SMED30001228

Overview
NameSMED30001228
Smed IDSMED30001228
Length (bp)377
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



SMED30001228

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30001228h1SMcG0017299 SmedASXL_004658SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30001228h1SMcG0017299 SmedASXL_004658SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30001228h1SMcG0017299 SmedASXL_013852SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30001228h1SMcG0017299 SmedASXL_013852SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30001228h1SMcG0017299 SmedASXL_013853SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30001228h1SMcG0017299 SmedASXL_013853SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
cephalic gangliaSMED30001228h1SMcG0017299 dd_Smed_v4_18888_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30001228h1SMcG0017299 dd_Smed_v4_18888_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30001228h1SMcG0017299 dd_Smed_v4_18326_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001228h1SMcG0017299 dd_Smed_v4_16722_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30001228h1SMcG0017299 dd_Smed_v4_16722_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
SMED30001228 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000249:31853..32210 -1436
Homology
[Close]
BLAST of SMED30001228 vs. Planmine SMEST
Match: SMESG000034251.1 (SMESG000034251.1)

HSP 1 Score: 174.096 bits (440), Expect = 2.638e-51
Identity = 108/124 (87.10%), Postives = 110/124 (88.71%), Query Frame = -1 
Query:    3 SSKRESNKDSQQVIDKKELARKDKINEYEINIKDKNITDSKSQTETLLQTDNENPSQTGTKSQNERREPSNENLDEIKQEIKNLTIGNQVRRIEKVQNDFXXXXXXXXXXKNNQQDSQLSYMES 374
            S K+ESN D QQVID KE+ R DKINEYEIN KDKNI DSKSQT      DNENPSQTGTKSQNERREPSNENLDEIKQEIKNLTIGNQVRRIEKVQNDFKKKEIKKESEKNNQQDSQLSYMES
Sbjct:  817 SLKQESNVDLQQVIDDKEVVRIDKINEYEINKKDKNIIDSKSQT------DNENPSQTGTKSQNERREPSNENLDEIKQEIKNLTIGNQVRRIEKVQNDFKKKEIKKESEKNNQQDSQLSYMES 934

HSP 2 Score: 96.2857 bits (238), Expect = 4.255e-24
Identity = 55/76 (72.37%), Postives = 60/76 (78.95%), Query Frame = -1 
Query:  147 SSKRESNKDSQQVIDKKELARKDKINEYEINIKDKNITDSKSQTETLLQTDNENPSQTGTKSQNERREPSNENLDE 374
            S K+ESN D QQVID KE+ R DKINEYEIN KDKNI DSKSQTETLLQ DNE PSQT  KS NER E SNE +++
Sbjct:  369 SLKQESNVDLQQVIDDKEVVRIDKINEYEINKKDKNIIDSKSQTETLLQIDNEKPSQTIKKSSNERNESSNETVND 444
The following BLAST results are available for this feature:
BLAST of SMED30001228 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 SMED30001228 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 SMED30001228 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 SMED30001228 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 SMED30001228 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 SMED30001228 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 SMED30001228 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 SMED30001228 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 SMED30001228 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 SMED30001228 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 SMED30001228 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 SMED30001228 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 SMED30001228 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 SMED30001228 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000034251.12.638e-5187.10SMESG000034251.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001228 ID=SMED30001228|Name=SMED30001228|organism=Schmidtea mediterranea sexual|type=transcript|length=377bp
TTGCTTTCCATATAAGACAGCTGTGAATCTTGTTGGTTATTCTTTTCCGA
TTCTTTTTTTATTTCTTTCTTTTTAAAATCATTTTGGACTTTTTCAATAC
GTCTAACCTGATTACCAATCGTTAGATTTTTAATTTCCTGCTTGATTTCA
TCTAAATTTTCGTTCGAGGGTTCCCTTCTTTCATTTTGTGATTTCGTACC
AGTTTGCGAAGGGTTTTCATTGTCAGTTTGTAGTAATGTTTCAGTTTGTG
ATTTTGAGTCGGTAATGTTTTTATCCTTTATATTTATTTCATATTCGTTT
ATTTTATCTTTTCTCGCTAGTTCTTTTTTGTCGATGACTTGCTGTGAATC
CTTATTACTTTCTCTTTTAGAACTTTT
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protein sequence of SMED30001228-orf-1

>SMED30001228-orf-1 ID=SMED30001228-orf-1|Name=SMED30001228-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
KSSKRESNKDSQQVIDKKELARKDKINEYEINIKDKNITDSKSQTETLLQ
TDNENPSQTGTKSQNERREPSNENLDEIKQEIKNLTIGNQVRRIEKVQND
FKKKEIKKESEKNNQQDSQLSYMES
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 83..103
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 29..65
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 89..103
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 89..114
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 38..54