SMED30010677

Overview
NameSMED30010677
Smed IDSMED30010677
Length (bp)618
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



SMED30010677

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30010677SMESG000022725.1 dd_Smed_v4_9435_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30010677SMESG000022725.1 dd_Smed_v4_9435_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30010677SMESG000022725.1 dd_Smed_v4_9435_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30010677SMESG000022725.1 dd_Smed_v4_9435_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30010677SMESG000022725.1 dd_Smed_v6_9435_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
SMED30010677 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001411:72078..72695 -3081
Homology
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BLAST of SMED30010677 vs. TrEMBL
Match: G7YQP5 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CLF_107516 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 8.202e-8
Identity = 31/69 (44.93%), Postives = 44/69 (63.77%), Query Frame = -3 
Query:  203 FLSIFIWTILFQSMAVVKCVTLGTALKEPDIYIKYDQTPFRIWFHIGISLAICYAILGTIWSMVNLIFK 409
            F+S+ +++IL QS   V+ VTL   LK P+ YI YDQ PF I  H GISL I Y+IL  + + + +I +
Sbjct:    4 FVSV-VFSILLQS---VQMVTLEEGLKNPEKYIFYDQNPFNIGMHAGISLLITYSILAIVLTFITIISR 68
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BLAST of SMED30010677 vs. TrEMBL
Match: A0A267EQR8 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig000783g2 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 1.985e-7
Identity = 30/63 (47.62%), Postives = 37/63 (58.73%), Query Frame = -3 
Query:  227 MSFLSIFIWTILFQSMAVVKCVTLGTALKEPDIYIKYDQTPFRIWFHIGISLAICYAILGTIW 415
            ++FL++    +L      V C+TL  A  +PD YI YD T F I  H GISL ICYAIL  IW
Sbjct:   29 VAFLAVIFVAVLPSG---VDCITLNDARADPDRYILYDTTQFHIGMHCGISLVICYAILCAIW 88
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BLAST of SMED30010677 vs. TrEMBL
Match: A0A267EL98 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig000783g4 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 2.052e-7
Identity = 30/63 (47.62%), Postives = 37/63 (58.73%), Query Frame = -3 
Query:  227 MSFLSIFIWTILFQSMAVVKCVTLGTALKEPDIYIKYDQTPFRIWFHIGISLAICYAILGTIW 415
            ++FL++    +L      V C+TL  A  +PD YI YD T F I  H GISL ICYAIL  IW
Sbjct:   30 VAFLAVIFVAVLPSG---VDCITLNDARADPDRYILYDTTQFHIGMHCGISLVICYAILCAIW 89
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BLAST of SMED30010677 vs. TrEMBL
Match: A0A074ZEH6 (Uncharacterized protein OS=Opisthorchis viverrini OX=6198 GN=T265_10094 PE=4 SV=1)

HSP 1 Score: 56.6102 bits (135), Expect = 6.524e-7
Identity = 32/69 (46.38%), Postives = 42/69 (60.87%), Query Frame = -3 
Query:  203 FLSIFIWTILFQSMAVVKCVTLGTALKEPDIYIKYDQTPFRIWFHIGISLAICYAILGTIWSMVNLIFK 409
            F+SI +++IL QS   V+ VTL   LK P+ YI YDQ PF I  H GISL I Y+IL  +   +  I +
Sbjct:    4 FVSI-VFSILLQS---VRMVTLEEGLKNPEKYIFYDQNPFNIGMHAGISLLITYSILAIVLGFIATISR 68
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BLAST of SMED30010677 vs. Planmine SMEST
Match: SMESG000022725.1 (SMESG000022725.1)

HSP 1 Score: 141.354 bits (355), Expect = 7.492e-44
Identity = 68/68 (100.00%), Postives = 68/68 (100.00%), Query Frame = -3 
Query:  167 MAVVKCVTLGTALKEPDIYIKYDQTPFRIWFHIGISLAICYAILGTIWSMVNLIFKIRELKKVGTELD 370
            MAVVKCVTLGTALKEPDIYIKYDQTPFRIWFHIGISLAICYAILGTIWSMVNLIFKIRELKKVGTELD
Sbjct:    1 MAVVKCVTLGTALKEPDIYIKYDQTPFRIWFHIGISLAICYAILGTIWSMVNLIFKIRELKKVGTELD 68
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BLAST of SMED30010677 vs. Planmine SMEST
Match: SMESG000035183.1 (SMESG000035183.1)

HSP 1 Score: 54.299 bits (129), Expect = 6.401e-10
Identity = 25/56 (44.64%), Postives = 37/56 (66.07%), Query Frame = -3 
Query:  194 VKCVTLGTALKEPDIYIKYDQTPFRIWFHIGISLAICYAILGTIWSMVNLIFKIRE 361
            V+ VTL    + P +YIKYD +   +  HIG+S+ I +AIL  IW +VN IFK+++
Sbjct:   24 VQSVTLEDGKQNPGLYIKYDTSEMNLGLHIGLSILITFAILTIIWCIVNAIFKLQK 79
The following BLAST results are available for this feature:
BLAST of SMED30010677 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 SMED30010677 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 SMED30010677 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 SMED30010677 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 SMED30010677 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 SMED30010677 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 SMED30010677 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 SMED30010677 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
G7YQP58.202e-844.93Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
A0A267EQR81.985e-747.62Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267EL982.052e-747.62Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A074ZEH66.524e-746.38Uncharacterized protein OS=Opisthorchis viverrini ... [more]
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BLAST of SMED30010677 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 SMED30010677 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 SMED30010677 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 SMED30010677 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 SMED30010677 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 SMED30010677 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000022725.17.492e-44100.00SMESG000022725.1[more]
SMESG000035183.16.401e-1044.64SMESG000035183.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010677 ID=SMED30010677|Name=SMED30010677|organism=Schmidtea mediterranea sexual|type=transcript|length=618bp
CTTATAAGCAATTTTAGTTCTATATAGTAAAGATAATCAATCAAAATATT
CAAATCTAACATTTTAAAATTTGAAATAAAAACTAATAAAATATAGGTAA
ATTTGCATAAAATTAAGCAAAGCATTTAAATATTTATAAACAAACAATTT
TCACATATAAACATCAATCTAATTCGGTTCCAACTTTTTTCAATTCTCGA
ATTTTAAATATTAAGTTGACCATACTCCATATTGTCCCTAAAATCGCATA
GCATATAGCCAAGGATATACCGATGTGGAACCAAATCCTAAAAGGGGTTT
GATCATATTTGATATAAATATCTGGCTCCTTCAAAGCTGTACCAAGAGTA
ACACATTTTACCACGGCCATACTTTGAAAAAGAATTGTCCATATAAAAAT
TGAAAGAAACGACATATTGGCATTAGTGATGAAGTGAGCTCTGAACGTTG
AATTATATAACAGAAGCTATTTACCAAATTAATTCGAAATGGAACCAAAT
TTGAATTTATAATTTTATTAATGAATAATGGTAAAATTTTGTATTTCGAT
GTGAAATTATGCAAATGAAAATCTTAAAGTTAAATCAGTTTGTAAATTAT
AAACGTGGAAAATTACAG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-TMSignalP-TMcoord: 1..21
score: 0.628
NoneNo IPR availableTMHMMTMhelixcoord: 44..66
NoneNo IPR availableTMHMMTMhelixcoord: 7..29