SMED30031825

Overview
NameSMED30031825
Smed IDSMED30031825
Length (bp)905
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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Alignments
SMED30031825 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008461:15242..16146 +4525
Homology
BLAST of SMED30031825 vs. Planmine SMEST
Match: SMESG000062966.1 (SMESG000062966.1)

HSP 1 Score: 55.4546 bits (132), Expect = 6.248e-9
Identity = 47/212 (22.17%), Postives = 93/212 (43.87%), Query Frame = 1
Query:    4 QQEMTQHQLDKCWICKEKFDTYILVKVNSCSHTFHYVCMMMTMIDFLNENCPKCCEYYSYVEFFVEKSRVKVKPLQRES-GVFIFHFYM-EKEKILGISSLFIKKYFAKPYILQIKVRNTPFRECVKVGKDFTVTHKHYNLLPFQKPLQ-----NVFLDFDFNAEFDVLDVKFKLFHHNEKLICLINFYGPFHEEFAKMQSTNVIERFARSL 618
            QQ +  +  D C IC +  +T   ++ N+C+H +HY C++  +       CP C   + Y +            ++R + G+ I+  Y  E   ++GI  L IKK    P ++ + V  T F +         +T K +  +    P++     N    F+ + E  ++D+K  L   ++++  L  FY   + +F++   +  +E   R +
Sbjct:   11 QQILQDNDEDLCPICLDTIETDRAIQTNNCNHLYHYNCVIDCVKVASLIKCPICRGVFKYFQPSAASIPTTNIIMKRNNEGIAIWQLYFDENRSVIGIECLRIKKNSVFPIVVDVTVSKTKFPKIF-----LLITDKSFREIVGTLPIEFSRTKNYKFKFNLSREMKIIDMKSSLLCTDKEISILTRFYFEKNGDFSEFPMSCELESIFRDV 217          
The following BLAST results are available for this feature:
BLAST of SMED30031825 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 SMED30031825 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 SMED30031825 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 SMED30031825 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 SMED30031825 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 SMED30031825 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 SMED30031825 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 SMED30031825 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 SMED30031825 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 SMED30031825 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 SMED30031825 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 SMED30031825 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 SMED30031825 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 SMED30031825 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000062966.16.248e-922.17SMESG000062966.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031825 ID=SMED30031825|Name=SMED30031825|organism=Schmidtea mediterranea sexual|type=transcript|length=905bp
CTACAACAAGAAATGACCCAACATCAACTTGATAAATGCTGGATTTGCAA
GGAAAAGTTTGACACATATATTCTCGTAAAAGTTAATTCATGTTCTCATA
CTTTTCATTATGTATGTATGATGATGACAATGATTGACTTTCTTAACGAA
AATTGTCCGAAATGTTGCGAATATTATAGCTATGTGGAGTTTTTTGTGGA
AAAGTCCAGAGTTAAAGTAAAGCCTTTGCAAAGAGAAAGTGGTGTTTTTA
TTTTTCATTTTTATATGGAAAAGGAAAAGATTCTAGGAATTAGTTCATTA
TTTATAAAGAAATACTTTGCTAAACCATATATCTTACAGATCAAAGTCCG
CAATACTCCATTTCGAGAATGCGTTAAAGTTGGTAAAGATTTCACTGTCA
CTCACAAACATTATAATTTGTTACCATTTCAAAAACCCTTACAAAATGTC
TTTCTTGATTTCGATTTTAATGCTGAATTCGATGTTTTGGATGTTAAATT
CAAATTGTTTCACCACAATGAAAAATTGATTTGTTTGATTAATTTCTACG
GTCCTTTTCACGAAGAATTTGCCAAAATGCAATCGACAAACGTTATTGAA
AGATTTGCACGAAGTCTTACCAATATTTTAGTTAAACCTAAATCATTTTA
ATTAAATTTAGAGTTTATATGATAAATTATTTTTAATAAATTTGTTTAAA
TAGTCGTCTCCTTTGTAATAACAATGATTGGAAATCAAGTAGTATTTCTA
TGCATAAATAATGGTGGTAATGAAATCAAGTATTTCGATATTTCTTGTAA
TCACTATTTCATTGCAAAATAATTTCATTATTATAATAATTATAATAAGA
TAATAATTATTATATAAGATAATAATTATTTATTCTTATGTCATTTCGAA
CTAAC
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protein sequence of SMED30031825-orf-1

>SMED30031825-orf-1 ID=SMED30031825-orf-1|Name=SMED30031825-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=217bp
LQQEMTQHQLDKCWICKEKFDTYILVKVNSCSHTFHYVCMMMTMIDFLNE
NCPKCCEYYSYVEFFVEKSRVKVKPLQRESGVFIFHFYMEKEKILGISSL
FIKKYFAKPYILQIKVRNTPFRECVKVGKDFTVTHKHYNLLPFQKPLQNV
FLDFDFNAEFDVLDVKFKLFHHNEKLICLINFYGPFHEEFAKMQSTNVIE
RFARSLTNILVKPKSF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR001841Znf_RING
IPR013083Znf_RING/FYVE/PHD
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0008270zinc ion binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001841Zinc finger, RING-typeSMARTSM00184ring_2coord: 13..55
e-value: 0.0066
score: 25.7
IPR001841Zinc finger, RING-typePROSITEPS50089ZF_RING_2coord: 13..55
score: 10.542
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 1..62
e-value: 3.4E-6
score: 28.2
NoneNo IPR availableSUPERFAMILYSSF57850RING/U-boxcoord: 12..61