SMED30035637

Overview
NameSMED30035637
Smed IDSMED30035637
Length (bp)559
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




SMED30035637

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
head regionSMED30035637SMESG000065407.1 SmedASXL_068778SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
head regionSMED30035637SMESG000065407.1 SmedASXL_044607SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
head regionSMED30035637SMESG000065407.1 dd_Smed_v6_56774_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
SMED30035637 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004396:17085..17643 +2732
v31.004396:14824..15382 +2723
v31.011437:15343..15901 -2001
Homology
BLAST of SMED30035637 vs. Planmine SMEST
Match: SMESG000065407.1 (SMESG000065407.1)

HSP 1 Score: 365.54 bits (937), Expect = 1.896e-130
Identity = 179/186 (96.24%), Postives = 180/186 (96.77%), Query Frame = 1
Query:    1 QDIYSRIIAPSCLLNVMENITINVSDVSSTKCGTLCSEKGKLCSGYLLRSFGCVSYVNEITLTTFKSCSSNNATFYKKRFKNDQDDYLAVKNIMINCNPPYSYSTADSLCRASNSMLAELTSPRTYQAALKWATNFGGPIWVGASCTSGPTNSTACYTWNISKQPFNATMWINNQPANIAGPAYVK 558
            QDIYSRIIAPSCLLNVMENITINVSDVSSTKCGT CSEKGKLCSGYLL SFGCVSYVNEITLTTFKSCSSNN TFYKKRFKNDQDDYL VKNIMINCNPPYS STADSLCRASNSMLAELTSPRTYQAALKWATNFGGPIWVGASCTSGPTNSTACYTWNISKQPFNATMWI+NQPANIAG AYVK
Sbjct:   17 QDIYSRIIAPSCLLNVMENITINVSDVSSTKCGTWCSEKGKLCSGYLLSSFGCVSYVNEITLTTFKSCSSNNVTFYKKRFKNDQDDYLVVKNIMINCNPPYSSSTADSLCRASNSMLAELTSPRTYQAALKWATNFGGPIWVGASCTSGPTNSTACYTWNISKQPFNATMWISNQPANIAGLAYVK 202          
BLAST of SMED30035637 vs. Planmine SMEST
Match: SMESG000032282.1 (SMESG000032282.1)

HSP 1 Score: 65.4698 bits (158), Expect = 3.155e-13
Identity = 44/167 (26.35%), Postives = 86/167 (51.50%), Query Frame = 1
Query:   28 PSCLLNVMENITINVSDVSSTKCGTLCSEKGKLCSGYLLRSFGCVSYVNEITLTTFKSCSSNNATFYKKRFKNDQDDYLAVKNIMINCNPPYSYSTADSLCRASNSMLAELTSPRTYQAALKWATNFGGPIWVGASCTSGPTNSTACYTWNISKQPFNATMWINNQP 528
            PSC+++++   T  ++   S  C  +C+     C+G+++    C+ ++NE+ L+  +SCSS++  FY+K F+N  +D+LAVK    +     + + A+S+C+ +N +LAE+ +   +              WVG     G   +   + W  S +P N T + + +P
Sbjct:    4 PSCVIDMINTKTHQLNRFGSVPCSLICNSDLH-CAGFIVNGNSCIIFINEVILSQSQSCSSSSVIFYRKVFQNKMEDFLAVK-YYFSLLTIINGANANSICQNNNGILAEVETSAAFNKVKGMCL---VESWVGGYQIPGSVGANG-WVWKSSNRPINMTYFSDGKP 164          
The following BLAST results are available for this feature:
BLAST of SMED30035637 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 SMED30035637 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 SMED30035637 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 SMED30035637 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 SMED30035637 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 SMED30035637 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 SMED30035637 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 SMED30035637 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 SMED30035637 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 SMED30035637 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 SMED30035637 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 SMED30035637 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 SMED30035637 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 SMED30035637 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000065407.11.896e-13096.24SMESG000065407.1[more]
SMESG000032282.13.155e-1326.35SMESG000032282.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035637 ID=SMED30035637|Name=SMED30035637|organism=Schmidtea mediterranea sexual|type=transcript|length=559bp
CAGGATATTTATTCAAGGATAATAGCTCCAAGTTGCCTGTTAAATGTCAT
GGAGAACATCACCATTAATGTTAGTGACGTAAGCTCTACCAAATGTGGTA
CTTTGTGTTCTGAGAAAGGTAAGTTATGTTCAGGATATTTATTGCGTTCA
TTCGGCTGCGTCAGCTACGTAAATGAGATCACGTTGACCACATTCAAAAG
TTGCTCGAGTAATAATGCCACATTTTATAAGAAAAGATTCAAGAATGATC
AAGATGATTACTTGGCAGTTAAGAACATAATGATTAATTGCAATCCACCT
TATTCCTACTCAACTGCCGATTCATTATGCAGAGCGTCAAACTCAATGCT
TGCTGAACTTACAAGTCCCAGAACCTATCAAGCTGCTCTAAAGTGGGCAA
CAAATTTTGGCGGTCCAATTTGGGTTGGAGCTTCTTGTACGTCCGGACCG
ACAAATTCCACAGCATGTTATACTTGGAACATATCGAAACAACCTTTCAA
TGCAACAATGTGGATAAACAATCAGCCAGCAAACATTGCAGGCCCAGCAT
ATGTTAAAG
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protein sequence of SMED30035637-orf-1

>SMED30035637-orf-1 ID=SMED30035637-orf-1|Name=SMED30035637-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=186bp
QDIYSRIIAPSCLLNVMENITINVSDVSSTKCGTLCSEKGKLCSGYLLRS
FGCVSYVNEITLTTFKSCSSNNATFYKKRFKNDQDDYLAVKNIMINCNPP
YSYSTADSLCRASNSMLAELTSPRTYQAALKWATNFGGPIWVGASCTSGP
TNSTACYTWNISKQPFNATMWINNQPANIAGPAYVK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR016186C-type_lectin-like/link_sf
IPR016187CTDL_fold