SMED30029160

Overview
NameSMED30029160
Smed IDSMED30029160
Length (bp)989
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 SMED30029160 (SMED30029160) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029160 (SMED30029160) 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.
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



SMED30029160

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X2 cellSMED30029160SMESG000071459.1 SmedASXL_009437SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30029160SMESG000071464.1 SMESG000071460.1 SMESG000071459.1 dd_Smed_v4_16180_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30029160SMESG000071464.1 SMESG000071460.1 SMESG000071459.1 dd_Smed_v4_16180_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029160SMESG000071464.1 SMESG000071460.1 SMESG000071459.1 dd_Smed_v4_16180_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30029160SMESG000071464.1 SMESG000071460.1 SMESG000071459.1 dd_Smed_v4_16180_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30029160SMESG000071464.1 SMESG000071460.1 SMESG000071459.1 dd_Smed_v4_16180_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30029160SMESG000071464.1 SMESG000071460.1 SMESG000071459.1 dd_Smed_v6_16180_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
SMED30029160 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.010054:12879..21191 +3988
Homology
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BLAST of SMED30029160 vs. Planmine SMEST
Match: SMESG000071459.1 (SMESG000071459.1)

HSP 1 Score: 248.44 bits (633), Expect = 1.877e-91
Identity = 118/119 (99.16%), Postives = 118/119 (99.16%), Query Frame = 2 
Query:   77 MINIQFRNGWSFVQKFAFLTKEGQSKVTLKVNNQYNTNFLMAMFIDNEDLWNLFLDTKPTCQQLRISKLSHIITSLNNTSSLSVVDNTTVYTNYLWFPSNDQSFYTFSVLLACDRTEIF 433
            MINIQFRNGWSFVQKFAFLTKEGQSKVTLKVNNQYNTNFLMAMFIDNEDLWNLFLDTKPTCQQLRISKLSHIITSLNNTSSLSVVDNTTVYTNYLWFPSNDQSFYTFSVLLACDRTE F
Sbjct:    1 MINIQFRNGWSFVQKFAFLTKEGQSKVTLKVNNQYNTNFLMAMFIDNEDLWNLFLDTKPTCQQLRISKLSHIITSLNNTSSLSVVDNTTVYTNYLWFPSNDQSFYTFSVLLACDRTEYF 119

HSP 2 Score: 107.071 bits (266), Expect = 1.877e-91
Identity = 74/76 (97.37%), Postives = 75/76 (98.68%), Query Frame = 1 
Query:  430 ILESSXXXXXXXXXXXXXXXXXRKMLKIEQRESILTILFGIVISIKFIVFFCQMWIYLNYAATGVYSYVAFVICKL 657
            ILESSIFFFITYLILIIIFGFYRKMLKIEQRESILTILFGIVISIKFIVFFCQMWIYLNYAATGVYSYVAFVI +L
Sbjct:  145 ILESSIFFFITYLILIIIFGFYRKMLKIEQRESILTILFGIVISIKFIVFFCQMWIYLNYAATGVYSYVAFVIFEL 220
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BLAST of SMED30029160 vs. Planmine SMEST
Match: SMESG000071459.1 (SMESG000071459.1)

HSP 1 Score: 166.777 bits (421), Expect = 5.392e-67
Identity = 78/79 (98.73%), Postives = 78/79 (98.73%), Query Frame = 2 
Query:  197 MAMFIDNEDLWNLFLDTKPTCQQLRISKLSHIITSLNNTSSLSVVDNTTVYTNYLWFPSNDQSFYTFSVLLACDRTEIF 433
            MAMFIDNEDLWNLFLDTKPTCQQLRISKLSHIITSLNNTSSLSVVDNTTVYTNYLWFPSNDQSFYTFSVLLACDRTE F
Sbjct:    1 MAMFIDNEDLWNLFLDTKPTCQQLRISKLSHIITSLNNTSSLSVVDNTTVYTNYLWFPSNDQSFYTFSVLLACDRTEYF 79

HSP 2 Score: 107.071 bits (266), Expect = 5.392e-67
Identity = 74/76 (97.37%), Postives = 75/76 (98.68%), Query Frame = 1 
Query:  430 ILESSXXXXXXXXXXXXXXXXXRKMLKIEQRESILTILFGIVISIKFIVFFCQMWIYLNYAATGVYSYVAFVICKL 657
            ILESSIFFFITYLILIIIFGFYRKMLKIEQRESILTILFGIVISIKFIVFFCQMWIYLNYAATGVYSYVAFVI +L
Sbjct:  105 ILESSIFFFITYLILIIIFGFYRKMLKIEQRESILTILFGIVISIKFIVFFCQMWIYLNYAATGVYSYVAFVIFEL 180
[Close]
BLAST of SMED30029160 vs. Planmine SMEST
Match: SMESG000071459.1 (SMESG000071459.1)

HSP 1 Score: 162.54 bits (410), Expect = 9.667e-66
Identity = 76/77 (98.70%), Postives = 76/77 (98.70%), Query Frame = 2 
Query:  203 MFIDNEDLWNLFLDTKPTCQQLRISKLSHIITSLNNTSSLSVVDNTTVYTNYLWFPSNDQSFYTFSVLLACDRTEIF 433
            MFIDNEDLWNLFLDTKPTCQQLRISKLSHIITSLNNTSSLSVVDNTTVYTNYLWFPSNDQSFYTFSVLLACDRTE F
Sbjct:    1 MFIDNEDLWNLFLDTKPTCQQLRISKLSHIITSLNNTSSLSVVDNTTVYTNYLWFPSNDQSFYTFSVLLACDRTEYF 77

HSP 2 Score: 107.071 bits (266), Expect = 9.667e-66
Identity = 74/76 (97.37%), Postives = 75/76 (98.68%), Query Frame = 1 
Query:  430 ILESSXXXXXXXXXXXXXXXXXRKMLKIEQRESILTILFGIVISIKFIVFFCQMWIYLNYAATGVYSYVAFVICKL 657
            ILESSIFFFITYLILIIIFGFYRKMLKIEQRESILTILFGIVISIKFIVFFCQMWIYLNYAATGVYSYVAFVI +L
Sbjct:  103 ILESSIFFFITYLILIIIFGFYRKMLKIEQRESILTILFGIVISIKFIVFFCQMWIYLNYAATGVYSYVAFVIFEL 178
The following BLAST results are available for this feature:
BLAST of SMED30029160 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 SMED30029160 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 SMED30029160 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 SMED30029160 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 SMED30029160 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 SMED30029160 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 SMED30029160 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 SMED30029160 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 SMED30029160 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 SMED30029160 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 SMED30029160 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 SMED30029160 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 SMED30029160 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 SMED30029160 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000071459.11.877e-9199.16SMESG000071459.1[more]
SMESG000071459.15.392e-6798.73SMESG000071459.1[more]
SMESG000071459.19.667e-6698.70SMESG000071459.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029160 ID=SMED30029160|Name=SMED30029160|organism=Schmidtea mediterranea sexual|type=transcript|length=989bp
GTTCTCCATTATGAAAATTATATTTTTGCTAAGCATAATTGTTTTTACTA
TTAGTAATGTTAATTCCAGGATTTCTATGATTAATATTCAATTTCGAAAT
GGTTGGAGTTTTGTTCAAAAATTTGCATTTTTAACTAAAGAAGGTCAATC
TAAAGTAACTCTGAAAGTGAACAATCAATATAATACAAACTTTTTAATGG
CAATGTTCATCGATAATGAAGATTTATGGAATTTATTCCTTGACACCAAA
CCGACTTGCCAACAATTGCGTATTTCAAAATTGTCTCATATTATTACATC
TTTGAATAACACTAGCTCATTATCCGTTGTTGATAATACTACAGTTTACA
CGAATTATTTGTGGTTTCCATCAAATGACCAATCATTTTACACTTTTTCA
GTACTTTTAGCATGTGATCGAACTGAAATATTTTGGAGTCGTCTATATTT
TTCTTCATCACGTATTTGATTCTTATCATCATATTCGGATTTTATAGAAA
AATGTTGAAGATTGAACAACGAGAATCCATTTTAACTATTTTATTTGGGA
TAGTCATCAGCATCAAATTCATTGTGTTTTTCTGTCAAATGTGGATTTAT
TTGAATTACGCAGCAACTGGAGTATATTCATATGTTGCATTTGTTATCTG
TAAGCTGATATTATTAATAAAATATTTAAACTATGAAAGAAATTCTTTCC
TAAATAACACAAAATACCATTTGAACAAAAATGAAATATATTTCAAAGAC
ATGGTCGTCATTAGCATTTCTATTTTCTCAACAATTTTAAAATATGAGAC
CTGTGTCGCGGTCAGAGCAGCCTCTTGAATTGCATCTTTTACTGCTAAAT
TTGAAGAACGGTCAAATTTCTCTACCTCTTAAAGCTTGGTAAAAGTCTTT
TAAATTTACTATTTAACCCTAAGCAACGACGCTTGGACTGTTCTTGCTCG
TCCAAATTTTTTTTTCAAAATCATCTTCTATAATGGCCC
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protein sequence of SMED30029160-orf-1

>SMED30029160-orf-1 ID=SMED30029160-orf-1|Name=SMED30029160-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=156bp
FSIMKIIFLLSIIVFTISNVNSRISMINIQFRNGWSFVQKFAFLTKEGQS
KVTLKVNNQYNTNFLMAMFIDNEDLWNLFLDTKPTCQQLRISKLSHIITS
LNNTSSLSVVDNTTVYTNYLWFPSNDQSFYTFSVLLACDRTEIFWSRLYF
SSSRI*
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protein sequence of SMED30029160-orf-2

>SMED30029160-orf-2 ID=SMED30029160-orf-2|Name=SMED30029160-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
MLKIEQRESILTILFGIVISIKFIVFFCQMWIYLNYAATGVYSYVAFVIC
KLILLIKYLNYERNSFLNNTKYHLNKNEIYFKDMVVISISIFSTILKYET
CVAVRAAS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0002032epidermal cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR003133T_Ag_DNA-bd
Vocabulary: biological process
TermDefinition
GO:0006260DNA replication
Vocabulary: molecular function
TermDefinition
GO:0003688DNA replication origin binding
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..22
score: 0.783