SMED30024515

Overview
NameSMED30024515
Smed IDSMED30024515
Length (bp)379
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 SMED30024515 (SMED30024515) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024515 (SMED30024515) 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



SMED30024515

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30024515SMESG000020136.1 dd_Smed_v4_3048_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30024515SMESG000020136.1 dd_Smed_v4_3048_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30024515SMESG000020136.1 dd_Smed_v4_3048_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30024515SMESG000020136.1 dd_Smed_v4_3048_0_1dd_Smed_v4PMID:30962434
Cote et al., 2019		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30024515 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001554:42674..45585 +1843
Homology
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BLAST of SMED30024515 vs. Planmine SMEST
Match: SMESG000020136.1 (SMESG000020136.1)

HSP 1 Score: 208.764 bits (530), Expect = 4.508e-71
Identity = 119/119 (100.00%), Postives = 119/119 (100.00%), Query Frame = -2 
Query:   13 MLKSLIVFSIIGYCSSLSCIPCNEVKCNDANLNCPKSQFVKGICGCCNVCGLQEGKICTSFSICMKGTLCETAFGCRYRNTLPFYIPFKGVCVXXXXXXXXXXXNCYNYKYVVSQIKYR 369
            MLKSLIVFSIIGYCSSLSCIPCNEVKCNDANLNCPKSQFVKGICGCCNVCGLQEGKICTSFSICMKGTLCETAFGCRYRNTLPFYIPFKGVCVKEKENEEPIEPNCYNYKYVVSQIKYR
Sbjct:    1 MLKSLIVFSIIGYCSSLSCIPCNEVKCNDANLNCPKSQFVKGICGCCNVCGLQEGKICTSFSICMKGTLCETAFGCRYRNTLPFYIPFKGVCVKEKENEEPIEPNCYNYKYVVSQIKYR 119
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BLAST of SMED30024515 vs. Planmine SMEST
Match: SMESG000039126.1 (SMESG000039126.1)

HSP 1 Score: 86.6557 bits (213), Expect = 6.328e-23
Identity = 54/116 (46.55%), Postives = 68/116 (58.62%), Query Frame = -2 
Query:   25 MLKSLIVFSIIGYCSSLSCIPCNEVKCNDANLNCPKSQFVKGICGCCNVCGLQEGKICTS-FSICMKGTLCETAFGCRYRNTLPFYIPFKGVCVXXXXXXXXXXXNCYNYKYVVSQ 369
            M  + I+  +IGY  SLSC  C    CN   LNCP+SQ ++  C CC VC   EG+IC S    C  G  C T +GCRY N LP+++P +GVC KE  NE P + NCY Y Y+  Q
Sbjct:    1 MKVAFILLLLIGYTYSLSC-KCFASSCNSVKLNCPRSQQIRDSCNCCYVCANLEGQICESNIKACAPGLRCVTEYGCRYSNHLPWFLPIQGVCEKELPNEPPADINCYRYSYLQQQ 115
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BLAST of SMED30024515 vs. Planmine SMEST
Match: SMESG000020144.1 (SMESG000020144.1)

HSP 1 Score: 83.5741 bits (205), Expect = 1.279e-21
Identity = 45/99 (45.45%), Postives = 61/99 (61.62%), Query Frame = -2 
Query:   25 CIPCNEVKCNDANLNCPKSQFVKGICGCCNVCGLQEGKICTSFS--ICMKGTLCETAFGCRYRNTLPFYIPFKGVCVXXXXXXXXXXXNCYNYKYVVSQ 315
            C PC+   C   + +CP+S+ V  IC CC VCGLQEG+ CTS S   C  G  CET+FGCRY+  LP+  P  G CV+EK +E+     CY+  +++ Q
Sbjct:   21 CPPCDMSSCTPVSSSCPESRIVPSICSCCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQ 119
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BLAST of SMED30024515 vs. Planmine SMEST
Match: SMESG000020144.1 (SMESG000020144.1)

HSP 1 Score: 77.0258 bits (188), Expect = 2.399e-19
Identity = 42/91 (46.15%), Postives = 57/91 (62.64%), Query Frame = -2 
Query:   25 CNDANLNCPKSQFVKGICGCCNVCGLQEGKICTSFS--ICMKGTLCETAFGCRYRNTLPFYIPFKGVCVXXXXXXXXXXXNCYNYKYVVSQ 291
            C   + +CP+S+ V  IC CC VCGLQEG+ CTS S   C  G  CET+FGCRY+  LP+  P  G CV+EK +E+     CY+  +++ Q
Sbjct:    4 CTPVSSSCPESRIVPSICSCCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQ 94
[Close]
BLAST of SMED30024515 vs. Planmine SMEST
Match: SMESG000020133.1 (SMESG000020133.1)

HSP 1 Score: 68.5514 bits (166), Expect = 8.755e-16
Identity = 43/100 (43.00%), Postives = 56/100 (56.00%), Query Frame = -2 
Query:   22 CIPCNEVKCNDANLNCPKSQFVKGICGCCNVCGLQEGKICTSF--SICMKGTLCETAFGCRYRNTLPFYIPFKGVCVXXXXXXXXXXXNCYNYKYVVSQI 315
            C PC + +C   +LNC     V   C CCNVCG+ EG+ICTS   S C  G  C T FGCRY+  LP  I  +G C KEK  E     +CY  ++++ Q+
Sbjct:   21 CPPCFQQECPKNDLNCRLENTVSDRCNCCNVCGITEGEICTSISSSRCANGLRCVTNFGCRYQYYLPTEIMVRGRCEKEKPKEPNTPDHCYKIEFIMKQV 120
The following BLAST results are available for this feature:
BLAST of SMED30024515 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 SMED30024515 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 SMED30024515 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 SMED30024515 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 SMED30024515 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 SMED30024515 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 SMED30024515 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 SMED30024515 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 SMED30024515 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 SMED30024515 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 SMED30024515 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 SMED30024515 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 SMED30024515 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 SMED30024515 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000020136.14.508e-71100.00SMESG000020136.1[more]
SMESG000039126.16.328e-2346.55SMESG000039126.1[more]
SMESG000020144.11.279e-2145.45SMESG000020144.1[more]
SMESG000020144.12.399e-1946.15SMESG000020144.1[more]
SMESG000020133.18.755e-1643.00SMESG000020133.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024515 ID=SMED30024515|Name=SMED30024515|organism=Schmidtea mediterranea sexual|type=transcript|length=379bp
TTTTTTACATTAACGATATTTTATTTGACTCACAACATATTTATAATTAT
AGCAATTTGGTTCTATTGGTTCTTCATTTTCTTTTTCTTTTACACAAACT
CCTTTGAATGGAATATAAAATGGAAGTGTATTCCTGTATCTACACCCGAA
CGCCGTCTCACATAAAGTGCCTTTCATGCATATACTAAATGAAGTGCAAA
TTTTTCCTTCTTGCAACCCACAGACATTGCAACATCCACAAATGCCTTTC
ACAAATTGACTCTTAGGACAATTGAGATTGGCATCGTTGCACTTCACTTC
GTTGCAAGGTATACAGGATAATGAAGAGCAGTAACCAATTATGCTAAATA
CTATCAATGACTTCAACATTTAAATGAAA
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protein sequence of SMED30024515-orf-1

>SMED30024515-orf-1 ID=SMED30024515-orf-1|Name=SMED30024515-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=120bp
MLKSLIVFSIIGYCSSLSCIPCNEVKCNDANLNCPKSQFVKGICGCCNVC
GLQEGKICTSFSICMKGTLCETAFGCRYRNTLPFYIPFKGVCVKEKENEE
PIEPNCYNYKYVVSQIKYR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000025nervous system
PLANA:0000099neuron
Vocabulary: INTERPRO
TermDefinition
IPR000867IGFBP-like
IPR009030Growth_fac_rcpt_cys_sf
Vocabulary: molecular function
TermDefinition
GO:0005520insulin-like growth factor binding
Vocabulary: biological process
TermDefinition
GO:0001558regulation of cell growth
Vocabulary: cellular component
TermDefinition
GO:0005576extracellular region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000867Insulin-like growth factor-binding protein, IGFBPPROSITEPS51323IGFBP_N_2coord: 15..79
score: 10.313
NoneNo IPR availablePROSITEPS51257PROKAR_LIPOPROTEINcoord: 1..19
score: 5.0
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..16
score: 0.798
IPR009030Growth factor receptor cysteine-rich domain superfamilySUPERFAMILYSSF57184Growth factor receptor domaincoord: 17..96