SMED30010024

Overview
NameSMED30010024
Smed IDSMED30010024
Length (bp)513
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 SMED30010024 (SMED30010024) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30010024 (SMED30010024) 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




SMED30010024

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
pharynxSMED30010024SMESG000038072.1 dd_Smed_v4_13847_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30010024SMESG000038072.1 dd_Smed_v4_13847_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30010024SMESG000038072.1 dd_Smed_v4_13847_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30010024SMESG000038072.1 dd_Smed_v6_13847_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30010024 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000552:102623..108238 -2485
Homology
BLAST of SMED30010024 vs. TrEMBL
Match: A0A1I8IR91 (WD_REPEATS_REGION domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 55.4546 bits (132), Expect = 3.845e-6
Identity = 38/169 (22.49%), Postives = 75/169 (44.38%), Query Frame = 1
Query:    1 GKLLCIGIVNADLKMFSVLDQGAFCRHMPQLEFQ-NSKDVVRIDWTLDSQVFRTEDIQFNNKIWLIYPKTKEIGAEKNSHMDFISDNCLVTFKNLSLWRSPLINE---LTAVNKGGNDDFVVYGTSNGAMGLVNLLKTDDPVDGEQMCFNNGPVKHLSVSFDNTYVLSS 495
            G LL +G  +  + +FSV + G   R   +   + +S  V+ +DW  D  V RT+      K+W +     ++  E  S + F ++ C ++F +++ W+ P +     L    +    D +  G  NG + L       +   G     +   +  ++ +FD++ V+SS
Sbjct:   24 GNLLALGAEDGSVFVFSVEENGLMYRRYREGAVKGHSAPVLCLDWATDCAVLRTQSADLVTKLWSV-SSLAQVSQEDASDIRFATETCYLSFNHVAAWQ-PYVGTDRGLVCAARSNTADKLCVGDDNGHLTLYRFPPHPELAQGISAPAHVRALHSVAFTFDDSAVISS 190          
BLAST of SMED30010024 vs. Planmine SMEST
Match: SMESG000038072.1 (SMESG000038072.1)

HSP 1 Score: 358.992 bits (920), Expect = 9.579e-119
Identity = 171/171 (100.00%), Postives = 171/171 (100.00%), Query Frame = 1
Query:    1 GKLLCIGIVNADLKMFSVLDQGAFCRHMPQLEFQNSKDVVRIDWTLDSQVFRTEDIQFNNKIWLIYPKTKEIGAEKNSHMDFISDNCLVTFKNLSLWRSPLINELTAVNKGGNDDFVVYGTSNGAMGLVNLLKTDDPVDGEQMCFNNGPVKHLSVSFDNTYVLSSCDDKSC 513
            GKLLCIGIVNADLKMFSVLDQGAFCRHMPQLEFQNSKDVVRIDWTLDSQVFRTEDIQFNNKIWLIYPKTKEIGAEKNSHMDFISDNCLVTFKNLSLWRSPLINELTAVNKGGNDDFVVYGTSNGAMGLVNLLKTDDPVDGEQMCFNNGPVKHLSVSFDNTYVLSSCDDKSC
Sbjct:  833 GKLLCIGIVNADLKMFSVLDQGAFCRHMPQLEFQNSKDVVRIDWTLDSQVFRTEDIQFNNKIWLIYPKTKEIGAEKNSHMDFISDNCLVTFKNLSLWRSPLINELTAVNKGGNDDFVVYGTSNGAMGLVNLLKTDDPVDGEQMCFNNGPVKHLSVSFDNTYVLSSCDDKSC 1003          
The following BLAST results are available for this feature:
BLAST of SMED30010024 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 SMED30010024 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 SMED30010024 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 SMED30010024 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 SMED30010024 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 SMED30010024 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 SMED30010024 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 SMED30010024 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A1I8IR913.845e-622.49WD_REPEATS_REGION domain-containing protein OS=Mac... [more]
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BLAST of SMED30010024 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 SMED30010024 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 SMED30010024 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 SMED30010024 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 SMED30010024 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 SMED30010024 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000038072.19.579e-119100.00SMESG000038072.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010024 ID=SMED30010024|Name=SMED30010024|organism=Schmidtea mediterranea sexual|type=transcript|length=513bp
GGAAAACTGCTCTGTATAGGAATCGTGAATGCTGATTTAAAAATGTTTTC
AGTCCTTGACCAAGGTGCGTTTTGCCGGCACATGCCACAGCTGGAATTCC
AGAATTCCAAGGACGTAGTGAGAATTGACTGGACTCTAGATTCCCAAGTG
TTTCGAACAGAAGACATACAGTTCAACAATAAAATATGGTTAATATATCC
AAAGACGAAAGAAATTGGAGCAGAAAAAAACTCTCATATGGATTTCATCT
CGGACAATTGTTTAGTGACATTCAAAAATTTAAGTTTGTGGCGGTCACCT
CTTATTAATGAGTTAACTGCTGTGAATAAGGGTGGGAATGATGATTTTGT
CGTTTATGGAACGTCAAATGGAGCTATGGGTTTGGTAAATTTGCTGAAAA
CCGATGATCCGGTCGACGGTGAACAAATGTGCTTTAATAATGGGCCGGTT
AAACATTTATCAGTATCATTTGATAATACTTACGTGTTGAGTTCGTGCGA
TGATAAGAGTTGT
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protein sequence of SMED30010024-orf-1

>SMED30010024-orf-1 ID=SMED30010024-orf-1|Name=SMED30010024-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=171bp
GKLLCIGIVNADLKMFSVLDQGAFCRHMPQLEFQNSKDVVRIDWTLDSQV
FRTEDIQFNNKIWLIYPKTKEIGAEKNSHMDFISDNCLVTFKNLSLWRSP
LINELTAVNKGGNDDFVVYGTSNGAMGLVNLLKTDDPVDGEQMCFNNGPV
KHLSVSFDNTYVLSSCDDKSC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR015943WD40/YVTN_repeat-like_dom_sf
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR015943WD40/YVTN repeat-like-containing domain superfamilyGENE3DG3DSA:2.130.10.10coord: 1..166
e-value: 8.1E-9
score: 36.5