X1.D.A5.1

Overview
NameX1.D.A5.1
Smed IDSMED30013682
Length (bp)374
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

 

 

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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of X1.D.A5.1 (SMED30013682) t-SNE clustered cells

Violin plots show distribution of expression levels for X1.D.A5.1 (SMED30013682) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30013682

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30013682 SmedASXL_004558SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30013682 SmedASXL_004558SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30013682h1SMcG0018592 dd_Smed_v6_571_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30013682h1SMcG0018587 dd_Smed_v6_571_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of X1.D.A5.1 vs. TrEMBL
Match: V9XTG6 (X1.D.A5.1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 201.445 bits (511), Expect = 6.227e-65
Identity = 98/98 (100.00%), Postives = 98/98 (100.00%), Query Frame = 1 
Query:   19 MNFIYSFVGLAMCLMSYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIEPAVSGEQPLFECEGPSLVRVDEKDIYLDPCQE 312
            MNFIYSFVGLAMCLMSYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIEPAVSGEQPLFECEGPSLVRVDEKDIYLDPCQE
Sbjct:    1 MNFIYSFVGLAMCLMSYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIEPAVSGEQPLFECEGPSLVRVDEKDIYLDPCQE 98
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BLAST of X1.D.A5.1 vs. Planmine SMEST
Match: SMESG000013036.1 (SMESG000013036.1)

HSP 1 Score: 64.3142 bits (155), Expect = 1.563e-14
Identity = 30/83 (36.14%), Postives = 52/83 (62.65%), Query Frame = 1 
Query:   61 MSYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIEPAVSGEQPLFECEGPSLVRVDEKDIYLDPCQ 309
            ++Y +++  +G G+ D +G+  V+I D+ F+A   +EV+VN   +CYKC I+   +G++P++EC GP    VD K  Y+  C 
Sbjct:   14 LNYISADEFFGYGYKDSNGKPFVKIADRIFEADTAREVKVNINSQCYKCSIK---TGDRPMYECSGPVPSFVDGKVTYVPVCT 93
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BLAST of X1.D.A5.1 vs. Planmine SMEST
Match: SMESG000055805.1 (SMESG000055805.1)

HSP 1 Score: 59.3066 bits (142), Expect = 1.401e-12
Identity = 33/93 (35.48%), Postives = 52/93 (55.91%), Query Frame = 1 
Query:   46 LAMCLM---SYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIEPAVSGE-QPLFECEGPSLVRVDEKDIYLDPCQE 312
            +A+C +    + +S + +G G+  KDG+  V+I + ++ A +  EVEV     C  C I P  S +  P FEC+GPS   +D + IYL  C+E
Sbjct:    5 IALCAIFCTKFVHSSVSFGNGYF-KDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKE 96
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BLAST of X1.D.A5.1 vs. Planmine SMEST
Match: SMESG000061917.1 (SMESG000061917.1)

HSP 1 Score: 58.9214 bits (141), Expect = 1.959e-12
Identity = 28/83 (33.73%), Postives = 45/83 (54.22%), Query Frame = 1 
Query:   58 LMSYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIEPAVSGEQPLFECEGPSLVRVDEKDIYLDPC 306
            L +  ++ L  GRG+ + +G   V+IFDQ F A +    ++   ++CY C I+   SG  P + C+GPS    + K  Y+ PC
Sbjct:   11 LSAMADASLFLGRGYRNSEGVPYVKIFDQVFKAEESSTQKIYQNERCYLCNIKAPGSGRLPRYTCQGPSPSSTNGKIKYISPC 93
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BLAST of X1.D.A5.1 vs. Planmine SMEST
Match: SMESG000013213.1 (SMESG000013213.1)

HSP 1 Score: 55.0694 bits (131), Expect = 7.094e-11
Identity = 29/96 (30.21%), Postives = 53/96 (55.21%), Query Frame = 1 
Query:   19 MNFIYSFVGLAMCLMSYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIEPAVSGEQPLFECEGPSLVRVDEKDIYLDPC 306
            MN I   + + +CL ++ +SE   G+G+ +  G  +V I  +++ A +   +++   +KC KC IE     + P +EC+GP LV   ++  Y+ PC
Sbjct:    1 MNKILYQIFIIICLNAFVHSEDSMGQGYTNSKGEPVVNINGKEYSAKQNNVIKIGEGEKCTKCSIE----SDPPFYECQGPVLV---DESKYVSPC 89
[Close]
BLAST of X1.D.A5.1 vs. Planmine SMEST
Match: SMESG000062897.1 (SMESG000062897.1)

HSP 1 Score: 51.9878 bits (123), Expect = 1.348e-9
Identity = 34/99 (34.34%), Postives = 55/99 (55.56%), Query Frame = 1 
Query:   13 ISMNFIYSFVGLAMCLMSYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIE-PAVSGEQPLFECEGPSLVRVDEKDIYLDPC 306
            I+M     FV ++ C+++   S L  G G+ + +G+ +V+I +Q F A K    ++    +C KC I  PA + E+P F+C GPS V +D K  Y+  C
Sbjct:    9 INMKLFVVFVFVSFCILNSKGS-LSRGIGYYE-NGKPVVKINNQVFPADKNSVQQIGSGDRCLKCFINAPANNDEKPKFQCHGPSPVYMDGKMAYISEC 105
The following BLAST results are available for this feature:
BLAST of X1.D.A5.1 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 X1.D.A5.1 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 X1.D.A5.1 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 X1.D.A5.1 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 X1.D.A5.1 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 X1.D.A5.1 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 X1.D.A5.1 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 X1.D.A5.1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XTG66.227e-65100.00X1.D.A5.1 OS=Schmidtea mediterranea OX=79327 PE=2 ... [more]
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BLAST of X1.D.A5.1 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 X1.D.A5.1 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 X1.D.A5.1 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 X1.D.A5.1 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 X1.D.A5.1 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 X1.D.A5.1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000013036.11.563e-1436.14SMESG000013036.1[more]
SMESG000055805.11.401e-1235.48SMESG000055805.1[more]
SMESG000061917.11.959e-1233.73SMESG000061917.1[more]
SMESG000013213.17.094e-1130.21SMESG000013213.1[more]
SMESG000062897.11.348e-934.34SMESG000062897.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013682 ID=SMED30013682|Name=X1.D.A5.1|organism=Schmidtea mediterranea sexual|type=transcript|length=374bp
AATATCCCTATTATCAGTATGAATTTTATATACAGCTTTGTCGGTCTAGC
GATGTGCCTGATGTCATATACGAATTCAGAATTGGTTTATGGACGAGGAT
TCGTTGACAAAGATGGTCGGCAGATTGTGGAGATATTCGATCAGCAATTT
GATGCATCCAAGCAAAAGGAGGTTGAAGTTAACTTCGTCAAAAAGTGTTA
CAAATGTTTAATAGAACCAGCAGTATCAGGAGAACAGCCTTTATTTGAGT
GTGAAGGACCTTCACTAGTTCGTGTGGATGAAAAAGACATTTATCTTGAT
CCTTGTCAGGAATAGAGGTCACTTGGACATAACATTTTGTATTTTCAAAA
AAAAAATTGTATTTCTATAAATAG
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protein sequence of SMED30013682-orf-1

>SMED30013682-orf-1 ID=SMED30013682-orf-1|Name=SMED30013682-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
NIPIISMNFIYSFVGLAMCLMSYTNSELVYGRGFVDKDGRQIVEIFDQQF
DASKQKEVEVNFVKKCYKCLIEPAVSGEQPLFECEGPSLVRVDEKDIYLD
PCQE*
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Aliases
The feature 'X1.D.A5.1' has the following synonyms
Synonym
X1.D.A5.1
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..26
score: 0.556