SMED30003821

Overview
NameSMED30003821
Smed IDSMED30003821
Length (bp)366
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



SMED30003821

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
head regionSMED30003821h1SMcG0008095 SmedASXL_003798SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
non-ciliated neuronSMED30003821h1SMcG0008095 dd_Smed_v4_78717_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30003821h1SMcG0008095 dd_Smed_v6_80306_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30003821h1SMcG0008095 dd_Smed_v6_88303_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30003821 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006212:720..4055 +1619
Homology
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BLAST of SMED30003821 vs. Planmine SMEST
Match: SMESG000079790.1 (SMESG000079790.1)

HSP 1 Score: 183.726 bits (465), Expect = 9.607e-59
Identity = 107/107 (100.00%), Postives = 107/107 (100.00%), Query Frame = 3 
Query:    3 QTVNASKETHYSKTLTRMSXXXXXXXXXXXXXXXVMWTILSLRADINVEIMSIIYSVSDILVYSHHSCNFILFMITGQRFRTSLKSLLRIRSKVGPLSEENQTIIRN 323
            QTVNASKETHYSKTLTRMSIAITILYITLITPAIVMWTILSLRADINVEIMSIIYSVSDILVYSHHSCNFILFMITGQRFRTSLKSLLRIRSKVGPLSEENQTIIRN
Sbjct:  212 QTVNASKETHYSKTLTRMSIAITILYITLITPAIVMWTILSLRADINVEIMSIIYSVSDILVYSHHSCNFILFMITGQRFRTSLKSLLRIRSKVGPLSEENQTIIRN 318
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BLAST of SMED30003821 vs. Planmine SMEST
Match: SMESG000079764.1 (SMESG000079764.1)

HSP 1 Score: 70.0922 bits (170), Expect = 3.443e-15
Identity = 41/74 (55.41%), Postives = 57/74 (77.03%), Query Frame = 3 
Query:   24 ETHYSKTLTRMSXXXXXXXXXXXXXXXVMWTILSLRADINVEIMSIIYSVSDILVYSHHSCNFILFMITGQRFR 245
            + HYSK+LT+MSIAI IL+  LITP+I +WT++S   DIN + +++ Y +++ILV+SHHS NF LF  TG RFR
Sbjct:  216 KNHYSKSLTKMSIAINILFFVLITPSITIWTLMSYAKDINADAIALCYDITNILVFSHHSLNFYLFFFTGPRFR 289
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BLAST of SMED30003821 vs. Planmine SMEST
Match: SMESG000079764.1 (SMESG000079764.1)

HSP 1 Score: 70.0922 bits (170), Expect = 3.611e-15
Identity = 41/74 (55.41%), Postives = 57/74 (77.03%), Query Frame = 3 
Query:   24 ETHYSKTLTRMSXXXXXXXXXXXXXXXVMWTILSLRADINVEIMSIIYSVSDILVYSHHSCNFILFMITGQRFR 245
            + HYSK+LT+MSIAI IL+  LITP+I +WT++S   DIN + +++ Y +++ILV+SHHS NF LF  TG RFR
Sbjct:  223 KNHYSKSLTKMSIAINILFFVLITPSITIWTLMSYAKDINADAIALCYDITNILVFSHHSLNFYLFFFTGPRFR 296
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BLAST of SMED30003821 vs. Planmine SMEST
Match: SMESG000079761.1 (SMESG000079761.1)

HSP 1 Score: 63.929 bits (154), Expect = 5.682e-13
Identity = 45/86 (52.33%), Postives = 63/86 (73.26%), Query Frame = 3 
Query:   27 THYSKTLTRMSXXXXXXXXXXXXXXXVMWTILSL-RADINVEIMSIIYSVSDILVYSHHSCNFILFMITGQRFRTSLKSLLRIRSK 281
             HYSK+LT+MSIAI IL++ L++P+I +WTI+S   A I  E +SI+Y  ++ILV+SHHS NF LF ++G RFR   K +L+I  K
Sbjct:  231 PHYSKSLTQMSIAINILFVLLLSPSIFIWTIISYWPASIQSEKISILYDSTNILVFSHHSLNFYLFFLSGPRFR---KEVLQIFGK 313
[Close]
BLAST of SMED30003821 vs. Planmine SMEST
Match: SMESG000011555.1 (SMESG000011555.1)

HSP 1 Score: 56.6102 bits (135), Expect = 2.188e-10
Identity = 36/92 (39.13%), Postives = 66/92 (71.74%), Query Frame = 3 
Query:   12 NASKETHYSKTLTRMSXXXXXXXXXXXXXXXVMWTILSL----RADINVEIMSIIYSVSDILVYSHHSCNFILFMITGQRFRTSLKSLLRIR 275
              S++T  SK+L +MS+ I ILY+  +TP++ +WT +++    + +I+ E++  ++SV+DIL Y  +S NF +++I+G+RFR  +K+LLRI+
Sbjct:  230 GKSQKTQ-SKSLLKMSLFIGILYLVFLTPSMTIWTTINMFTYYQVEISGEMIDFLFSVTDILAYLQYSTNFFVYVISGKRFRLEIKNLLRIK 320
The following BLAST results are available for this feature:
BLAST of SMED30003821 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 SMED30003821 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 SMED30003821 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 SMED30003821 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 SMED30003821 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 SMED30003821 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 SMED30003821 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 SMED30003821 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 SMED30003821 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 SMED30003821 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 SMED30003821 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 SMED30003821 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 SMED30003821 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 SMED30003821 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000079790.19.607e-59100.00SMESG000079790.1[more]
SMESG000079764.13.443e-1555.41SMESG000079764.1[more]
SMESG000079764.13.611e-1555.41SMESG000079764.1[more]
SMESG000079761.15.682e-1352.33SMESG000079761.1[more]
SMESG000011555.12.188e-1039.13SMESG000011555.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003821 ID=SMED30003821|Name=SMED30003821|organism=Schmidtea mediterranea sexual|type=transcript|length=366bp
ATCAGACTGTAAATGCTTCTAAAGAAACTCATTATTCGAAAACTCTAACC
CGAATGTCAATTGCGATAACCATTCTGTATATAACATTAATTACTCCAGC
CATAGTTATGTGGACAATTCTTAGCCTTCGTGCCGATATCAATGTGGAGA
TTATGTCCATCATATATTCCGTCAGTGATATTCTCGTTTATTCCCATCAT
AGCTGCAATTTCATTCTTTTCATGATTACTGGACAGAGATTTCGGACGTC
TTTAAAATCCCTACTTAGAATTAGAAGCAAAGTCGGTCCCTTGTCGGAGG
AAAATCAAACAATTATTAGAAACTAAACCTGAATAATGACAAAAATAGCA
AGCACCATAAACATTG
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protein sequence of SMED30003821-orf-1

>SMED30003821-orf-1 ID=SMED30003821-orf-1|Name=SMED30003821-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=108bp
QTVNASKETHYSKTLTRMSIAITILYITLITPAIVMWTILSLRADINVEI
MSIIYSVSDILVYSHHSCNFILFMITGQRFRTSLKSLLRIRSKVGPLSEE
NQTIIRN*
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.20.1070.10coord: 1..94
e-value: 2.5E-12
score: 48.3
NoneNo IPR availablePANTHERPTHR24243G-PROTEIN COUPLED RECEPTORcoord: 4..92
NoneNo IPR availablePANTHERPTHR24243:SF214G-PROTEIN COUPLED RECEPTOR 19-RELATEDcoord: 4..92
NoneNo IPR availableCDDcd149787tmA_FMRFamide_R-likecoord: 15..84
e-value: 3.70184E-6
score: 41.4644
NoneNo IPR availableSUPERFAMILYSSF81321Family A G protein-coupled receptor-likecoord: 9..94
NoneNo IPR availableTMHMMTMhelixcoord: 51..73
NoneNo IPR availableTMHMMTMhelixcoord: 19..41