SMED30008969

Overview
NameSMED30008969
Smed IDSMED30008969
Length (bp)659
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 SMED30008969 (SMED30008969) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008969 (SMED30008969) 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




SMED30008969

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
epidermisSMED30008969SMESG000074923.1 dd_Smed_v4_11974_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30008969SMESG000074923.1 dd_Smed_v4_11974_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30008969 vs. Planmine SMEST
Match: SMESG000074923.1 (SMESG000074923.1)

HSP 1 Score: 398.667 bits (1023), Expect = 2.117e-136
Identity = 198/198 (100.00%), Postives = 198/198 (100.00%), Query Frame = 3
Query:   66 MSTLFGIVIFICTIEISLEELPTTSCPSSRPFQTLGIRCANFQEVCVKTNDIKCKKFQNICAQCPPSNFSTLTYLNIENMKEQLKNNVKRTSSIFILLWIIIAFNILMAILLILEIRFGIITKLFHRRKLSDEKQYISLKRAERYEKQYVPIEREQRDDSNDSNIIILNKIDILTTNVNKLIKSIKEKTKICMNGQII 659
            MSTLFGIVIFICTIEISLEELPTTSCPSSRPFQTLGIRCANFQEVCVKTNDIKCKKFQNICAQCPPSNFSTLTYLNIENMKEQLKNNVKRTSSIFILLWIIIAFNILMAILLILEIRFGIITKLFHRRKLSDEKQYISLKRAERYEKQYVPIEREQRDDSNDSNIIILNKIDILTTNVNKLIKSIKEKTKICMNGQII
Sbjct:    1 MSTLFGIVIFICTIEISLEELPTTSCPSSRPFQTLGIRCANFQEVCVKTNDIKCKKFQNICAQCPPSNFSTLTYLNIENMKEQLKNNVKRTSSIFILLWIIIAFNILMAILLILEIRFGIITKLFHRRKLSDEKQYISLKRAERYEKQYVPIEREQRDDSNDSNIIILNKIDILTTNVNKLIKSIKEKTKICMNGQII 198          
BLAST of SMED30008969 vs. Planmine SMEST
Match: SMESG000074915.1 (SMESG000074915.1)

HSP 1 Score: 139.813 bits (351), Expect = 1.561e-39
Identity = 83/202 (41.09%), Postives = 122/202 (60.40%), Query Frame = 3
Query:   66 MSTLFGIVI-FICTIEISLEELPTTSCPSSRPFQTLGIRCANFQEVCVKTNDIKCKKFQNICAQCPPSNFSTLTYLNIENMKEQLKNNVKRTSSIFILLWIIIAFNILMAILLILEIRFGIITKLFHR---RKLSDEKQYISLKRAERYEKQYVPIEREQRDDSNDSNIIILNKIDILTTNVNKLIKSIKEKTKICMNGQII 659
            MS L GI+  FI +I+IS EELP + C   +PF+T+   CANF +VCVKT D +C+ FQ +C QCP  N+S  TYL++  + +Q+K +  R   I    ++I+   IL   L I EIRF I+TK+F     + ++   + +  +++E        I  E+R +SN     I + ++ LT N++ LI+ IKEKTKICMNGQII
Sbjct:    1 MSILLGIIFTFIYSIKISREELPLSMCGIVKPFKTMNNSCANFVDVCVKTGDKECQNFQRLCQQCPAYNYSIQTYLDVRTISDQIKRSYDRIERIHSNFYLIVGLIILFLFLSIFEIRFKILTKVFSAICGQSINHMYRILQSRKSEEL------ILMEKRINSN-----ITSNLNSLTANIDILIQKIKEKTKICMNGQII 191          
BLAST of SMED30008969 vs. Planmine SMEST
Match: SMESG000074915.1 (SMESG000074915.1)

HSP 1 Score: 119.013 bits (297), Expect = 9.488e-32
Identity = 69/176 (39.20%), Postives = 104/176 (59.09%), Query Frame = 3
Query:  141 CPSSRPFQTLGIRCANFQEVCVKTNDIKCKKFQNICAQCPPSNFSTLTYLNIENMKEQLKNNVKRTSSIFILLWIIIAFNILMAILLILEIRFGIITKLFHR---RKLSDEKQYISLKRAERYEKQYVPIEREQRDDSNDSNIIILNKIDILTTNVNKLIKSIKEKTKICMNGQII 659
            C   +PF+T+   CANF +VCVKT D +C+ FQ +C QCP  N+S  TYL++  + +Q+K +  R   I    ++I+   IL   L I EIRF I+TK+F     + ++   + +  +++E        I  E+R +SN     I + ++ LT N++ LI+ IKEKTKICMNGQII
Sbjct:    2 CGIVKPFKTMNNSCANFVDVCVKTGDKECQNFQRLCQQCPAYNYSIQTYLDVRTISDQIKRSYDRIERIHSNFYLIVGLIILFLFLSIFEIRFKILTKVFSAICGQSINHMYRILQSRKSEEL------ILMEKRINSN-----ITSNLNSLTANIDILIQKIKEKTKICMNGQII 166          
BLAST of SMED30008969 vs. Planmine SMEST
Match: SMESG000074921.1 (SMESG000074921.1)

HSP 1 Score: 98.9821 bits (245), Expect = 9.365e-24
Identity = 51/134 (38.06%), Postives = 84/134 (62.69%), Query Frame = 3
Query:   66 MSTLFGIVI-FICTIEISLEELPTTSCPSSRPFQTLGIRCANFQEVCVKTNDIKCKKFQNICAQCPPSNFSTLTYLNIENMKEQL--------KNNVKRTSSIFILLWIIIAFNILMAILLILEIRFGIITKLF 440
            MS L GI+  FI +I+IS EELP + C   +PF+T+   CANF +VCVKT D +C+ FQN+C QCP  N+S  T+L++  + +++        +N     ++  +L++ I+    L+ ++L +E+RF + TK+F
Sbjct:    1 MSILLGIIFTFIYSIKISREELPLSMCGIVKPFKTMNNSCANFVDVCVKTGDKECQNFQNVCQQCPAYNYSIQTFLDVRTINDRMSKIEDKMFQNQNIIINTTLVLVYCIMFMICLILVVLFVEVRFKLCTKIF 134          
BLAST of SMED30008969 vs. Planmine SMEST
Match: SMESG000074921.1 (SMESG000074921.1)

HSP 1 Score: 93.5893 bits (231), Expect = 8.016e-22
Identity = 55/152 (36.18%), Postives = 85/152 (55.92%), Query Frame = 3
Query:   66 MSTLFGIVI-FICTIEISLEELPTTSCPSSRPFQTLGIRCANFQEVCVKTNDIKCKKFQNICAQCPPSNFSTLTYLNIENMKEQL--------KNN---VKRTSSI---------------FILLWIIIAFNILMAILLILEIRFGIITKLF 440
            MS L GI+  FI +I+IS EELP + C   +PF+T+   CANF +VCVKT D +C+ FQN+C QCP  N+S  T+L++  + +++        KN      R S I                +L++ I+    L+ ++L +E+RF + TK+F
Sbjct:    1 MSILLGIIFTFIYSIKISREELPLSMCGIVKPFKTMNNSCANFVDVCVKTGDKECQNFQNVCQQCPAYNYSIQTFLDVRTINDRMSKIEEKINKNQNIITYRMSKIEDKMFQNQNIIINTTLVLVYCIMFMICLILVVLFVEVRFKLCTKIF 152          
The following BLAST results are available for this feature:
BLAST of SMED30008969 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 SMED30008969 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 SMED30008969 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 SMED30008969 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 SMED30008969 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 SMED30008969 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 SMED30008969 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 SMED30008969 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 SMED30008969 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 SMED30008969 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 SMED30008969 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 SMED30008969 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 SMED30008969 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 SMED30008969 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000074923.12.117e-136100.00SMESG000074923.1[more]
SMESG000074915.11.561e-3941.09SMESG000074915.1[more]
SMESG000074915.19.488e-3239.20SMESG000074915.1[more]
SMESG000074921.19.365e-2438.06SMESG000074921.1[more]
SMESG000074921.18.016e-2236.18SMESG000074921.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008969 ID=SMED30008969|Name=SMED30008969|organism=Schmidtea mediterranea sexual|type=transcript|length=659bp
ATTATTATCATTATTAATATCGCTATGTTTAGTTTAGTTTTTCTTGTGAG
TTCATAAACTACAAAATGTCAACTTTATTTGGAATTGTCATTTTCATATG
TACAATCGAGATAAGCTTGGAAGAGCTTCCGACGACATCATGCCCAAGTT
CCAGGCCATTCCAAACGTTGGGAATCCGTTGCGCAAATTTTCAGGAAGTC
TGCGTGAAAACTAATGATATAAAATGTAAAAAATTTCAAAATATCTGCGC
TCAATGTCCACCGTCCAATTTCAGTACCTTAACTTACTTAAATATAGAAA
ATATGAAAGAGCAACTGAAGAACAATGTGAAACGAACAAGTTCAATTTTT
ATTCTTTTGTGGATTATTATTGCATTTAACATTTTAATGGCCATCTTGCT
GATATTGGAAATAAGATTCGGGATCATAACGAAATTATTTCATCGCAGAA
AATTATCTGATGAGAAACAATATATATCTTTAAAAAGAGCTGAAAGATAT
GAGAAACAATATGTACCTATAGAAAGAGAGCAAAGAGATGATTCCAATGA
TTCCAATATTATAATACTAAACAAAATAGACATCTTGACCACCAATGTGA
ATAAATTAATAAAAAGCATAAAAGAGAAAACAAAGATTTGCATGAATGGA
CAAATAATT
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protein sequence of SMED30008969-orf-1

>SMED30008969-orf-1 ID=SMED30008969-orf-1|Name=SMED30008969-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=198bp
MSTLFGIVIFICTIEISLEELPTTSCPSSRPFQTLGIRCANFQEVCVKTN
DIKCKKFQNICAQCPPSNFSTLTYLNIENMKEQLKNNVKRTSSIFILLWI
IIAFNILMAILLILEIRFGIITKLFHRRKLSDEKQYISLKRAERYEKQYV
PIEREQRDDSNDSNIIILNKIDILTTNVNKLIKSIKEKTKICMNGQII
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
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..19
score: 0.662
NoneNo IPR availableTMHMMTMhelixcoord: 94..116