SMED30026746

Overview
NameSMED30026746
Smed IDSMED30026746
Length (bp)468
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 SMED30026746 (SMED30026746) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026746 (SMED30026746) 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




SMED30026746

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
intestinal phagocyteSMED30026746SMESG000061917.1 Contig1936newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30026746SMESG000061917.1 Contig1936uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30026746SMESG000007405.1 SMESG000034704.1 Contig1936newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30026746SMESG000007405.1 SMESG000034704.1 Contig1936uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
nervous systemSMED30026746SMESG000061917.1 dd_Smed_v4_588_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026746SMESG000061917.1 dd_Smed_v4_588_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30026746SMESG000061917.1 dd_Smed_v4_588_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
SMED30026746 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000666:85366..85923 +2216
Homology
BLAST of SMED30026746 vs. TrEMBL
Match: V9XTG6 (X1.D.A5.1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 3.050e-8
Identity = 28/85 (32.94%), Postives = 46/85 (54.12%), Query Frame = 2
Query:  122 IVLSAMADASLFLGRGYRNSEGVPYVKIFDQVFKAEESSTQKIYQNERCYLCNIKAPGSGRLPRYTCQGPSPGSTNGKIKYISPC 376
            + L +  ++ L  GRG+ + +G   V+IFDQ F A +    ++   ++CY C I+   SG  P + C+GPS    + K  Y+ PC
Sbjct:   12 MCLMSYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIEPAVSGEQPLFECEGPSLVRVDEKDIYLDPC 96          
BLAST of SMED30026746 vs. Planmine SMEST
Match: SMESG000061917.1 (SMESG000061917.1)

HSP 1 Score: 189.504 bits (480), Expect = 2.044e-63
Identity = 92/93 (98.92%), Postives = 92/93 (98.92%), Query Frame = 2
Query:   98 MLLILSGIIVLSAMADASLFLGRGYRNSEGVPYVKIFDQVFKAEESSTQKIYQNERCYLCNIKAPGSGRLPRYTCQGPSPGSTNGKIKYISPC 376
            MLLILSGIIVLSAMADASLFLGRGYRNSEGVPYVKIFDQVFKAEESSTQKIYQNERCYLCNIKAPGSGRLPRYTCQGPSP STNGKIKYISPC
Sbjct:    1 MLLILSGIIVLSAMADASLFLGRGYRNSEGVPYVKIFDQVFKAEESSTQKIYQNERCYLCNIKAPGSGRLPRYTCQGPSPSSTNGKIKYISPC 93          
BLAST of SMED30026746 vs. Planmine SMEST
Match: SMESG000028873.1 (SMESG000028873.1)

HSP 1 Score: 74.7146 bits (182), Expect = 3.880e-18
Identity = 37/93 (39.78%), Postives = 52/93 (55.91%), Query Frame = 2
Query:   98 MLLILSGIIVLSAMADASLFLGRGYRNSEGVPYVKIFDQVFKAEESSTQKIYQNERCYLCNIKAPGSGRLPRYTCQGPSPGSTNGKIKYISPC 376
            M++ +  ++  S+ +DAS   G G  N +G P V IF   FKAE+ + +K+++   CYLC IK      LP +TC GP P    GKI Y S C
Sbjct:    1 MIIFVLFVLAFSSFSDASFIKGFGRINEKGNPEVVIFGYTFKAEDIAIKKLFRGNTCYLCVIKPRQGEMLPTFTCIGPDPIKVKGKIYYKSAC 93          
BLAST of SMED30026746 vs. Planmine SMEST
Match: SMESG000039587.1 (SMESG000039587.1)

HSP 1 Score: 73.1738 bits (178), Expect = 1.619e-17
Identity = 41/96 (42.71%), Postives = 55/96 (57.29%), Query Frame = 2
Query:   92 EKMLLILSGIIVLSAMADASLFLGRGYRNSEGVPYVKIFDQVFKAEESSTQKIYQNERCYLCNIKAPGS-GRLPRYTCQGPSPGSTNGKIKYISPC 376
            + ++ +L    VL+++ADA +F G G  + +G PYV I   VF A  S   +  +   C +CNI AP S   LPR+ CQG SP S NGK  Y SPC
Sbjct:    2 KNIISLLVFAFVLASIADAHVFRGTGNFDRKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNGKQAYKSPC 97          
BLAST of SMED30026746 vs. Planmine SMEST
Match: SMESG000006666.1 (SMESG000006666.1)

HSP 1 Score: 73.1738 bits (178), Expect = 1.619e-17
Identity = 41/96 (42.71%), Postives = 55/96 (57.29%), Query Frame = 2
Query:   92 EKMLLILSGIIVLSAMADASLFLGRGYRNSEGVPYVKIFDQVFKAEESSTQKIYQNERCYLCNIKAPGS-GRLPRYTCQGPSPGSTNGKIKYISPC 376
            + ++ +L    VL+++ADA +F G G  + +G PYV I   VF A  S   +  +   C +CNI AP S   LPR+ CQG SP S NGK  Y SPC
Sbjct:    2 KNIISLLVFAFVLASIADAHVFRGTGNFDRKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFECQGASPVSLNGKQAYKSPC 97          
BLAST of SMED30026746 vs. Planmine SMEST
Match: SMESG000013036.1 (SMESG000013036.1)

HSP 1 Score: 69.3218 bits (168), Expect = 4.041e-16
Identity = 32/77 (41.56%), Postives = 47/77 (61.04%), Query Frame = 2
Query:  146 ASLFLGRGYRNSEGVPYVKIFDQVFKAEESSTQKIYQNERCYLCNIKAPGSGRLPRYTCQGPSPGSTNGKIKYISPC 376
            A  F G GY++S G P+VKI D++F+A+ +   K+  N +CY C+IK   +G  P Y C GP P   +GK+ Y+  C
Sbjct:   19 ADEFFGYGYKDSNGKPFVKIADRIFEADTAREVKVNINSQCYKCSIK---TGDRPMYECSGPVPSFVDGKVTYVPVC 92          
The following BLAST results are available for this feature:
BLAST of SMED30026746 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 SMED30026746 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 SMED30026746 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 SMED30026746 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 SMED30026746 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 SMED30026746 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 SMED30026746 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 SMED30026746 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XTG63.050e-832.94X1.D.A5.1 OS=Schmidtea mediterranea OX=79327 PE=2 ... [more]
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BLAST of SMED30026746 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 SMED30026746 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 SMED30026746 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 SMED30026746 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 SMED30026746 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 SMED30026746 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000061917.12.044e-6398.92SMESG000061917.1[more]
SMESG000028873.13.880e-1839.78SMESG000028873.1[more]
SMESG000039587.11.619e-1742.71SMESG000039587.1[more]
SMESG000006666.11.619e-1742.71SMESG000006666.1[more]
SMESG000013036.14.041e-1641.56SMESG000013036.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026746 ID=SMED30026746|Name=SMED30026746|organism=Schmidtea mediterranea sexual|type=transcript|length=468bp
CTACTTNTAATTAGTCAAATAGATCTAAGATAACTAGACAAATATCCAAC
TATAAAAGAGTGGATTTTGGACAAATTTTCCTTGTTTCTGTGAAAAAATG
CTTTTGATTCTTTCTGGAATAATTGTTCTCAGTGCCATGGCAGATGCATC
GCTATTTCTTGGGCGAGGATATCGCAATTCTGAAGGTGTTCCATATGTTA
AAATATTTGACCAAGTATTTAAAGCCGAAGAATCATCAACCCAAAAAATA
TATCAAAATGAACGTTGTTATCTCTGTAACATTAAAGCTCCGGGGTCTGG
AAGACTACCAAGATACACTTGTCAAGGACCAAGTCCGGGTTCTACAAATG
GGAAAATAAAATATATTTCGCCATGCTAAATTTGTGAACTTTTGAAAAAT
AATGACAAAAAATAATTTGTTTTATTAAATCAATTTTAATAAATATATTT
AACAAAANNNNNAAAAAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
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..17
score: 0.774