATTAGCATCAAC
AGACAAATCGTCCAAATTATCATCTAATTCAGATTTCATTTCGAAATCAA
CTTCAAGAGTGACAAAGAATCAAGATATAAATTTAAACAATCAAACCATT
CATCAAGTTCCCAACTAAATTCTCCACGGGTAATGATTAACTTATGGCCC
ACCCTTTTTACAAAGTTCTTATTTACAAAAGTAAATTCAACACAAACCAC
ACCCTTATAAAAGCTAAACATTTCACTTTCATTAATTAATTCAATGTTAT
CATCTAAAGTCATGAAAGTATGATACTTTAACATTCCAGAAATTCCAAAG
TAATTCGGAGGTGCTAATCTATTGGAAACTATGTATTAGAACCTTTGAAT
GTTACTAATAATGTAACTAATGAATGTAACTAATAAAGATAACATTCGGT
TTTGGTGGATGAAAATAAAAGTCTCACATATTGGTATCATTGCGTAAACT
CGTATATTCATCGACATGAGATTTAAAGGAACGATATAATTGTTAATGCC
TTTGGAGATAACAATGATGAATTTAGC
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protein sequence of SMED30004172-orf-1

>SMED30004172-orf-1 ID=SMED30004172-orf-1|Name=SMED30004172-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=289bp
AIKNKMHSKKIFGTIIFCITQICICEFNKKDFSDHIFLQNFSSLVLTPSI
EICDYSATIMKFEIKFGKTSGLIFYAEDSLTNTFSSLKLLDRGRVRLDMG
IFSSKNQSDIIPDYISCYIDLSDNVPLIHNLSTGWCHVEIQISQQKLTLI
IEKSKNTQTFPNHYYKKFQLHKNPIGKYLYFAGLPQKMKQDATKRVQFSS
AVESYNKGEIKHLQTWNCHNKTFSKPSVVNGEFYNNFETGNPGFILLAST
DKSSKLSSNSDFISKSTSRVTKNQDINLNNQTIHQVPN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR013320ConA-like_dom_sf