SMED30016457

Overview
NameSMED30016457
Smed IDSMED30016457
Length (bp)997
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 SMED30016457 (SMED30016457) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016457 (SMED30016457) 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




SMED30016457

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30016457SMESG000040036.1 SmedASXL_009157SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
protonephridiaSMED30016457SMESG000040036.1 dd_Smed_v4_21280_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30016457 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000799:115929..116925 -4985
Homology
BLAST of SMED30016457 vs. Planmine SMEST
Match: SMESG000040036.1 (SMESG000040036.1)

HSP 1 Score: 357.451 bits (916), Expect = 4.874e-125
Identity = 206/206 (100.00%), Postives = 206/206 (100.00%), Query Frame = -3
Query:  306 YDDLSSQNRNASETNLGFISDIYVNSSNIDPSMLRANETRFTPNVPLPNQNFSTTKSKKIVNINNPVLFKWFXXXXXXXXXXIFVTEIAVIFENCYNEMNMRFYVGTWVSWFLIVCGILQIRISQHHAEIEISFXXXXXXXXXXXXXXLFVGFILALIMRVIVGNNLCQNITVLVIFEISLSLAPIIWSALFILKYLLFEYIPSRK 923
            YDDLSSQNRNASETNLGFISDIYVNSSNIDPSMLRANETRFTPNVPLPNQNFSTTKSKKIVNINNPVLFKWFGLMILIGGLLIFVTEIAVIFENCYNEMNMRFYVGTWVSWFLIVCGILQIRISQHHAEIEISFLILTLIMTLICCLILFVGFILALIMRVIVGNNLCQNITVLVIFEISLSLAPIIWSALFILKYLLFEYIPSRK
Sbjct:    9 YDDLSSQNRNASETNLGFISDIYVNSSNIDPSMLRANETRFTPNVPLPNQNFSTTKSKKIVNINNPVLFKWFGLMILIGGLLIFVTEIAVIFENCYNEMNMRFYVGTWVSWFLIVCGILQIRISQHHAEIEISFLILTLIMTLICCLILFVGFILALIMRVIVGNNLCQNITVLVIFEISLSLAPIIWSALFILKYLLFEYIPSRK 214          
BLAST of SMED30016457 vs. Planmine SMEST
Match: SMESG000040041.1 (SMESG000040041.1)

HSP 1 Score: 80.1073 bits (196), Expect = 2.024e-17
Identity = 64/201 (31.84%), Postives = 108/201 (53.73%), Query Frame = -3
Query:  339 YDDLSSQNRNASETNLGFISDIYVNSSNIDPSML----RANETRFTPNVPLPNQNFSTTKSKKIVNINNPVLFKWFXXXXXXXXXXIFVTEIAVIFENCYNEMNMRFYVGTWVSWFLIVCGILQIRISQHHAEIEISFXXXXXXXXXXXXXXLFVGFILALIMR--VIVGNNLCQNITVLVIFEISLSLAPIIWSALFILK 923
            YDDLS        TN+     +Y   +N D  ++    R    +    V   N+  ++T  K  +N  +P  F W G+MI+IG   I  TE+ +IF+ CY  +   FY+G W+SW L++ G LQIR+S HH  + I + I     T++  + L +GFIL+L++R  + +   +C N+  + +FEI++ + P++ S + + K
Sbjct:    7 YDDLSQLPNILRNTNMDN-EVVYAVPTNNDIDVVTVDSRQTARQSKNRVSFINKEDNSTVKK--INFKHPENFLWLGIMIVIGATTILFTEMGMIFQGCY-MIGYGFYLGIWISWILLITGFLQIRLSVHHQNVRIFYQIFVCFSTILSGVFLIIGFILSLVIRFNIPLLYGVCYNLPAVFLFEITIIMVPVVISLVCLFK 203          
The following BLAST results are available for this feature:
BLAST of SMED30016457 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 SMED30016457 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 SMED30016457 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 SMED30016457 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 SMED30016457 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 SMED30016457 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 SMED30016457 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 SMED30016457 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 SMED30016457 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 SMED30016457 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 SMED30016457 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 SMED30016457 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 SMED30016457 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 SMED30016457 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000040036.14.874e-125100.00SMESG000040036.1[more]
SMESG000040041.12.024e-1731.84SMESG000040041.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016457 ID=SMED30016457|Name=SMED30016457|organism=Schmidtea mediterranea sexual|type=transcript|length=997bp
CAGTATTTTTTCTTTTTACAAATCCCATAATCCATGACAAAGCAAACTCC
TAACAATATTTTATTTATGCGGTTCTAAGGTTTCTGTTTCAAAATGTTGT
CCGTGGAAAATTTACAAATTCAAATCTTATGAGTGAAATTATGATCAAAT
TATGAGCTTTCGAGAAAAAAATATTTATATCTATAGTAAATTACACAAAT
AAAAATGTCATTTAATTCATTGCAATGTTTTTATACAAGATGCGATAATC
CTTGAATATAGTAAAACAAAGATCTCAATACATAATGTTTTCTTCCTTAA
AATCATTTTCTTGATGGAATGTATTCAAACAATAAATACTTCAGAATAAA
TAATGCGCTCCAGATTATTGGAGCCAAAGAAAGAGATATTTCAAAAATTA
CTAAAACAGTAATATTTTGACAAAGATTGTTCCCAACGATGACTCGCATG
ATCAGAGCTAGAATAAATCCAACAAATAGTATCAGGCAACATATCAAAGT
CATTATAAGCGTTAAAATTAAAAAAGAAATCTCAATTTCTGCGTGATGTT
GGCTGATTCTTATTTGAAGAATCCCACAGACAATTAAAAACCACGAAACC
CAAGTCCCAACATAAAATCTCATATTCATTTCATTGTAACAGTTTTCAAA
AATGACTGCTATTTCCGTGACAAATATCAACAGGCCTCCTATAAGGATCA
TCAAACCAAACCATTTGAAAAGAACAGGGTTGTTGATGTTGACAATTTTT
TTTGATTTTGTCGTTGAAAAATTTTGATTTGGCAAAGGCACATTCGGAGT
GAAACGCGTTTCATTTGCCCTGAGCATCGAAGGGTCAATGTTTGAGGAGT
TCACATAAATATCCGAAATAAAACCCAAATTTGTTTCACTGGCATTCCGG
TTTTGAGACGACAAATCATCATAAATCTCTTCTTCGATTTCCGACATTGA
AATAAATATGAATTGGAATTGAACTAAACTTAATTTATTCTAAAAAT
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protein sequence of SMED30016457-orf-1

>SMED30016457-orf-1 ID=SMED30016457-orf-1|Name=SMED30016457-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=215bp
MSEIEEEIYDDLSSQNRNASETNLGFISDIYVNSSNIDPSMLRANETRFT
PNVPLPNQNFSTTKSKKIVNINNPVLFKWFGLMILIGGLLIFVTEIAVIF
ENCYNEMNMRFYVGTWVSWFLIVCGILQIRISQHHAEIEISFLILTLIMT
LICCLILFVGFILALIMRVIVGNNLCQNITVLVIFEISLSLAPIIWSALF
ILKYLLFEYIPSRK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 112..129
NoneNo IPR availableTMHMMTMhelixcoord: 79..100
NoneNo IPR availableTMHMMTMhelixcoord: 179..201
NoneNo IPR availableTMHMMTMhelixcoord: 144..166