SMED30008225

Overview
NameSMED30008225
Smed IDSMED30008225
Length (bp)449
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 SMED30008225 (SMED30008225) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008225 (SMED30008225) 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.
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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



SMED30008225

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30008225SMESG000039587.1 SMESG000006666.1 SmedASXL_051097SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parenchymaSMED30008225SMESG000039587.1 SMESG000006666.1 dd_Smed_v4_313_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30008225 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.031687:3598..4133 -2161
v31.020784:5243..5763 +2002
v31.020784:2000..2464 -1181
Homology
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BLAST of SMED30008225 vs. Planmine SMEST
Match: SMESG000039587.1 (SMESG000039587.1)

HSP 1 Score: 201.445 bits (511), Expect = 4.638e-68
Identity = 98/99 (98.99%), Postives = 98/99 (98.99%), Query Frame = 1 
Query:   49 MKNIISLLVFAFVLVSIADAHVFRGTGNFDRKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNGKQAYKSPCYV 345
            MKNIISLLVFAFVL SIADAHVFRGTGNFDRKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNGKQAYKSPCYV
Sbjct:    1 MKNIISLLVFAFVLASIADAHVFRGTGNFDRKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNGKQAYKSPCYV 99
[Close]
BLAST of SMED30008225 vs. Planmine SMEST
Match: SMESG000006666.1 (SMESG000006666.1)

HSP 1 Score: 201.445 bits (511), Expect = 4.638e-68
Identity = 98/99 (98.99%), Postives = 98/99 (98.99%), Query Frame = 1 
Query:   49 MKNIISLLVFAFVLVSIADAHVFRGTGNFDRKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNGKQAYKSPCYV 345
            MKNIISLLVFAFVL SIADAHVFRGTGNFDRKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNGKQAYKSPCYV
Sbjct:    1 MKNIISLLVFAFVLASIADAHVFRGTGNFDRKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNGKQAYKSPCYV 99
[Close]
BLAST of SMED30008225 vs. Planmine SMEST
Match: SMESG000006744.1 (SMESG000006744.1)

HSP 1 Score: 141.354 bits (355), Expect = 2.148e-44
Identity = 65/97 (67.01%), Postives = 79/97 (81.44%), Query Frame = 1 
Query:   49 MKNIISLLVFAFVLVSIADAHVFRGTGNFDRKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNGKQAYKSPC 339
            MKNIISLLVFA  L SI+DA++FRGTG+FD +G PYVIIKGI+FSA  SRNV+ GEG +C+ CNI AP+  SDLP FEC+GASP  ++GK+ YKS C
Sbjct:    1 MKNIISLLVFALTLASISDAYMFRGTGDFDLEGTPYVIIKGIMFSAANSRNVKLGEGADCVNCNISAPQLSSDLPTFECRGASPAFIDGKRIYKSAC 97
[Close]
BLAST of SMED30008225 vs. Planmine SMEST
Match: SMESG000006744.1 (SMESG000006744.1)

HSP 1 Score: 108.997 bits (271), Expect = 6.563e-32
Identity = 49/76 (64.47%), Postives = 61/76 (80.26%), Query Frame = 1 
Query:  112 VFRGTGNFDRKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNGKQAYKSPC 339
            +FRGTG+FD +G PYVIIKGI+FSA  SRNV+ GEG +C+ CNI AP+  SDLP FEC+GASP  ++GK+ YKS C
Sbjct:    1 MFRGTGDFDLEGTPYVIIKGIMFSAANSRNVKLGEGADCVNCNISAPQLSSDLPTFECRGASPAFIDGKRIYKSAC 76
[Close]
BLAST of SMED30008225 vs. Planmine SMEST
Match: SMESG000006559.1 (SMESG000006559.1)

HSP 1 Score: 77.411 bits (189), Expect = 7.524e-19
Identity = 41/90 (45.56%), Postives = 57/90 (63.33%), Query Frame = 1 
Query:   49 MKNII-SLLVFAFVLVSIADAHVFRGTGNFDRKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNG 315
            MK+II +L   AF  +SIADA  F G G+FD+ G+P+V I G  FSA +S  VR GEG+ C+ C I  P S+ + P + C+ A+ V + G
Sbjct:    1 MKSIIFALFAIAFA-ISIADAAEFGGVGSFDQSGSPFVKINGQRFSAAKSLVVRIGEGIKCVKCEISPPSSKGEKPSYVCETANAVKVGG 89
The following BLAST results are available for this feature:
BLAST of SMED30008225 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 SMED30008225 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 SMED30008225 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 SMED30008225 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 SMED30008225 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 SMED30008225 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 SMED30008225 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 SMED30008225 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 SMED30008225 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 SMED30008225 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 SMED30008225 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 SMED30008225 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 SMED30008225 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 SMED30008225 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000039587.14.638e-6898.99SMESG000039587.1[more]
SMESG000006666.14.638e-6898.99SMESG000006666.1[more]
SMESG000006744.12.148e-4467.01SMESG000006744.1[more]
SMESG000006744.16.563e-3264.47SMESG000006744.1[more]
SMESG000006559.17.524e-1945.56SMESG000006559.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008225 ID=SMED30008225|Name=SMED30008225|organism=Schmidtea mediterranea sexual|type=transcript|length=449bp
TATAAATTGAATGTAATTTCACCGGTATTTCATACACTTGAATAAATCAT
GAAAAACATTATTTCTTTGCTAGTTTTCGCATTTGTTTTGGTTTCAATAG
CTGATGCTCATGTTTTTAGAGGAACTGGTAACTTCGATCGCAAAGGTAAC
CCATATGTAATCATCAAAGGAATAGTGTTTTCGGCCACCCGTTCAAGAAA
TGTAAGATTCGGTGAAGGCGTCAACTGTATCATTTGCAATATTTATGCTC
CTAAGTCGAGATCTGATTTACCAAGATTCGAATGTCAAGGAGCGTCTCCA
GTTTCCCTTAATGGTAAACAAGCTTACAAATCTCCATGTTACGTTTAACA
ATCAAATATTTAACAATCAAATATACAATCAAATAATTATTATTTTCAAA
TCTTGATTAAAAACCAATTTTAATAAAATCAATTAATTTTTAAAAAAAA
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protein sequence of SMED30008225-orf-1

>SMED30008225-orf-1 ID=SMED30008225-orf-1|Name=SMED30008225-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp
MKNIISLLVFAFVLVSIADAHVFRGTGNFDRKGNPYVIIKGIVFSATRSR
NVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNGKQAYKSPCYV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
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..20
score: 0.875
NoneNo IPR availableTMHMMTMhelixcoord: 4..23