SMED30016916

Overview
NameSMED30016916
Smed IDSMED30016916
Length (bp)614
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 SMED30016916 (SMED30016916) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016916 (SMED30016916) 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



SMED30016916

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
prepharyngeal regionSMED30016916h1SMcG0022474 SmedASXL_019068SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30016916h1SMcG0022474 SmedASXL_019068SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pigment cellSMED30016916h1SMcG0022474 SmedASXL_019068SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30016916h1SMcG0022474 OX_Smed_1.0.22186ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30016916h1SMcG0022474 KF134120smed_ncbi_20240424PMID:23903188
Currie et al., 2013		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30016916 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001374:53883..54539 -3046
Homology
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BLAST of SMED30016916 vs. TrEMBL
Match: S5VQ20 (Upps (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 166.777 bits (421), Expect = 6.104e-49
Identity = 147/155 (94.84%), Postives = 150/155 (96.77%), Query Frame = -2 
Query:  107 MGFTLLSILFFMVFTLSNGERRDSLTEENILALPDDGGDDNTNIAFRYIKYLSKNEDEQVAKXXXXXXXXXXXXXXXSGSEFXXXXXXXXXXXXXXXXXXXXXXDKPVKTMKKEDSVXXXXXXXXXXXXXXXXXTHEWNGVGKDLRSNKNRAVDS 571
            +  +LLSILFFMVFTLSNGERRDSLTEENILALPDDGGDDNTNIAFRYIKYLSKNEDEQVA+ SDEDDEESHLHHLDSGSEFDKEEIIEIEINNNKNDELILLEDKPVKTMKKEDSVETEIEITSESEEEEIEITHEWNGVGKD RSNKNR VDS
Sbjct:    2 LPISLLSILFFMVFTLSNGERRDSLTEENILALPDDGGDDNTNIAFRYIKYLSKNEDEQVAEGSDEDDEESHLHHLDSGSEFDKEEIIEIEINNNKNDELILLEDKPVKTMKKEDSVETEIEITSESEEEEIEITHEWNGVGKDFRSNKNRVVDS 156
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BLAST of SMED30016916 vs. Planmine SMEST
Match: SMESG000010015.1 (SMESG000010015.1)

HSP 1 Score: 179.489 bits (454), Expect = 1.355e-57
Identity = 155/155 (100.00%), Postives = 155/155 (100.00%), Query Frame = -2 
Query:  107 MGFTLLSILFFMVFTLSNGERRDSLTEENILALPDDGGDDNTNIAFRYIKYLSKNEDEQVAKXXXXXXXXXXXXXXXSGSEFXXXXXXXXXXXXXXXXXXXXXXDKPVKTMKKEDSVXXXXXXXXXXXXXXXXXTHEWNGVGKDLRSNKNRAVDS 571
            MGFTLLSILFFMVFTLSNGERRDSLTEENILALPDDGGDDNTNIAFRYIKYLSKNEDEQVAKDSDEDDEESHLHHLDSGSEFDKEEIIEIEINNNKNDELILLEDKPVKTMKKEDSVETEIEITSESEEEEIEITHEWNGVGKDLRSNKNRAVDS
Sbjct:    1 MGFTLLSILFFMVFTLSNGERRDSLTEENILALPDDGGDDNTNIAFRYIKYLSKNEDEQVAKDSDEDDEESHLHHLDSGSEFDKEEIIEIEINNNKNDELILLEDKPVKTMKKEDSVETEIEITSESEEEEIEITHEWNGVGKDLRSNKNRAVDS 155
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BLAST of SMED30016916 vs. Planmine SMEST
Match: SMESG000010015.1 (SMESG000010015.1)

HSP 1 Score: 157.532 bits (397), Expect = 4.857e-49
Identity = 144/144 (100.00%), Postives = 144/144 (100.00%), Query Frame = -2 
Query:  107 MVFTLSNGERRDSLTEENILALPDDGGDDNTNIAFRYIKYLSKNEDEQVAKXXXXXXXXXXXXXXXSGSEFXXXXXXXXXXXXXXXXXXXXXXDKPVKTMKKEDSVXXXXXXXXXXXXXXXXXTHEWNGVGKDLRSNKNRAVDS 538
            MVFTLSNGERRDSLTEENILALPDDGGDDNTNIAFRYIKYLSKNEDEQVAKDSDEDDEESHLHHLDSGSEFDKEEIIEIEINNNKNDELILLEDKPVKTMKKEDSVETEIEITSESEEEEIEITHEWNGVGKDLRSNKNRAVDS
Sbjct:    1 MVFTLSNGERRDSLTEENILALPDDGGDDNTNIAFRYIKYLSKNEDEQVAKDSDEDDEESHLHHLDSGSEFDKEEIIEIEINNNKNDELILLEDKPVKTMKKEDSVETEIEITSESEEEEIEITHEWNGVGKDLRSNKNRAVDS 144
The following BLAST results are available for this feature:
BLAST of SMED30016916 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 SMED30016916 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 SMED30016916 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 SMED30016916 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 SMED30016916 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 SMED30016916 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 SMED30016916 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 SMED30016916 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
S5VQ206.104e-4994.84Upps (Fragment) OS=Schmidtea mediterranea OX=79327... [more]
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BLAST of SMED30016916 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 SMED30016916 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 SMED30016916 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 SMED30016916 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 SMED30016916 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 SMED30016916 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000010015.11.355e-57100.00SMESG000010015.1[more]
SMESG000010015.14.857e-49100.00SMESG000010015.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016916 ID=SMED30016916|Name=SMED30016916|organism=Schmidtea mediterranea sexual|type=transcript|length=614bp
AAAAATAAAATTTTATTTAATCACAAAATTATCCAATTTAATTGTTAAAT
ACAAAATGATTTTATTTGGATTTTTTCTTCTTGTGAGATTTTTGTTCCTC
GTTTTTACTATCCACCGCTCTGTTCTTATTCGATCTCAAATCTTTGCCAA
CTCCATTCCATTCGTGGGTTATCTCGATCTCCTCTTCCTCTGATTCAGAT
GTAATTTCTATTTCCGTTTCAACACTGTCTTCCTTTTTCATTGTTTTGAC
CGGTTTGTCCTCCAACAATATCAGTTCATCATTTTTATTATTGTTTATTT
CGATTTCAATAATTTCCTCTTTATCGAATTCTGAGCCGGAGTCCAAGTGA
TGCAGGTGACTCTCTTCATCATCTTCATCCGAATCTTTGGCGACTTGTTC
GTCTTCATTTTTGCTTAAATATTTTATGTATCTGAAAGCGATGTTTGTAT
TGTCATCACCTCCATCGTCAGGGAGAGCCAAAATATTTTCTTCTGTCAAA
GAATCTCGCCTTTCTCCATTGGATAAAGTAAAGACCATAAAAAATAGAAT
AGAAAGTAAAGTAAACCCCATTTTAATGCACCTCCTTAATATATTTCACC
TCTTTATAACAAAT
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protein sequence of SMED30016916-orf-1

>SMED30016916-orf-1 ID=SMED30016916-orf-1|Name=SMED30016916-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=170bp
MGFTLLSILFFMVFTLSNGERRDSLTEENILALPDDGGDDNTNIAFRYIK
YLSKNEDEQVAKDSDEDDEESHLHHLDSGSEFDKEEIIEIEINNNKNDEL
ILLEDKPVKTMKKEDSVETEIEITSESEEEEIEITHEWNGVGKDLRSNKN
RAVDSKNEEQKSHKKKKSK*
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Aliases
The feature 'SMED30016916' has the following synonyms
Synonym
upps
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0002075pigment cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 113..169
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 134..161
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 58..82
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.836