SMED30022764

Overview
NameSMED30022764
Smed IDSMED30022764
Length (bp)598
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 SMED30022764 (SMED30022764) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022764 (SMED30022764) 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



SMED30022764

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30022764SMESG000049990.1 SMESG000010934.1 dd_Smed_v4_64358_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022764SMESG000049990.1 SMESG000010934.1 dd_Smed_v4_64358_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30022764SMESG000049990.1 SMESG000010934.1 dd_Smed_v4_64358_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30022764 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.013691:14988..15585 -2990
Homology
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BLAST of SMED30022764 vs. Ensembl Celegans
Match: Y19D2B.1 (pep chromosome:WBcel235:II:10922672:10922974:-1 gene:WBGene00012489.1 transcript:Y19D2B.1.1 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:Y19D2B.1)

HSP 1 Score: 44.2838 bits (103), Expect = 2.347e-6
Identity = 23/40 (57.50%), Postives = 27/40 (67.50%), Query Frame = -2 
Query:  478 VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKE 597
            VGEGMEEGEFTEARED + L++DY+ V       L  D E
Sbjct:   44 VGEGMEEGEFTEAREDLAALEKDYEEVGADSNEGLEEDGE 83
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BLAST of SMED30022764 vs. Ensembl Fly
Match: alphaTub85E (gene:FBgn0003886 transcript:FBtr0082087)

HSP 1 Score: 50.8322 bits (120), Expect = 1.915e-7
Identity = 25/40 (62.50%), Postives = 30/40 (75.00%), Query Frame = -2 
Query:  478 VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKE 597
            VGEGMEEGEF EARED + L++DY+ V    TTEL  D+E
Sbjct:  409 VGEGMEEGEFAEAREDLAALEKDYEEVGIDSTTELGEDEE 448
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BLAST of SMED30022764 vs. Ensembl Zebrafish
Match: tuba4l (tubulin, alpha 4 like [Source:ZFIN;Acc:ZDB-GENE-030131-5588])

HSP 1 Score: 47.3654 bits (111), Expect = 3.982e-6
Identity = 23/40 (57.50%), Postives = 30/40 (75.00%), Query Frame = -2 
Query:  478 VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKE 597
            VGEGMEEGEF+EARED + L++DY+ VA   T +   D+E
Sbjct:  408 VGEGMEEGEFSEAREDMAALEKDYEEVAADSTDDCGEDEE 447
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BLAST of SMED30022764 vs. Ensembl Zebrafish
Match: tuba4l (tubulin, alpha 4 like [Source:ZFIN;Acc:ZDB-GENE-030131-5588])

HSP 1 Score: 47.3654 bits (111), Expect = 4.003e-6
Identity = 23/40 (57.50%), Postives = 30/40 (75.00%), Query Frame = -2 
Query:  478 VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKE 597
            VGEGMEEGEF+EARED + L++DY+ VA   T +   D+E
Sbjct:  415 VGEGMEEGEFSEAREDMAALEKDYEEVAADSTDDCGEDEE 454
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BLAST of SMED30022764 vs. UniProt/SwissProt
Match: sp|P06604|TBA2_DROME (Tubulin alpha-2 chain OS=Drosophila melanogaster OX=7227 GN=alphaTub85E PE=1 SV=1)

HSP 1 Score: 50.8322 bits (120), Expect = 1.920e-6
Identity = 25/40 (62.50%), Postives = 30/40 (75.00%), Query Frame = -2 
Query:  478 VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKE 597
            VGEGMEEGEF EARED + L++DY+ V    TTEL  D+E
Sbjct:  409 VGEGMEEGEFAEAREDLAALEKDYEEVGIDSTTELGEDEE 448
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BLAST of SMED30022764 vs. Ensembl Yeast
Match: TUB1 (Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules; relative distribution to nuclear foci increases upon DNA replication stress; TUB1 has a paralog, TUB3, that arose from the whole genome duplication [Source:SGD;Acc:S000004550])

HSP 1 Score: 44.669 bits (104), Expect = 3.484e-6
Identity = 19/24 (79.17%), Postives = 21/24 (87.50%), Query Frame = -2 
Query:  526 VGEGMEEGEFTEAREDFSILQEDY 597
            VGEGMEEGEFTEARED + L+ DY
Sbjct:  410 VGEGMEEGEFTEAREDLAALERDY 433
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BLAST of SMED30022764 vs. Ensembl Yeast
Match: TUB3 (Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules; expressed at lower level than Tub1p; TUB3 has a paralog, TUB1, that arose from the whole genome duplication [Source:SGD;Acc:S000004593])

HSP 1 Score: 44.669 bits (104), Expect = 3.925e-6
Identity = 19/24 (79.17%), Postives = 21/24 (87.50%), Query Frame = -2 
Query:  526 VGEGMEEGEFTEAREDFSILQEDY 597
            VGEGMEEGEFTEARED + L+ DY
Sbjct:  410 VGEGMEEGEFTEAREDLAALERDY 433
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BLAST of SMED30022764 vs. Planmine SMEST
Match: SMESG000010934.1 (SMESG000010934.1)

HSP 1 Score: 291.582 bits (745), Expect = 8.677e-97
Identity = 158/158 (100.00%), Postives = 158/158 (100.00%), Query Frame = -2 
Query:  124 VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKEMVKNNISFENYSILSSDNKIYENFEDENIHLNKLNKDQKLSSTYDNCKLDDLGNYCIENSKNSDVIKKRPLKPEIKSVEFKTNDIIITXXXXXXXXXNKRLFNFLKLEDNTQSDISTL 597
            VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKEMVKNNISFENYSILSSDNKIYENFEDENIHLNKLNKDQKLSSTYDNCKLDDLGNYCIENSKNSDVIKKRPLKPEIKSVEFKTNDIIITEESNEERERNKRLFNFLKLEDNTQSDISTL
Sbjct:  383 VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKEMVKNNISFENYSILSSDNKIYENFEDENIHLNKLNKDQKLSSTYDNCKLDDLGNYCIENSKNSDVIKKRPLKPEIKSVEFKTNDIIITEESNEERERNKRLFNFLKLEDNTQSDISTL 540
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BLAST of SMED30022764 vs. Planmine SMEST
Match: SMESG000049990.1 (SMESG000049990.1)

HSP 1 Score: 213.001 bits (541), Expect = 6.066e-67
Identity = 106/114 (92.98%), Postives = 108/114 (94.74%), Query Frame = -2 
Query:  256 VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKEMVKNNISFENYSILSSDNKIYENFEDENIHLNKLNKDQKLSSTYDNCKLDDLGNYCIENSKNSDVIKKRPLKPE 597
            VGEGMEEGEF EAREDFSILQEDYKCVAE ETTELNNDKEMVKNNISFENYSILSSDNKIYENFEDENIHLNKLNKDQKLSSTYDNCKLDDLGNYCIENSKNSDVIKK+  +  
Sbjct:  369 VGEGMEEGEFAEAREDFSILQEDYKCVAEDETTELNNDKEMVKNNISFENYSILSSDNKIYENFEDENIHLNKLNKDQKLSSTYDNCKLDDLGNYCIENSKNSDVIKKKSFEAR 482
[Close]
BLAST of SMED30022764 vs. Planmine SMEST
Match: SMESG000049990.1 (SMESG000049990.1)

HSP 1 Score: 213.001 bits (541), Expect = 1.184e-65
Identity = 106/109 (97.25%), Postives = 107/109 (98.17%), Query Frame = -2 
Query:  271 VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKEMVKNNISFENYSILSSDNKIYENFEDENIHLNKLNKDQKLSSTYDNCKLDDLGNYCIENSKNSDVIKKR 597
            VGEGMEEGEF EAREDFSILQEDYKCVAE ETTELNNDKEMVKNNISFENYSILSSDNKIYENFEDENIHLNKLNKDQKLSSTYDNCKLDDLGNYCIENSKNSDVIKK+
Sbjct:  508 VGEGMEEGEFAEAREDFSILQEDYKCVAEDETTELNNDKEMVKNNISFENYSILSSDNKIYENFEDENIHLNKLNKDQKLSSTYDNCKLDDLGNYCIENSKNSDVIKKK 616
[Close]
BLAST of SMED30022764 vs. Planmine SMEST
Match: SMESG000079004.1 (SMESG000079004.1)

HSP 1 Score: 45.8246 bits (107), Expect = 9.173e-6
Identity = 24/44 (54.55%), Postives = 33/44 (75.00%), Query Frame = -2 
Query:  466 VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKEMVKN 597
            VGEGMEEGEF+EARED + L++DY+    G  TE+ N+ E+ +N
Sbjct:  410 VGEGMEEGEFSEAREDLAALEKDYE--EAGLDTEIVNEDELNEN 451
The following BLAST results are available for this feature:
BLAST of SMED30022764 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 SMED30022764 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 1
Match NameE-valueIdentityDescription
Y19D2B.12.347e-657.50pep chromosome:WBcel235:II:10922672:10922974:-1 ge... [more]
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BLAST of SMED30022764 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
alphaTub85E1.915e-762.50gene:FBgn0003886 transcript:FBtr0082087[more]
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BLAST of SMED30022764 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
tuba4l3.982e-657.50tubulin, alpha 4 like [Source:ZFIN;Acc:ZDB-GENE-03... [more]
tuba4l4.003e-657.50tubulin, alpha 4 like [Source:ZFIN;Acc:ZDB-GENE-03... [more]
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BLAST of SMED30022764 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 SMED30022764 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 SMED30022764 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|P06604|TBA2_DROME1.920e-662.50Tubulin alpha-2 chain OS=Drosophila melanogaster O... [more]
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BLAST of SMED30022764 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 SMED30022764 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 SMED30022764 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 SMED30022764 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 2
Match NameE-valueIdentityDescription
TUB13.484e-679.17Alpha-tubulin; associates with beta-tubulin (Tub2p... [more]
TUB33.925e-679.17Alpha-tubulin; associates with beta-tubulin (Tub2p... [more]
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BLAST of SMED30022764 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 SMED30022764 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 SMED30022764 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000010934.18.677e-97100.00SMESG000010934.1[more]
SMESG000049990.16.066e-6792.98SMESG000049990.1[more]
SMESG000049990.11.184e-6597.25SMESG000049990.1[more]
SMESG000079004.19.173e-654.55SMESG000079004.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022764 ID=SMED30022764|Name=SMED30022764|organism=Schmidtea mediterranea sexual|type=transcript|length=598bp
TTCAAAAATATGTATAAATTTATTAATGTTTTTACACAAAATTTGTTCAC
CCAATAAATCTTTGAAAAACTTATTTTCGCCGACACCAAATTGATGTGAA
TGAAACATAATAAAATTTACTCACAGTGTAGAAATATCCGACTGTGTATT
GTCTTCTAGTTTTAAAAAGTTAAATAATCTTTTATTTCTTTCTCTTTCTT
CATTGCTTTCTTCAGTGATAATTATATCGTTTGTTTTGAATTCAACGCTT
TTTATTTCTGGCTTCAAAGGACGTTTTTTAATGACGTCTGAATTCTTGGA
ATTTTCGATACAGTAATTTCCTAGATCGTCAAGTTTACAATTATCATAGG
TCGATGAAAGTTTCTGATCTTTATTAAGTTTGTTTAAATGAATATTTTCA
TCTTCGAAATTTTCATATATTTTGTTGTCTGATGATAATATACTGTAGTT
TTCAAAGCTGATATTGTTTTTAACCATTTCTTTATCGTTATTTAATTCAG
TCGTTTCGCCTTCTGCAACACATTTGTAATCTTCTTGAAGAATTGAAAAA
TCTTCTCTAGCCTCAGTGAATTCCCCTTCTTCCATTCCTTCGCCAACA
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protein sequence of SMED30022764-orf-1

>SMED30022764-orf-1 ID=SMED30022764-orf-1|Name=SMED30022764-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=159bp
VGEGMEEGEFTEAREDFSILQEDYKCVAEGETTELNNDKEMVKNNISFEN
YSILSSDNKIYENFEDENIHLNKLNKDQKLSSTYDNCKLDDLGNYCIENS
KNSDVIKKRPLKPEIKSVEFKTNDIIITEESNEERERNKRLFNFLKLEDN
TQSDISTL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR023123Tubulin_C
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR023123Tubulin, C-terminalGENE3DG3DSA:1.10.287.600coord: 1..28
e-value: 1.4E-8
score: 36.2