SMED30015008

Overview
NameSMED30015008
Smed IDSMED30015008
Length (bp)1778
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.
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



SMED30015008

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30015008SMESG000001496.1 SMESG000001495.1 SmedASXL_014725SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30015008 SmedASXL_020994SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30015008SMESG000001496.1 SMESG000001495.1 dd_Smed_v4_14943_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30015008SMESG000001496.1 SMESG000001495.1 dd_Smed_v4_14943_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30015008SMESG000001496.1 SMESG000001495.1 dd_Smed_v4_14943_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30015008SMESG000001496.1 SMESG000001495.1 dd_Smed_v4_14943_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30015008SMESG000001496.1 SMESG000001495.1 dd_Smed_v6_14943_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30015008 dd_Smed_v6_27917_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30015008SMESG000001496.1 SMESG000001495.1 dd_Smed_v4_14943_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
SMED30015008 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007448:25835..33817 +8789
v31.006908:21208..29090 +8780
Homology
[Close]
BLAST of SMED30015008 vs. Planmine SMEST
Match: SMESG000001495.1 (SMESG000001495.1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.638e-9
Identity = 25/27 (92.59%), Postives = 26/27 (96.30%), Query Frame = 1 
Query:  100 MKYYGVKLIFGYWFLIYSLVQSQTTNV 180
            MKYYGVKLIFGYWFLIYSLVQSQTT +
Sbjct:    1 MKYYGVKLIFGYWFLIYSLVQSQTTGI 27
The following BLAST results are available for this feature:
BLAST of SMED30015008 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 SMED30015008 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 SMED30015008 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 SMED30015008 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 SMED30015008 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 SMED30015008 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 SMED30015008 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 SMED30015008 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 SMED30015008 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 SMED30015008 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 SMED30015008 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 SMED30015008 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 SMED30015008 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 SMED30015008 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000001495.11.638e-992.59SMESG000001495.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015008 ID=SMED30015008|Name=SMED30015008|organism=Schmidtea mediterranea sexual|type=transcript|length=1778bp
TAACAATTGAAATTTAATCAAAATATTTATTTTAAATTATTTTCTGTGAA
TAATTGATTTTATTAAGCCATTTAAGATTTATTCAAATAGATTATAAATA
TGAAGTATTATGGTGTTAAGTTAATTTTTGGATACTGGTTTCTTATATAT
TCATTGGTACAAAGTCAAACAACGAATGTGGAGAACAGTACCAGTTCACC
AGTTATAATATCTACTGGTTCAATGTCTGTAACTTCTGCAGATACAACAT
CTGTAACTGGCATTATACAGACCCAAACAAACTCATCTGTAATAACAATT
ACATCTTCACCAAATGCAACAACATCTTCTAATTCAACTCTTACTTTAAA
CAATTTAACAAATTCTTCATATGAAGTAACAACTCAATCCTTTTTAATGA
AAACTTCGAACTTAATTCAATCTACACCAGAACAATCTTCGTCGAACAGT
ACTTTTTCAATAGCATCTTCTAATTTTATTACGTCTTCATCAATACAACC
TTCATCTAATCTCACATCTATAAGTACGCCCTTGCCCTTTTCCTCCACAG
ACAATAACGTATCGTCTACTATAATTTCTGATATTAAAACTTCGATGTTA
CCGACATCTACGCTCGCATCGTCTACCATTATTTCCGTAGGATCTTCTTC
TCAAGGTTTATCATCATCAAATACAACGCAGGTATAACCACCATGTAGAT
AATTGGTGTAAATAACCCTTTTGAATTACTAGTATTACATGTGATGTATT
GTTGTCTTTTTAACACTGGTATTATATTTATACACCTGTAGACAAAACAG
ATTTGGCTTTGAAAATATTTAATAAAATCAGTAGTTCAATTAGATCATGG
GTGGGCAACCCTTTTTGTGCCGAAGGCCGCGTAATAATTTTCTTTGAAAA
CCAGACAAAAAGTTTGTCTAAAATAAAGAAATTATTAAAAAAAAATTAAC
AAAGTACGCAGGCCGTAGGTTGCCCAGTCCTGATTTAGACAAACAATGCT
TAGCATATAAACAATCTACTTTAAATTGTGAAATTTAATGTGGAAATCAT
ATATTGCAGATGTACGGCCTTATGAGTACTAATAACCTAACCTTCTTCTG
CATAACTCTAACTGCTAGAGTCTAGCATATTCATAATGAAGGATACATTT
GTATTTATAGGCAAACGGTTAAATGTGTCACATTTTCATAGCATTGATGG
TCATCCTCTCAGAAAATATCAAACCCCTTATTTGTCTGTTGAAAGTCACT
GAGTGTTGCTCGAGGACAACTGTTTCTTTCATCAACAAAAAAAGGTAAAC
ATGTCGATTTCAAGATTAGGAATGAAGATGATTAGAAAGCATCGTATGCA
AGAAAGTTCAACAGAAATGTGGCACGATTGTGAAACGCTAACAAAAACGA
TAAACAAATTAACATAGTGGTAGCACAATAATTTTGTGTGGTGCAATTAC
ATTATTAGTTATACTTCCATTGAATGCAATTGAAAGAAAACGAACTACCT
AAAGATGGACAGAATATCATTTTTTTTGTGATCATTTCAAATAATCTAGT
CATTTTTCCAATATTTGAAAGAAAACAATATATGGATTGTCCAGTTATAT
AAATAAGTTAATCTACATATGTATAGGTCATGGAACCCCCCCCTTCCATT
ACCGAGATAAATGCTATTTTTAAGATATTAATGAATTGCAAGTATTAATT
TTAGGAAAGTGTTTATTTTATTCAATAGTGCTTTGATTGCATGCTAACCA
CCTTATATATACTCCATGAACTCTTGAA
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002032epidermal cell
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: 0.69