SMED30012843

Overview
NameSMED30012843
Smed IDSMED30012843
Length (bp)1325
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ 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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30012843 (SMED30012843) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012843 (SMED30012843) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 SMED30012843 (SMED30012843) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30012843 (SMED30012843) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30012843

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30012843h1SMcG0002456 Contig5150GPL15192PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30012843h1SMcG0002456 Contig5150GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30012843h1SMcG0001452 Contig5150GPL15192PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30012843h1SMcG0001452 Contig5150GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Smed sexual biotypeSMED30012843h1SMcG0001452 Contig1904GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30012843h1SMcG0001452 dd_Smed_v4_727_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30012843h1SMcG0001452 dd_Smed_v4_727_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30012843h1SMcG0001452 dd_Smed_v4_727_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30012843h1SMcG0001452 dd_Smed_v4_727_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30012843h1SMcG0001452 dd_Smed_v4_727_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30012843h1SMcG0001452 dd_Smed_v4_727_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30012843h1SMcG0001452 dd_Smed_v4_727_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30012843h1SMcG0001452 dd_Smed_v6_727_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30012843h1SMcG0001452 dd_Smed_v4_727_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
Alignments
SMED30012843 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007218:29853..34041 +6448
v31.015808:5629..9823 +6399
Homology
[Close]
BLAST of SMED30012843 vs. TrEMBL
Match: A0A212F1V6 (Adenylyl cyclase-associated protein OS=Danaus plexippus plexippus OX=278856 GN=KGM_215799 PE=3 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 4.295e-6
Identity = 33/96 (34.38%), Postives = 57/96 (59.38%), Query Frame = 3 
Query:   93 SCDLENLVKRLETLTSRLEKLPQL-------SESGDMKSVKSN---SSSVAINEYANLLSSELHHFLQISDKIGGDVKTQVHFLFDAFLSLLNYLH 350
            + DLE+L++RLE +TSRLE+LP L         S    +V+ +   + +++IN Y  L+   L  +LQ+S+++GGD+ T  + + +AF   L Y+ 
Sbjct:   59 AADLESLIERLERVTSRLERLPVLLSTTLTPPSSPTPLTVQIDLIETDNMSINGYQELMQGPLQSYLQLSNQLGGDIATHANLVNEAFQEQLRYIQ 154
[Close]
BLAST of SMED30012843 vs. Ensembl Nematostella
Match: EDO46368 (Adenylyl cyclase-associated protein [Source:UniProtKB/TrEMBL;Acc:A7RQH5])

HSP 1 Score: 48.1358 bits (113), Expect = 4.223e-6
Identity = 34/97 (35.05%), Postives = 54/97 (55.67%), Query Frame = 3 
Query:   90 MSCDLENLVKRLETLTSRLEKLPQLSESGDMKSVKSNSSSVAINEYANLLSSELHHFLQISDKIGGDVKTQVHFLFDAFLSLLNYLHAIKIIISLHE 380
            M+ +L+ LV RLE +TSRLE +   S SG     ++N   V+   Y   LS  +   L+IS +IGGDV +Q   +  AF +  ++L    +++S H+
Sbjct:    1 MAGNLDPLVVRLEAVTSRLEAMASKSGSGGSGGTEANEEIVSF--YDKFLSESVAKCLKISSEIGGDVGSQAKLVDQAFKAQRDFL----VLVSKHQ 91
[Close]
BLAST of SMED30012843 vs. Planmine SMEST
Match: SMESG000032321.1 (SMESG000032321.1)

HSP 1 Score: 128.642 bits (322), Expect = 1.297e-32
Identity = 74/86 (86.05%), Postives = 78/86 (90.70%), Query Frame = 3 
Query:   90 MSCDLENLVKRLETLTSRLEKLPQLSESGDMKSVKSNSSSVAINEYANLLSSELHHFLQISDKIGGDVKTQVHFLFDAFLSLLNYL 347
            MSCDLENLVKRLET+TSRLEKLPQLSESGDMKSVKSNSSSVAINEYANLLSSELHHFLQISDKIGGDVKTQ   +  AF + L +L
Sbjct:    1 MSCDLENLVKRLETITSRLEKLPQLSESGDMKSVKSNSSSVAINEYANLLSSELHHFLQISDKIGGDVKTQAALVEKAFSAQLEFL 86
The following BLAST results are available for this feature:
BLAST of SMED30012843 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012843 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012843 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012843 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012843 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012843 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012843 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012843 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A212F1V64.295e-634.38Adenylyl cyclase-associated protein OS=Danaus plex... [more]
back to top
BLAST of SMED30012843 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012843 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012843 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012843 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO463684.223e-635.05Adenylyl cyclase-associated protein [Source:UniPr... [more]
back to top
BLAST of SMED30012843 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30012843 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000032321.11.297e-3286.05SMESG000032321.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012843 ID=SMED30012843|Name=SMED30012843|organism=Schmidtea mediterranea sexual|type=transcript|length=1325bp
AAATTATTAACAAAAAAACATTTGTTTGTATAAACTAAATAAATAAATTT
AATATTTCATTTCTAGTTATTTCAGGAAAAGAAATAAAGATGTCCTGTGA
TTTAGAGAATTTAGTTAAAAGATTAGAAACTCTTACGAGCCGATTAGAAA
AACTACCCCAATTATCAGAAAGTGGTGATATGAAATCTGTTAAATCTAAT
TCAAGTAGCGTTGCTATTAACGAGTACGCAAATTTGTTAAGTAGTGAGTT
GCATCATTTTCTGCAAATCAGTGACAAAATTGGCGGAGATGTTAAAACTC
AGGTTCATTTTTTATTTGATGCATTTTTATCTCTACTAAATTATTTACAT
GCCATTAAAATTATTATTAGCCTGCATGAATTTTGCTTGATGTGATTAAT
TTTCATTGATTTATTATTAATAATAATATGTGAATCTATGTGTGCATTAA
TCTAAATCTGTCAATAGTTACACAATTTAGTTACGTATTTCATATTTTCA
TATAACGGACATTTTGATCATAAAATTTCTGCTTTTAACAAAAATATATA
ATCTATTTCGCATTCAAATTTCATTCTATTGAGAAAAAAACAGCATTTTT
ATTGATCTTATAGTATAGGTCCCAAAACTTTTCTGCATAAAATACATAAT
TATATTTTTATAGAAAAAAATAACATGTAGTGAGAAAATATAAAAAAGGG
TTTTGTCTATTTTGTGACTTTATTTACCACAAAAACAATTAAAACTGTAG
TATTTGTTATACGCTGAGTATTATAATTTTGTATTAGTTGCTCTTTGTGT
CTTGTCATTCCAGATCTGTTGCAAATATTTTTTATAACATTATATTTGTA
AAATAGTTTTCTTCTGGATTTTCTGTAGTAAAGTTGTTGATTGTCAAAGT
TCATTACACAGTTTCTGTTTGAATTTTGTCATTCAATTTTTTACATCAGA
AAATGTAATATAATCATCTACTATCGTCGACCCATAAATTTATAGCCTGT
CAAGTTTCCTATACCATTTTATACCCCGTTCCAAAGAAGGATTATAATGG
TCAAAAAGGCATAATGAATTATCAGTAATTGTAGCAATCTACAATTCTAA
ATTTTCGTACTGTTTTTTTCTTAATTTTCCACTTAAAGATTACAAACTAC
TGTTACTTTCCCTGTCAATAATATTACCGTTGTTTAGTTGTACAACAATA
ACATCTTCGGGGTTGTATTTGCGATTTTTTTAAGTGTTCCACCTAAATGA
GTTCTTGTCCAAGAAGTTGCTGTGTAGTCGGTGTTAAACGGATCTTTATC
TTAAAAATAATAATCCTCCTATAGG
back to top

protein sequence of SMED30012843-orf-1

>SMED30012843-orf-1 ID=SMED30012843-orf-1|Name=SMED30012843-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
MSCDLENLVKRLETLTSRLEKLPQLSESGDMKSVKSNSSSVAINEYANLL
SSELHHFLQISDKIGGDVKTQVHFLFDAFLSLLNYLHAIKIIISLHEFCL
M*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR013992Adenylate_cyclase-assoc_CAP_N
IPR018106CAP_CS_N
Vocabulary: biological process
TermDefinition
GO:0007010cytoskeleton organization
GO:0000902cell morphogenesis
Vocabulary: molecular function
TermDefinition
GO:0003779actin binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013992Adenylate cyclase-associated CAP, N-terminalPFAMPF01213CAP_Ncoord: 7..88
e-value: 1.0E-11
score: 44.9
IPR018106CAP, conserved site, N-terminalPROSITEPS01088CAP_1coord: 8..20