SMED30006968

Overview
NameSMED30006968
Smed IDSMED30006968
Length (bp)588
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



SMED30006968

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Category 3 cellSMED30006968 dd_Smed_v4_55350_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30006968 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001820:33149..33731 +2446
v31.000673:7033..7877 +2278
v31.000996:14126..14895 +1899
v31.001375:87005..87782 -1719
v31.002642:67014..67791 -1718
v31.009854:7585..8320 +1627
Homology
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BLAST of SMED30006968 vs. Planmine SMEST
Match: SMESG000026049.1 (SMESG000026049.1)

HSP 1 Score: 154.451 bits (389), Expect = 2.744e-46
Identity = 74/115 (64.35%), Postives = 91/115 (79.13%), Query Frame = 2 
Query:  206 REPGRNPARESRHRAEYILARLEERQRQTNWQVAMARLHLAKINEDIATGRIPSTDGYAPSYGISYELDDSMLGQLSRSMNVVIPKKLLPKDMRDTDRSLIERQYHSYAPERTRW 550
            R P RNPAR+++ RAE+ LAR+E  QRQTNWQV MAR  LAKIN DIA GRIP+TD YAP+YGIS+ELDD    + +  M+VVIP++LLPKDM+D+DRS  ERQ HSYA  R+R+
Sbjct:   38 RNPARNPARKTQQRAEFTLARIELHQRQTNWQVVMARRRLAKINADIAAGRIPNTDRYAPAYGISFELDDPAFAEPTMLMDVVIPRRLLPKDMQDSDRSPAERQEHSYARGRSRY 152
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BLAST of SMED30006968 vs. Planmine SMEST
Match: SMESG000060158.1 (SMESG000060158.1)

HSP 1 Score: 132.494 bits (332), Expect = 5.793e-40
Identity = 61/97 (62.89%), Postives = 79/97 (81.44%), Query Frame = 2 
Query:  206 REPGRNPARESRHRAEYILARLEERQRQTNWQVAMARLHLAKINEDIATGRIPSTDGYAPSYGISYELDDSMLGQLSRSMNVVIPKKLLPKDMRDTD 496
            REPGR PARE+R RAE+ L RLE  Q+QTNWQV++AR  L ++N DIA GRIPSTD Y+P+YG+SYELDDS L ++   MNVVIP++LLP++M++ D
Sbjct:    5 REPGRKPAREARKRAEFTLVRLEIHQKQTNWQVSIARRRLDRVNVDIAAGRIPSTDDYSPNYGVSYELDDSALVEMYTLMNVVIPRRLLPREMQNYD 101
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BLAST of SMED30006968 vs. Planmine SMEST
Match: SMESG000019832.1 (SMESG000019832.1)

HSP 1 Score: 130.954 bits (328), Expect = 8.659e-39
Identity = 70/125 (56.00%), Postives = 87/125 (69.60%), Query Frame = 2 
Query:  209 EPGRNPARESRHRAEYILARLEERQRQTNWQVAMARLHLAKINEDIATGRIPSTDGYAPSYGISYELDDSMLGQLSRSMNVVIPKKLLPKDMRDTDRSLIERQYHSYAPERTRWNPSSHHRNSMR 583
            EPGRNP RE R  AEYILARL E QR+T+ QV  AR +L +I  DIA G IPSTDGYAPSYGIS+ELD+  L + +RSMNV +P+K+LPK+MR+ + S      HSY    +  NP + +RN  R
Sbjct:   35 EPGRNPVRELRGHAEYILARLGEHQRRTDIQVERARRYLDQIKADIAAGLIPSTDGYAPSYGISFELDNPRLNRPTRSMNVTVPRKILPKEMREENESRPTEWDHSYTRRPSTRNPRNSYRNPHR 159
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BLAST of SMED30006968 vs. Planmine SMEST
Match: SMESG000036641.1 (SMESG000036641.1)

HSP 1 Score: 134.42 bits (337), Expect = 1.644e-38
Identity = 64/104 (61.54%), Postives = 79/104 (75.96%), Query Frame = 2 
Query:  206 REPGRNPARESRHRAEYILARLEERQRQTNWQVAMARLHLAKINEDIATGRIPSTDGYAPSYGISYELDDSMLGQLSRSMNVVIPKKLLPKDMRDTDRSLIERQ 517
            +EPGRNPARE+R RAE  L  LE  Q+QTNWQVAMAR  L K+N DIA G+IPSTDGYAP  G+S+ELDD  L ++   MNV+IP++LLP DM++ DR   +RQ
Sbjct:   34 QEPGRNPAREARQRAESTLDCLEIHQKQTNWQVAMARQWLDKVNADIAAGKIPSTDGYAPECGVSFELDDPALMEMDTPMNVLIPRRLLPIDMKNYDRRSPQRQ 137
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BLAST of SMED30006968 vs. Planmine SMEST
Match: SMESG000066467.1 (SMESG000066467.1)

HSP 1 Score: 134.806 bits (338), Expect = 1.335e-37
Identity = 68/124 (54.84%), Postives = 83/124 (66.94%), Query Frame = 2 
Query:  206 REPGRNPARESRHRAEYILARLEERQRQTNWQVAMARLHLAKINEDIATGRIPSTDGYAPSYGISYELDDSMLGQLSRSMNVVIPKKLLPKDMRDTDRSLIERQYHSYAPERTRWNPSSHHRNS 577
            REPGRNPARE R + E++LARLEE QRQTN QVA ARL+LA +NEDIA GRI  TDGYAP Y  S+ LDD  L   + +MNVVIP+K LP+ MR  +        H YA   ++ +   HHR +
Sbjct:  273 REPGRNPAREIRGQTEFLLARLEEHQRQTNLQVARARLYLANVNEDIAAGRIACTDGYAPPYNTSFNLDDERLNVNAEAMNVVIPRKALPRKMRRNEGPAERHNEHPYARTVSKSDSFQHHRKT 396
The following BLAST results are available for this feature:
BLAST of SMED30006968 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 SMED30006968 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 SMED30006968 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 SMED30006968 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 SMED30006968 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 SMED30006968 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 SMED30006968 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 SMED30006968 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 SMED30006968 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 SMED30006968 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 SMED30006968 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 SMED30006968 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 SMED30006968 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 SMED30006968 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000026049.12.744e-4664.35SMESG000026049.1[more]
SMESG000060158.15.793e-4062.89SMESG000060158.1[more]
SMESG000019832.18.659e-3956.00SMESG000019832.1[more]
SMESG000036641.11.644e-3861.54SMESG000036641.1[more]
SMESG000066467.11.335e-3754.84SMESG000066467.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006968 ID=SMED30006968|Name=SMED30006968|organism=Schmidtea mediterranea sexual|type=transcript|length=588bp
TGCACAAGTTCTACCATCGTCAAAAGCCATACCACTAATTACAACCCCAA
ACAAACGACAAATCACGACCAATTGTTCGCGGTTTTAGTATAATAGAAAT
TCACCGACTTACAGATACAGTAAAACTTAAACCGGCTTGACTCATCCACT
ACAGGTATTTACATCAACCTGCACATTTACACTCCGACCAAATAGAATGA
GATTAAGAGAGCCAGGCCGAAACCCAGCCCGTGAAAGCCGACACCGCGCG
GAATACATTCTGGCTCGCCTCGAAGAACGGCAGAGACAAACTAATTGGCA
GGTGGCAATGGCAAGACTACACCTGGCCAAGATCAATGAAGACATTGCAA
CTGGAAGAATTCCCAGTACGGACGGATATGCCCCATCTTATGGCATATCG
TATGAACTGGATGATTCGATGTTAGGACAACTTTCCAGATCTATGAACGT
GGTGATTCCAAAAAAATTACTTCCCAAGGATATGCGGGACACCGACAGAA
GCCTGATAGAACGACAATACCATTCATACGCTCCAGAACGCACAAGATGG
AACCCAAGTTCGCATCACCGAAATTCTATGCGACGTTA
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protein sequence of SMED30006968-orf-1

>SMED30006968-orf-1 ID=SMED30006968-orf-1|Name=SMED30006968-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp
MRLREPGRNPARESRHRAEYILARLEERQRQTNWQVAMARLHLAKINEDI
ATGRIPSTDGYAPSYGISYELDDSMLGQLSRSMNVVIPKKLLPKDMRDTD
RSLIERQYHSYAPERTRWNPSSHHRNSMRR
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
Vocabulary: INTERPRO
TermDefinition
IPR029027Single_a-helix_sf