SMED30015799

Overview
NameSMED30015799
Smed IDSMED30015799
Length (bp)656
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 SMED30015799 (SMED30015799) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30015799 (SMED30015799) 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




SMED30015799

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 systemSMED30015799h1SMcG0018038 dd_Smed_v4_895_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30015799h1SMcG0018038 dd_Smed_v4_895_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30015799h1SMcG0018038 dd_Smed_v4_895_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30015799h1SMcG0018038 dd_Smed_v4_895_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
SMED30015799 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001050:6339..7042 +3220
Homology
BLAST of SMED30015799 vs. Planmine SMEST
Match: SMESG000039126.1 (SMESG000039126.1)

HSP 1 Score: 248.44 bits (633), Expect = 3.223e-85
Identity = 122/122 (100.00%), Postives = 122/122 (100.00%), Query Frame = 2
Query:   35 MKVAFILLLLIGYTYSLSCKCFASSCNSVKLNCPRSQQIRDSCNCCYVCANLEGQICESNIKACAPGLRCVTEYGCRYSNHLPWFLPIQGVCEKELPNEPPADINCYRYSYLQQQKLKLRRE 400
            MKVAFILLLLIGYTYSLSCKCFASSCNSVKLNCPRSQQIRDSCNCCYVCANLEGQICESNIKACAPGLRCVTEYGCRYSNHLPWFLPIQGVCEKELPNEPPADINCYRYSYLQQQKLKLRRE
Sbjct:    1 MKVAFILLLLIGYTYSLSCKCFASSCNSVKLNCPRSQQIRDSCNCCYVCANLEGQICESNIKACAPGLRCVTEYGCRYSNHLPWFLPIQGVCEKELPNEPPADINCYRYSYLQQQKLKLRRE 122          
BLAST of SMED30015799 vs. Planmine SMEST
Match: SMESG000020136.1 (SMESG000020136.1)

HSP 1 Score: 101.679 bits (252), Expect = 1.347e-27
Identity = 54/116 (46.55%), Postives = 68/116 (58.62%), Query Frame = 2
Query:   35 MKVAFILLLLIGYTYSLSC-KCFASSCNSVKLNCPRSQQIRDSCNCCYVCANLEGQICESNIKACAPGLRCVTEYGCRYSNHLPWFLPIQGVCEKELPNEPPADINCYRYSYLQQQ 379
            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 MLKSLIVFSIIGYCSSLSCIPCNEVKCNDANLNCPKSQFVKGICGCCNVCGLQEGKICTS-FSICMKGTLCETAFGCRYRNTLPFYIPFKGVCVKEKENEEPIEPNCYNYKYVVSQ 115          
BLAST of SMED30015799 vs. Planmine SMEST
Match: SMESG000020133.1 (SMESG000020133.1)

HSP 1 Score: 82.8037 bits (203), Expect = 2.593e-20
Identity = 43/96 (44.79%), Postives = 56/96 (58.33%), Query Frame = 2
Query:   95 CFASSCNSVKLNCPRSQQIRDSCNCCYVCANLEGQICES-NIKACAPGLRCVTEYGCRYSNHLPWFLPIQGVCEKELPNEPPADINCYRYSYLQQQ 379
            CF   C    LNC     + D CNCC VC   EG+IC S +   CA GLRCVT +GCRY  +LP  + ++G CEKE P EP    +CY+  ++ +Q
Sbjct:   24 CFQQECPKNDLNCRLENTVSDRCNCCNVCGITEGEICTSISSSRCANGLRCVTNFGCRYQYYLPTEIMVRGRCEKEKPKEPNTPDHCYKIEFIMKQ 119          
BLAST of SMED30015799 vs. Planmine SMEST
Match: SMESG000020144.1 (SMESG000020144.1)

HSP 1 Score: 78.9518 bits (193), Expect = 8.359e-19
Identity = 41/99 (41.41%), Postives = 55/99 (55.56%), Query Frame = 2
Query:   95 CFASSCNSVKLNCPRSQQIRDSCNCCYVCANLEGQICESNIKA-CAPGLRCVTEYGCRYSNHLPWFLPIQGVCEKELPNEPPADINCYRYSYLQQQKLK 388
            C  SSC  V  +CP S+ +   C+CC VC   EG+ C SN    CA GLRC T +GCRY  +LPW  P+ G C +E P+E      CY   ++ +Q  +
Sbjct:   24 CDMSSCTPVSSSCPESRIVPSICSCCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQSGR 122          
BLAST of SMED30015799 vs. Planmine SMEST
Match: SMESG000020144.1 (SMESG000020144.1)

HSP 1 Score: 77.7962 bits (190), Expect = 1.138e-18
Identity = 40/96 (41.67%), Postives = 54/96 (56.25%), Query Frame = 2
Query:  104 SSCNSVKLNCPRSQQIRDSCNCCYVCANLEGQICESNIKA-CAPGLRCVTEYGCRYSNHLPWFLPIQGVCEKELPNEPPADINCYRYSYLQQQKLK 388
            SSC  V  +CP S+ +   C+CC VC   EG+ C SN    CA GLRC T +GCRY  +LPW  P+ G C +E P+E      CY   ++ +Q  +
Sbjct:    2 SSCTPVSSSCPESRIVPSICSCCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQSGR 97          
The following BLAST results are available for this feature:
BLAST of SMED30015799 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 SMED30015799 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 SMED30015799 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 SMED30015799 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 SMED30015799 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 SMED30015799 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 SMED30015799 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 SMED30015799 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 SMED30015799 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 SMED30015799 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 SMED30015799 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 SMED30015799 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 SMED30015799 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 SMED30015799 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000039126.13.223e-85100.00SMESG000039126.1[more]
SMESG000020136.11.347e-2746.55SMESG000020136.1[more]
SMESG000020133.12.593e-2044.79SMESG000020133.1[more]
SMESG000020144.18.359e-1941.41SMESG000020144.1[more]
SMESG000020144.11.138e-1841.67SMESG000020144.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015799 ID=SMED30015799|Name=SMED30015799|organism=Schmidtea mediterranea sexual|type=transcript|length=656bp
AAATTCAAGTTGCAATAGGCAAACTTGAATTAAAATGAAAGTAGCTTTTA
TCCTTCTCCTTTTAATTGGGTACACTTATTCACTTTCGTGCAAATGTTTC
GCAAGTTCGTGTAACTCAGTGAAACTAAACTGTCCAAGAAGTCAACAAAT
TAGAGACTCGTGTAATTGTTGCTATGTTTGTGCGAACTTAGAGGGCCAGA
TTTGTGAATCGAACATAAAAGCATGCGCTCCTGGTTTGAGATGCGTCACT
GAATATGGGTGCCGTTATTCCAACCATTTGCCTTGGTTTCTTCCGATTCA
AGGAGTTTGTGAAAAAGAATTACCGAATGAGCCACCAGCGGACATAAACT
GCTATCGATATAGTTATCTACAACAGCAAAAGTTGAAACTCAGAAGAGAA
TAGACAGAACTTATTAATTTATGTTTAATTATTTTAAAATTCTTTTTAAT
TTTCGATTTTTATTATTATTTTATACATGAATAGGATTCAACATATAAAA
TCAGTGTATAAATGTGATTTTTCCATATGAAAGTTGGCAATCTAACCCTT
TCAATTCAATCAGTGACGTAGGACATTTCAAGAATAACAAAATATTTTAT
GTGTCAAACGTTAATTATAATCAAAAATAATATTGAATTATGTCTAAATA
ATATGC
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protein sequence of SMED30015799-orf-1

>SMED30015799-orf-1 ID=SMED30015799-orf-1|Name=SMED30015799-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
MKVAFILLLLIGYTYSLSCKCFASSCNSVKLNCPRSQQIRDSCNCCYVCA
NLEGQICESNIKACAPGLRCVTEYGCRYSNHLPWFLPIQGVCEKELPNEP
PADINCYRYSYLQQQKLKLRRE*
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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: biological process
TermDefinition
GO:0001558regulation of cell growth
GO:0007155cell adhesion
GO:0048839inner ear development
Vocabulary: cellular component
TermDefinition
GO:0005576extracellular region
GO:0005615extracellular space
GO:0070062extracellular exosome
Vocabulary: molecular function
TermDefinition
GO:0005520insulin-like growth factor binding
GO:0019838growth factor binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:3.30.60.30coord: 17..106
e-value: 4.9E-6
score: 29.1
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..16
score: 0.914
IPR000867Insulin-like growth factor-binding protein, IGFBPPFAMPF00219IGFBPcoord: 20..70
e-value: 2.7E-8
score: 34.3
IPR000867Insulin-like growth factor-binding protein, IGFBPPROSITEPS51323IGFBP_N_2coord: 13..95
score: 12.424
IPR009030Growth factor receptor cysteine-rich domain superfamilySUPERFAMILYSSF57184Growth factor receptor domaincoord: 16..94