SMED30029999

Overview
NameSMED30029999
Smed IDSMED30029999
Length (bp)675
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30029999 (SMED30029999) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029999 (SMED30029999) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30029999

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
parapharyngeal regionSMED30029999h1SMcG0020714 SmedASXL_009142SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30029999h1SMcG0020714 dd_Smed_v4_12708_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029999h1SMcG0020714 Contig54473newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029999h1SMcG0020714 Contig54473uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30029999h1SMcG0020714 dd_Smed_v6_12708_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30029999 vs. Planmine SMEST
Match: SMESG000017257.1 (SMESG000017257.1)

HSP 1 Score: 388.652 bits (997), Expect = 8.322e-139
Identity = 183/187 (97.86%), Postives = 186/187 (99.47%), Query Frame = 2 
Query:   56 SQMNYSISERTSNKNYGSFYGSSDLNRYVFTDRRPCNHAFHGVSDPLTDRIYFKNRNGITTNSSYGSFLDHLSDASHPKWKLRPDLMNSICQTVQKHAKENQGNKESIIEKIHDLEQLEHLYQETEKRSPRKDENVVRNQVAQLRETRNQTIQHIQCDPPFSWSLVDKVEIQMLDGSTLFLTKADLD 616
            SQMNYSISERTSNKNYGSFYGSSDLN+YVFTDRRPCNHAFHGVSDPLTDRIYFKNRNGITTNSSYGSFLDHLSDASHPKWKLRPDLMNSICQTVQK+AKENQGNKESIIEKIHDLEQLEHLYQE EKRSPRKDENVVRNQVAQLRETR+QTIQHIQCDPPFSWSLVDKVEIQMLDGSTLFLTKADLD
Sbjct:   42 SQMNYSISERTSNKNYGSFYGSSDLNKYVFTDRRPCNHAFHGVSDPLTDRIYFKNRNGITTNSSYGSFLDHLSDASHPKWKLRPDLMNSICQTVQKNAKENQGNKESIIEKIHDLEQLEHLYQEIEKRSPRKDENVVRNQVAQLRETRDQTIQHIQCDPPFSWSLVDKVEIQMLDGSTLFLTKADLD 228
The following BLAST results are available for this feature:
BLAST of SMED30029999 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029999 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000017257.18.322e-13997.86SMESG000017257.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029999 ID=SMED30029999|Name=SMED30029999|organism=Schmidtea mediterranea sexual|type=transcript|length=675bp
AAACATTTGAAAAACTGGAAAAAAATATTCAAGAAAAAAAAAGAAAGAAA
AAAAATCACAAATGAATTACAGCATAAGTGAAAGAACTAGCAACAAAAAT
TACGGATCATTTTACGGAAGCAGTGATCTCAACAGGTATGTCTTTACAGA
TAGAAGGCCATGCAATCACGCCTTTCACGGGGTCAGTGATCCGTTGACAG
ATCGGATTTATTTCAAAAACAGAAACGGCATAACCACCAATTCCAGCTAC
GGCTCCTTTCTCGATCACTTATCTGATGCCTCCCATCCAAAATGGAAATT
GAGACCAGATTTAATGAACTCAATTTGTCAAACCGTTCAAAAGCACGCGA
AGGAAAATCAAGGAAACAAAGAATCAATCATCGAAAAAATTCACGACTTA
GAACAACTGGAACATTTGTATCAAGAAACAGAGAAAAGATCTCCAAGAAA
AGATGAAAATGTCGTCCGAAATCAGGTCGCTCAACTTCGTGAAACACGGA
ACCAAACTATCCAACACATTCAGTGTGATCCACCATTCAGTTGGAGTCTG
GTTGACAAGGTCGAGATTCAGATGCTTGATGGGTCAACATTATTCCTGAC
CAAGGCTGACCTTGATAACATTAATTTCATAGAATAATATAACAACTAAA
TTGACAGATATTTTTATTATTAAAA
back to top

protein sequence of SMED30029999-orf-1

>SMED30029999-orf-1 ID=SMED30029999-orf-1|Name=SMED30029999-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=192bp
MNYSISERTSNKNYGSFYGSSDLNRYVFTDRRPCNHAFHGVSDPLTDRIY
FKNRNGITTNSSYGSFLDHLSDASHPKWKLRPDLMNSICQTVQKHAKENQ
GNKESIIEKIHDLEQLEHLYQETEKRSPRKDENVVRNQVAQLRETRNQTI
QHIQCDPPFSWSLVDKVEIQMLDGSTLFLTKADLDNINFIE*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000418head
PLANA:0000420parapharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 7..21
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..21