SMED30017762

Overview
NameSMED30017762
Smed IDSMED30017762
Length (bp)675
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell 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 SMED30017762 (SMED30017762) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017762 (SMED30017762) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30017762 (SMED30017762) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017762 (SMED30017762) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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



SMED30017762

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30017762SMESG000016810.1 dd_Smed_v4_783_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30017762SMESG000016810.1 dd_Smed_v4_783_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30017762SMESG000016810.1 dd_Smed_v4_783_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30017762SMESG000016810.1 dd_Smed_v4_783_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30017762SMESG000016810.1 dd_Smed_v4_783_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30017762SMESG000016810.1 dd_Smed_v4_783_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30017762SMESG000016810.1 dd_Smed_v6_783_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30017762SMESG000016810.1 dd_Smed_v4_783_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
SMED30017762 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001202:41609..42329 +3247
Homology
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BLAST of SMED30017762 vs. Planmine SMEST
Match: SMESG000016810.1 (SMESG000016810.1)

HSP 1 Score: 261.536 bits (667), Expect = 1.092e-89
Identity = 147/152 (96.71%), Postives = 150/152 (98.68%), Query Frame = 1 
Query:  130 DSDGSASRSYEDNVNRSISIKELKNKWSDKFNIAIQSVKFNNQILXXXXXXXXXXXXXXXTVQLIQDKSNDQITLVVELQSINTNQRSIQIPVNPNITTEELMSVIRNRISFDLGSAYLTHHGQQLRSAVSLKDQNVKNNDRIQVLMRTRGG 585
            DSDGS SRSYEDNVNRSISIKELK KWSDKFNIAIQSVKFNNQILS+DSNCSSCSIINGSTV+LIQDKSNDQITL+VELQSINTNQRSIQIPVNPNITTEELMSVIRNRISFDLGSAYLTHHGQQLRSAVSLKDQNVKNNDRIQVLMRTRGG
Sbjct:   12 DSDGSVSRSYEDNVNRSISIKELKKKWSDKFNIAIQSVKFNNQILSDDSNCSSCSIINGSTVKLIQDKSNDQITLLVELQSINTNQRSIQIPVNPNITTEELMSVIRNRISFDLGSAYLTHHGQQLRSAVSLKDQNVKNNDRIQVLMRTRGG 163
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BLAST of SMED30017762 vs. Planmine SMEST
Match: SMESG000016811.1 (SMESG000016811.1)

HSP 1 Score: 187.578 bits (475), Expect = 1.261e-60
Identity = 101/163 (61.96%), Postives = 131/163 (80.37%), Query Frame = 1 
Query:   97 MSTITIKIEIIDSDGSASRSYEDNVNRSISIKELKNKWSDKFNIAIQSVKFNNQILXXXXXXXXXXXXXXXTVQLIQDKSNDQITLVVELQSINTNQRSIQIPVNPNITTEELMSVIRNRISFDLGSAYLTHHGQQLRSAVSLKDQNVKNNDRIQVLMRTRGG 585
            MS I +KIEI           +DNV+ S+S++++K  WSDK+N+ IQSV++NNQILS+++NC+   I  GSTVQLI ++S+DQI L+VELQS+N NQRS QI VNPNITTEELMSVIRN++ FD+GSAYL+HH ++L S VSLKDQ+VKNND I+VLM+TRGG
Sbjct:    1 MSMIAVKIEI------GKNVLQDNVDPSMSLRDVKRNWSDKYNVDIQSVRYNNQILSDENNCNFYKIRTGSTVQLISNESDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLSHHNEELPSGVSLKDQSVKNNDTIKVLMKTRGG 157
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BLAST of SMED30017762 vs. Planmine SMEST
Match: SMESG000016811.1 (SMESG000016811.1)

HSP 1 Score: 183.726 bits (465), Expect = 4.418e-59
Identity = 99/160 (61.88%), Postives = 129/160 (80.62%), Query Frame = 1 
Query:  106 ITIKIEIIDSDGSASRSYEDNVNRSISIKELKNKWSDKFNIAIQSVKFNNQILXXXXXXXXXXXXXXXTVQLIQDKSNDQITLVVELQSINTNQRSIQIPVNPNITTEELMSVIRNRISFDLGSAYLTHHGQQLRSAVSLKDQNVKNNDRIQVLMRTRGG 585
            I +KIEI           +DNV+ S+S++++K  WSDK+N+ IQSV++NNQILS+++NC+   I  GSTVQLI ++S+DQI L+VELQS+N NQRS QI VNPNITTEELMSVIRN++ FD+GSAYL+HH ++L S VSLKDQ+VKNND I+VLM+TRGG
Sbjct:    2 IAVKIEI------GKNVLQDNVDPSMSLRDVKRNWSDKYNVDIQSVRYNNQILSDENNCNFYKIRTGSTVQLISNESDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLSHHNEELPSGVSLKDQSVKNNDTIKVLMKTRGG 155
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BLAST of SMED30017762 vs. Planmine SMEST
Match: SMESG000016780.1 (SMESG000016780.1)

HSP 1 Score: 165.236 bits (417), Expect = 2.906e-52
Identity = 87/135 (64.44%), Postives = 107/135 (79.26%), Query Frame = 1 
Query:  181 ISIKELKNKWSDKFNIAIQSVKFNNQILXXXXXXXXXXXXXXXTVQLIQDKSNDQITLVVELQSINTNQRSIQIPVNPNITTEELMSVIRNRISFDLGSAYLTHHGQQLRSAVSLKDQNVKNNDRIQVLMRTRGG 585
            + I+EL+ K   KFN+ IQS++FNNQ+LS+D +  S       TV L  DKS+DQI L+VELQS+N NQRS QI VNPNITTEELMSVIRN++ FD+GSAYLTHH ++L S +SLKDQNVKNND I+VLM+TRGG
Sbjct:    1 MHIRELRRKLKYKFNVDIQSIQFNNQLLSDDRHSGS-------TVSLTLDKSDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLTHHNEELPSGISLKDQNVKNNDTIKVLMKTRGG 128
[Close]
BLAST of SMED30017762 vs. Planmine SMEST
Match: SMESG000016772.1 (SMESG000016772.1)

HSP 1 Score: 164.466 bits (415), Expect = 1.751e-51
Identity = 89/163 (54.60%), Postives = 121/163 (74.23%), Query Frame = 1 
Query:   97 MSTITIKIEIIDSDGSASRSYEDNVNRSISIKELKNKWSDKFNIAIQSVKFNNQILXXXXXXXXXXXXXXXTVQLIQDKSNDQITLVVELQSINTNQRSIQIPVNPNITTEELMSVIRNRISFDLGSAYLTHHGQQLRSAVSLKDQNVKNNDRIQVLMRTRGG 585
            MS I + ++I +S+G   + Y+ N N S+SI  LK  WSDK+ + IQSV+FN Q LS+D NC+  +I +G+T++LI  KS+ +I L+VE+QSIN  QR IQ+ VNP+I TE+LM VI+ +I F+  SAYLTHHG+ LR  VSL+DQ VKNND IQVL+RT+GG
Sbjct:    1 MSNIKLNLQITNSNGEPMKIYQVNANPSMSISVLKGNWSDKYGVDIQSVRFNGQTLSDDKNCNFYNIRDGATLELISSKSDSKINLIVEVQSINPGQRPIQVRVNPSIKTEDLMKVIKEKIYFNFDSAYLTHHGETLREGVSLRDQCVKNNDMIQVLVRTKGG 163
The following BLAST results are available for this feature:
BLAST of SMED30017762 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 SMED30017762 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 SMED30017762 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 SMED30017762 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 SMED30017762 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 SMED30017762 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 SMED30017762 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 SMED30017762 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 SMED30017762 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 SMED30017762 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 SMED30017762 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 SMED30017762 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 SMED30017762 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 SMED30017762 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000016810.11.092e-8996.71SMESG000016810.1[more]
SMESG000016811.11.261e-6061.96SMESG000016811.1[more]
SMESG000016811.14.418e-5961.88SMESG000016811.1[more]
SMESG000016780.12.906e-5264.44SMESG000016780.1[more]
SMESG000016772.11.751e-5154.60SMESG000016772.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017762 ID=SMED30017762|Name=SMED30017762|organism=Schmidtea mediterranea sexual|type=transcript|length=675bp
TGTAATTTTACTGGTTTTTCCAAATTAATTATAGATTTGGATTTCCAAAG
ATGTTGAATAAATTTGAATGAAATTTTAATATTATCATTTAATACAATGT
CAACTATAACTATAAAAATTGAAATCATTGATTCTGACGGAAGTGCGTCG
AGAAGTTACGAAGACAATGTCAACCGTTCAATCTCAATAAAGGAATTGAA
AAATAAATGGTCTGATAAATTTAATATTGCTATCCAATCGGTTAAATTTA
ACAATCAAATTCTAAGCAACGACAGCAATTGCAGCTCTTGTAGTATTATC
AATGGATCAACTGTGCAACTCATCCAGGATAAATCGAACGATCAGATCAC
TTTGGTTGTGGAACTGCAGTCAATAAATACCAACCAAAGATCGATTCAAA
TCCCAGTGAATCCAAATATCACAACCGAAGAACTGATGAGCGTTATCCGA
AATAGAATTTCATTCGATTTAGGGTCGGCTTATCTAACTCATCATGGCCA
ACAACTTCGTTCTGCGGTCAGTTTAAAAGACCAAAATGTCAAAAATAATG
ACAGGATCCAAGTATTGATGAGAACCAGAGGTGGATAAATTAATTTGAGA
AAACATTAACATTAAACAGATCTTCAATTTTATTATTAATTAAATAATCA
ATTTTATTAAAATTCAATTTTTATT
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protein sequence of SMED30017762-orf-1

>SMED30017762-orf-1 ID=SMED30017762-orf-1|Name=SMED30017762-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=164bp
MSTITIKIEIIDSDGSASRSYEDNVNRSISIKELKNKWSDKFNIAIQSVK
FNNQILSNDSNCSSCSIINGSTVQLIQDKSNDQITLVVELQSINTNQRSI
QIPVNPNITTEELMSVIRNRISFDLGSAYLTHHGQQLRSAVSLKDQNVKN
NDRIQVLMRTRGG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000418head
PLANA:0002032epidermal cell
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR041207NUB1_ubiquitin-like_dom
IPR000626Ubiquitin-like_dom
IPR029071Ubiquitin-like_domsf
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000626Ubiquitin-like domainPFAMPF00240ubiquitincoord: 20..77
e-value: 1.5E-5
score: 24.6
IPR000626Ubiquitin-like domainPROSITEPS50053UBIQUITIN_2coord: 86..163
score: 13.162
IPR000626Ubiquitin-like domainPROSITEPS50053UBIQUITIN_2coord: 4..82
score: 9.308
NoneNo IPR availableGENE3DG3DSA:3.10.20.90coord: 2..81
e-value: 2.2E-8
score: 35.7
NoneNo IPR availableGENE3DG3DSA:3.10.20.90coord: 82..162
e-value: 3.8E-10
score: 41.4
NoneNo IPR availableCDDcd17062Ubl_NUB1coord: 85..158
e-value: 6.71337E-7
score: 42.8958
IPR041207NEDD8 ultimate buster 1, ubiquitin-like domainPFAMPF18037Ubiquitin_5coord: 95..158
e-value: 1.8E-5
score: 25.0
IPR029071Ubiquitin-like domain superfamilySUPERFAMILYSSF54236Ubiquitin-likecoord: 6..81
IPR029071Ubiquitin-like domain superfamilySUPERFAMILYSSF54236Ubiquitin-likecoord: 82..163