SMED30015450

Overview
NameSMED30015450
Smed IDSMED30015450
Length (bp)1594
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



SMED30015450

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30015450 SmedASXL_062850SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30015450 SmedASXL_062850SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30015450 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002010:13515..16200 +4845
Homology
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BLAST of SMED30015450 vs. Planmine SMEST
Match: SMESG000056267.1 (SMESG000056267.1)

HSP 1 Score: 82.4185 bits (202), Expect = 4.023e-16
Identity = 40/56 (71.43%), Postives = 42/56 (75.00%), Query Frame = -2 
Query: 1426 GAIGLGRVPIPTLIDSWI*YYGQSREPAMPDLVLFFSSSYECKKKITSNILTQMSQ 1593
            GAI  GRVPIPTLID WI  YGQ+REPAM DL+ FF S   CK KITS IL QMSQ
Sbjct:  159 GAIRFGRVPIPTLIDEWIEQYGQNREPAMLDLMQFFISCCGCKGKITSEILAQMSQ 214
The following BLAST results are available for this feature:
BLAST of SMED30015450 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 SMED30015450 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 SMED30015450 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 SMED30015450 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 SMED30015450 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 SMED30015450 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 SMED30015450 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 SMED30015450 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 SMED30015450 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 SMED30015450 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 SMED30015450 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 SMED30015450 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 SMED30015450 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 SMED30015450 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000056267.14.023e-1671.43SMESG000056267.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015450 ID=SMED30015450|Name=SMED30015450|organism=Schmidtea mediterranea sexual|type=transcript|length=1594bp
ATCAAATGTGACTGAAGGAATACCTGCACGAAAAATGAAATAAATTTTAC
AAATATTCCATGCATAGCAGTTAAAATAATTACAAATCAAAAAATATTAA
GTCCCAAAACCGGAAATTACTCGAGATTATCAAAATTTCCGGTTACCTAA
ATACTAATTGAAAAAGCAAATAAATGGATCAAAAAGATTTAATTATTTAA
TTAAAATAACGTGAAAGCAAAAAAGTGAAACTCAAACCAATTATTCGGCC
CTATTTAAGTTGACACGGAAATTACGTTTTGCTTTGTAATTTAATTTCGC
AGCTTTGTTTGATCACATTTGAGTGCCACTTTAGTCCATTTGAGCCATGT
TTAAGCCCCATCACATCTTCCAAACTAAATATATGATTCTATGACTCAAG
ATACCTTATCTTGGAAAAAAGATTTACATGGTATTCTTACAGAAATTTCC
GTGCAATATTTCAAATCCAGATTTATACTCCTAAGAACAAATTCTTGATC
AGCATTCATGTCTTTGGAAATGTTTGATTTTCTCATTCGCAACCACTCAG
AAATGACAAAAAGAAATTTTTGAGAAAGTTAATTGGTTACAAAACTCAAT
ATGGGTGCTTGTATTGTTAGCAGAAATGTATCGTTCTATTTATACTGTAC
TTTACATCCATTTCTTCGACGTCAGAAGTCAGTATTGGGCCCAACTCAAT
TCACTCGAGAAAGCTTTCTTGCTGTTGTTTATAGGTCAAACTCGACCACC
TCAAGGCTTACGTTTGATTTTGAGGCTTGGCAATTTTCTCCATATTCTAG
TTTCTCACTACATTGGGGCCACTCCTTGTCACCCGGCGAGATCACCTTGT
TGTATAACACATCTCACAACGCTGGACTGAGGCATGCGGAAGCCTCGTTA
TCTAATTGAGTGAAATCTCCTCTCATCGGATTTCTGATGTTTATGTTGTT
CTCTGTCTGTTGAATGGATTTTTTGTTGCATGGTTTAATTCTGACACGGT
ATGTTTATTTATCCTCTGTACCTCGGTCTCGTCTTCACTTTCGTTTTNTN
TGNTNNNATNAAATNANNNNNNTNNNNNNNNNNNATNNTCANANNTNTNC
NATTAGNCNTNNNTNACGATTTTTACGGTTTTATAAAAATGAATNNNNNN
NNNNTNANNNNNTNNNNTTACAATATTTATTNTANNATAGCATTAATATT
GCTAATATAATGCAAGTGTAATTTAGATATCTGCTATTCCAAACGGCATG
TTATTAAATTGTTTTGTTTGTTCTTCGTTGAAAATGTAGTTTTAATTTTC
GGTAATACGCGTTTCCAGGTTCAATTGTCGAAAAATATTTCGCACCATTT
AATATATACATTCAGTAATTCATTCATGTTATATTATTCCGTTGATGATT
TGTGCTAATTGTTCTTGTAAAAACATTGAGACATCTGAGTAAGTATGTTT
GAAGTTATCTTCTTTTTACATTCATAGGATGAGCTGAAAAAGAGAACTAA
ATCCGGCATCGCTGGCTCACGACTTTGGCCATAATATCATATCCAACTAT
CAATTAGAGTTGGAATTGGAACTCTTCCTAATCCTATAGCACCA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..21
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..35