SMED30020582

Overview
NameSMED30020582
Smed IDSMED30020582
Length (bp)565
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30020582

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30020582h1SMcG0000942 PL08001A1E08smed_ncbi_20240424PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30020582h1SMcG0000942 PL08001A1E08smed_ncbi_20240424PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
secretory cellSMED30020582h1SMcG0000942 PL08001A1E08smed_ncbi_20240424PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30020582h1SMcG0000942 PL08001A1E08smed_ncbi_20240424PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
testis primordiumSMED30020582h1SMcG0000942 PL06004B1B10_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism juvenile stagecDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020582 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007562:18626..19190 +2825
Homology
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BLAST of SMED30020582 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: 43.5134 bits (101), Expect = 4.948e-6
Identity = 17/29 (58.62%), Postives = 23/29 (79.31%), Query Frame = 2 
Query:    2 WFVGEGMEEAEFTEAKENMVGLIEDYRSI 88
            W+VGEGMEE EFTEA+E++  L +DY  +
Sbjct:   42 WYVGEGMEEGEFTEAREDLAALEKDYEEV 70
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BLAST of SMED30020582 vs. Ensembl Celegans
Match: tba-9 (Tubulin alpha chain [Source:UniProtKB/TrEMBL;Acc:Q20221])

HSP 1 Score: 45.4394 bits (106), Expect = 8.554e-6
Identity = 17/34 (50.00%), Postives = 25/34 (73.53%), Query Frame = 2 
Query:    2 WFVGEGMEEAEFTEAKENMVGLIEDYRSIEIHPG 103
            W+VGEGMEE EF+EA+E++  L +DY  + +  G
Sbjct:  412 WYVGEGMEEGEFSEAREDLAALEKDYEEVGLDAG 445
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BLAST of SMED30020582 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: 44.2838 bits (103), Expect = 4.358e-6
Identity = 17/26 (65.38%), Postives = 21/26 (80.77%), Query Frame = 2 
Query:    2 WFVGEGMEEAEFTEAKENMVGLIEDY 79
            W+VGEGMEE EFTEA+E++  L  DY
Sbjct:  408 WYVGEGMEEGEFTEAREDLAALERDY 433
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BLAST of SMED30020582 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: 44.2838 bits (103), Expect = 4.603e-6
Identity = 17/26 (65.38%), Postives = 21/26 (80.77%), Query Frame = 2 
Query:    2 WFVGEGMEEAEFTEAKENMVGLIEDY 79
            W+VGEGMEE EFTEA+E++  L  DY
Sbjct:  408 WYVGEGMEEGEFTEAREDLAALERDY 433
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BLAST of SMED30020582 vs. Ensembl Medaka
Match: ENSORLT00000020148.2 (protein O-fucosyltransferase 2 [Source:NCBI gene;Acc:100125468])

HSP 1 Score: 45.8246 bits (107), Expect = 9.486e-6
Identity = 18/31 (58.06%), Postives = 24/31 (77.42%), Query Frame = 2 
Query:    2 WFVGEGMEEAEFTEAKENMVGLIEDYRSIEI 94
            W+VGEGMEE EF+EA+E+M  L +DY  + I
Sbjct:  439 WYVGEGMEEGEFSEAREDMAALEKDYEEVGI 469
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BLAST of SMED30020582 vs. Planmine SMEST
Match: SMESG000074897.1 (SMESG000074897.1)

HSP 1 Score: 245.743 bits (626), Expect = 2.729e-79
Identity = 119/119 (100.00%), Postives = 119/119 (100.00%), Query Frame = 2 
Query:    2 WFVGEGMEEAEFTEAKENMVGLIEDYRSIEIHPGRNNTMDIEINLNMPQYTKNIQPQNFSEKNTQPLIKVEEVGNNVTQPNTPLPNAEEMTNDPPIIPPNSDKLTTVSRLTDEDSVSDI 358
            WFVGEGMEEAEFTEAKENMVGLIEDYRSIEIHPGRNNTMDIEINLNMPQYTKNIQPQNFSEKNTQPLIKVEEVGNNVTQPNTPLPNAEEMTNDPPIIPPNSDKLTTVSRLTDEDSVSDI
Sbjct:  408 WFVGEGMEEAEFTEAKENMVGLIEDYRSIEIHPGRNNTMDIEINLNMPQYTKNIQPQNFSEKNTQPLIKVEEVGNNVTQPNTPLPNAEEMTNDPPIIPPNSDKLTTVSRLTDEDSVSDI 526
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BLAST of SMED30020582 vs. Planmine SMEST
Match: SMESG000009421.1 (SMESG000009421.1)

HSP 1 Score: 47.7506 bits (112), Expect = 1.623e-6
Identity = 21/36 (58.33%), Postives = 24/36 (66.67%), Query Frame = 2 
Query:    2 WFVGEGMEEAEFTEAKENMVGLIEDYRSIEIHPGRN 109
            W+VGEGMEE EF EAK+ M  LI+DY  I    G N
Sbjct:  406 WYVGEGMEEGEFNEAKDEMTSLIQDYEEIASDEGGN 441
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BLAST of SMED30020582 vs. Planmine SMEST
Match: SMESG000010934.1 (SMESG000010934.1)

HSP 1 Score: 46.595 bits (109), Expect = 4.609e-6
Identity = 18/29 (62.07%), Postives = 23/29 (79.31%), Query Frame = 2 
Query:    2 WFVGEGMEEAEFTEAKENMVGLIEDYRSI 88
            W+VGEGMEE EFTEA+E+   L EDY+ +
Sbjct:  381 WYVGEGMEEGEFTEAREDFSILQEDYKCV 409
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BLAST of SMED30020582 vs. Planmine SMEST
Match: SMESG000027786.1 (SMESG000027786.1)

HSP 1 Score: 45.8246 bits (107), Expect = 6.142e-6
Identity = 19/30 (63.33%), Postives = 24/30 (80.00%), Query Frame = 2 
Query:    2 WFVGEGMEEAEFTEAKENMVGLIEDYRSIE 91
            W+VGEGMEE EF EAK+ + GLI+D+  IE
Sbjct:  374 WYVGEGMEEGEFNEAKDEIDGLIKDFEEIE 403
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BLAST of SMED30020582 vs. Planmine SMEST
Match: SMESG000069843.1 (SMESG000069843.1)

HSP 1 Score: 44.669 bits (104), Expect = 6.655e-6
Identity = 17/31 (54.84%), Postives = 24/31 (77.42%), Query Frame = 2 
Query:    2 WFVGEGMEEAEFTEAKENMVGLIEDYRSIEI 94
            W+VGEGMEE EF+EA+E++  L +DY  + I
Sbjct:  117 WYVGEGMEEGEFSEAREDLAALEKDYEKVGI 147
The following BLAST results are available for this feature:
BLAST of SMED30020582 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 SMED30020582 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 2
Match NameE-valueIdentityDescription
Y19D2B.14.948e-658.62pep chromosome:WBcel235:II:10922672:10922974:-1 ge... [more]
tba-98.554e-650.00Tubulin alpha chain [Source:UniProtKB/TrEMBL;Acc:... [more]
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BLAST of SMED30020582 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 SMED30020582 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 SMED30020582 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 SMED30020582 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 SMED30020582 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 SMED30020582 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 SMED30020582 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 SMED30020582 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 SMED30020582 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 2
Match NameE-valueIdentityDescription
TUB14.358e-665.38Alpha-tubulin; associates with beta-tubulin (Tub2p... [more]
TUB34.603e-665.38Alpha-tubulin; associates with beta-tubulin (Tub2p... [more]
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BLAST of SMED30020582 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 SMED30020582 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSORLT00000020148.29.486e-658.06protein O-fucosyltransferase 2 [Source:NCBI gene;A... [more]
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BLAST of SMED30020582 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000074897.12.729e-79100.00SMESG000074897.1[more]
SMESG000009421.11.623e-658.33SMESG000009421.1[more]
SMESG000010934.14.609e-662.07SMESG000010934.1[more]
SMESG000027786.16.142e-663.33SMESG000027786.1[more]
SMESG000069843.16.655e-654.84SMESG000069843.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020582 ID=SMED30020582|Name=SMED30020582|organism=Schmidtea mediterranea sexual|type=transcript|length=565bp
TTGGTTTGTTGGCGAAGGAATGGAAGAAGCGGAATTTACTGAAGCAAAAG
AAAATATGGTCGGCTTAATAGAAGATTATAGGTCAATTGAAATTCATCCA
GGTCGAAATAATACGATGGATATAGAAATAAATTTAAATATGCCACAATA
TACGAAAAACATTCAACCCCAAAATTTTTCTGAAAAGAATACTCAACCAC
TAATTAAAGTTGAAGAAGTTGGCAATAACGTTACCCAACCAAATACACCT
TTGCCAAACGCAGAAGAAATGACAAATGATCCTCCAATTATTCCGCCAAA
CTCCGACAAGCTTACCACTGTGTCACGCCTAACTGACGAAGATTCAGTTT
CAGACATCTAAATGGAAAATCGAAACGAATTCCTCATCCTATTTGTTACC
TTTTATCAGATTTAATTTTTTTGAAAATATTTAACAAAATATTTTTAATT
GAAATCAAAAAATATCCTAATCAAGATATAAGAGAAAATTTTAAAAAAAA
TTCACAATTAATCAAAAGTTCCATATAATCATTATTTCATTTGGAAAATG
ATTCTTAAAATATTC
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protein sequence of SMED30020582-orf-1

>SMED30020582-orf-1 ID=SMED30020582-orf-1|Name=SMED30020582-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=120bp
WFVGEGMEEAEFTEAKENMVGLIEDYRSIEIHPGRNNTMDIEINLNMPQY
TKNIQPQNFSEKNTQPLIKVEEVGNNVTQPNTPLPNAEEMTNDPPIIPPN
SDKLTTVSRLTDEDSVSDI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000105secretory cell
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR023123Tubulin_C
IPR008280Tub_FtsZ_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..40
e-value: 4.3E-10
score: 41.4
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 73..88
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 73..119
IPR008280Tubulin/FtsZ, C-terminalSUPERFAMILYSSF55307Tubulin C-terminal domain-likecoord: 1..29