SMED30035419

Overview
NameSMED30035419
Smed IDSMED30035419
Length (bp)1080
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ 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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30035419 (SMED30035419) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035419 (SMED30035419) in cells (dots) of each of the 12 neoblast clusters.

 

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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 SMED30035419 (SMED30035419) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035419 (SMED30035419) 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.
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

 

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Anatomical Expression

PAGE et. al., 2020



SMED30035419

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30035419SMESG000056435.1 dd_Smed_v4_11454_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035419SMESG000056435.1 dd_Smed_v4_11454_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30035419SMESG000056435.1 dd_Smed_v4_11454_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
SMED30035419 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008031:15603..20156 +5027
v31.005993:20144..24698 -4989
Homology
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BLAST of SMED30035419 vs. TrEMBL
Match: A0A3S2NEB6 (DALR_1 domain-containing protein OS=Chilo suppressalis OX=168631 GN=evm_006458 PE=4 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 9.877e-8
Identity = 48/169 (28.40%), Postives = 85/169 (50.30%), Query Frame = 1 
Query:  520 LRDNVLVFQFLRQNPRKSIKL--PASMIGNSISDSIFVCYNYARICGLLK---KIVLNFECTTIVDFPNGKVQNFINDDFWFLVWGEIDSFSDMISSVLPSNDCGHEYRIYKICVYLIKLSRHFSLFYDKVKILIKMRGDEENFRLAMCYQLLVGLRNIYEFCFNILGM 1011
            L ++ +VF+ L+  P  ++K+    S  G+S   + FV YN AR+  L++   + V+     T+ D  N  +    N+D W LV+  I  F  M+ + +  N+   E+R + +C +L  + R FS +Y KV++L + R        A  + L + L +  + C NIL +
Sbjct:  248 LGESAVVFELLQTKPGSAVKINFECSSAGSS-KGAAFVLYNCARLEALIRSYNEKVVEGIYPTLPDIENTDLSLLTNEDEWCLVFNYIMGFPSMLENCVEVNEKTCEFRPHLLCSFLCSMVRVFSQYYRKVRVLTEPRKHLLPVLFARLHMLTI-LNDTLKTCLNILNI 414
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BLAST of SMED30035419 vs. TrEMBL
Match: A0A1B6C7T6 (DALR_1 domain-containing protein OS=Clastoptera arizonana OX=38151 GN=g.10188 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 6.721e-6
Identity = 44/141 (31.21%), Postives = 67/141 (47.52%), Query Frame = 1 
Query:  604 SISDSIFVCYNYARICGLLKKIVLNFECTTIVDFPNGKVQNF---INDDFWFLVWGEIDSFSDMISSVLPSNDCGH--EYRIYKICVYLIKLSRHFSLFYDKVKILIKMRGDEENFRLAMCYQLLVGLRNIYEFCFNILGM 1011
            S   S FV YNYARIC +L++             P+    +F   I ++ W L++  I  + +++      N C H    R + IC +L  LS  FS FY K +IL +          A  + LL+GLR +Y+  FN+L +
Sbjct:   51 STKGSTFVLYNYARICAILQQFQDKVAMEYYDPLPSVLETSFSPLIQEEEWNLMFDYILEWPNVL------NKCQHLSSLRFHYICGFLSSLSLCFSRFYRKYRILTEPLPQLLPLMTARLH-LLLGLRQVYQNAFNLLSI 184
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BLAST of SMED30035419 vs. TrEMBL
Match: A0A1B6DXP0 (DALR_1 domain-containing protein OS=Clastoptera arizonana OX=38151 GN=g.10189 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 9.804e-6
Identity = 44/141 (31.21%), Postives = 67/141 (47.52%), Query Frame = 1 
Query:  604 SISDSIFVCYNYARICGLLKKIVLNFECTTIVDFPNGKVQNF---INDDFWFLVWGEIDSFSDMISSVLPSNDCGH--EYRIYKICVYLIKLSRHFSLFYDKVKILIKMRGDEENFRLAMCYQLLVGLRNIYEFCFNILGM 1011
            S   S FV YNYARIC +L++             P+    +F   I ++ W L++  I  + +++      N C H    R + IC +L  LS  FS FY K +IL +          A  + LL+GLR +Y+  FN+L +
Sbjct:   66 STKGSTFVLYNYARICAILQQFQDKVAMEYYDPLPSVLETSFSPLIQEEEWNLMFDYILEWPNVL------NKCQHLSSLRFHYICGFLSSLSLCFSRFYRKYRILTEPLPQLLPLMTARLH-LLLGLRQVYQNAFNLLSI 199
[Close]
BLAST of SMED30035419 vs. Planmine SMEST
Match: SMESG000056435.1 (SMESG000056435.1)

HSP 1 Score: 550.051 bits (1416), Expect = 0.000e+0
Identity = 274/283 (96.82%), Postives = 278/283 (98.23%), Query Frame = 1 
Query:  184 ERIKIKVDRYIIFDILKSVSCLTSIENVPTLYENESFLDFHNKVFIQSINNFQKIFTEYNKNDIIQLLLTDPNIMNDSFQKHVENIHFNVQMAFIEKFRDESEKFLELNSSLLRDNVLVFQFLRQNPRKSIKLPASMIGNSISDSIFVCYNYARICGLLKKIVLN-FECTTIVDFPNGKVQNFINDDFWFLVWGEIDSFSDMISSVLPSNDCGHEYRIYKICVYLIKLSRHFSLFYDKVKILIKMRGDEENFRLAMCYQLLVGLRNIYEFCFNILGMSFLNVI 1029
            +  KIKVDRYIIFDILKSVSCLTSIENVPTLYENESFLDFHNKVFIQSINNFQKIFTEYNKN+IIQ LLT+PNIMN+SFQKHVENIHFNVQMAFIEKFRDESEKFLELNSSLLRDNVLVFQFLRQNPRKSIKLPASMIGNSISDSIFVCYNYARICGLLKKIVLN FECTTIVDFPNGKVQNFINDDFWFLVWGEIDSFSDMISSVLPSNDCGHEYRIYKICVYLIKLSRHFSLFYDKVKILIKM GDEENFRLAMCYQLLVGLRNIYEFCFNILGMSFLNVI
Sbjct:   62 KEFKIKVDRYIIFDILKSVSCLTSIENVPTLYENESFLDFHNKVFIQSINNFQKIFTEYNKNEIIQPLLTNPNIMNNSFQKHVENIHFNVQMAFIEKFRDESEKFLELNSSLLRDNVLVFQFLRQNPRKSIKLPASMIGNSISDSIFVCYNYARICGLLKKIVLNYFECTTIVDFPNGKVQNFINDDFWFLVWGEIDSFSDMISSVLPSNDCGHEYRIYKICVYLIKLSRHFSLFYDKVKILIKMSGDEENFRLAMCYQLLVGLRNIYEFCFNILGMSFLNVI 344

HSP 2 Score: 129.413 bits (324), Expect = 2.523e-34
Identity = 63/68 (92.65%), Postives = 67/68 (98.53%), Query Frame = 2 
Query:    2 MNITDSAFLKLKNSIISCNEKSLFNSIVKYSNNSNFDILVYHSNTPIIELPRFCRVIEGNLKELKLRL 205
            MNITDSAFLKLKNSIISCNEKSLFNSIVKYSNNSNFDILVYHSNTPIIELPRFCRVI+GNLKE K+++
Sbjct:    1 MNITDSAFLKLKNSIISCNEKSLFNSIVKYSNNSNFDILVYHSNTPIIELPRFCRVIQGNLKEFKIKV 68
The following BLAST results are available for this feature:
BLAST of SMED30035419 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 SMED30035419 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 SMED30035419 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 SMED30035419 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 SMED30035419 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 SMED30035419 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 SMED30035419 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 SMED30035419 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A3S2NEB69.877e-828.40DALR_1 domain-containing protein OS=Chilo suppress... [more]
A0A1B6C7T66.721e-631.21DALR_1 domain-containing protein OS=Clastoptera ar... [more]
A0A1B6DXP09.804e-631.21DALR_1 domain-containing protein OS=Clastoptera ar... [more]
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BLAST of SMED30035419 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 SMED30035419 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 SMED30035419 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 SMED30035419 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 SMED30035419 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 SMED30035419 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000056435.12.523e-3496.82SMESG000056435.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035419 ID=SMED30035419|Name=SMED30035419|organism=Schmidtea mediterranea sexual|type=transcript|length=1080bp
AATGAATATAACTGACAGCGCTTTTCTAAAGTTAAAAAATTCAATTATTT
CATGTAATGAAAAAAGTTTATTTAACTCTATTGTCAAGTATAGTAACAAT
TCCAATTTTGATATATTAGTGTATCATTCGAATACACCAATTATTGAATT
ACCAAGATTTTGTCGCGTCATTGAAGGAAATCTGAAAGAATTAAAATTAA
GGTTGACCGATACATTATTTTTGATATCTTGAAATCAGTTAGTTGTCTAA
CATCCATAGAAAACGTTCCGACCTTATATGAAAATGAAAGTTTTCTTGAT
TTTCATAATAAAGTTTTTATTCAATCTATTAATAACTTTCAAAAAATATT
TACAGAATATAACAAAAATGATATAATACAGCTTTTATTAACCGATCCAA
ACATAATGAATGACTCATTTCAAAAACACGTAGAAAATATTCATTTTAAT
GTTCAAATGGCATTTATTGAGAAATTTCGGGATGAATCTGAGAAATTTCT
AGAACTAAATTCCAGTTTGCTTAGAGATAATGTTTTAGTGTTTCAATTTC
TTCGCCAAAACCCAAGAAAATCAATTAAATTACCGGCAAGCATGATTGGA
AATAGTATTTCAGATTCCATTTTTGTCTGTTATAACTACGCTAGAATTTG
CGGGCTGTTGAAAAAGATTGTTTTGAATTTTGAGTGCACAACAATAGTCG
ATTTTCCCAACGGAAAGGTTCAGAACTTTATTAATGATGATTTTTGGTTC
CTGGTTTGGGGAGAAATCGATTCATTTTCTGACATGATTTCATCTGTGCT
GCCAAGCAATGACTGTGGACACGAATATCGGATATATAAAATATGTGTTT
ATTTAATCAAGCTGTCGAGGCATTTCAGTTTGTTCTATGACAAAGTCAAA
ATTTTGATTAAAATGAGAGGCGATGAAGAAAACTTCCGGTTAGCAATGTG
CTATCAGCTGTTGGTTGGCTTGCGCAATATTTATGAATTTTGTTTTAATA
TTCTAGGAATGTCTTTTTTAAACGTTATATGAACTTTGATTTTATTGGAT
AATAAATTTCCACTTGTTTTTAAAAAAAAA
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protein sequence of SMED30035419-orf-1

>SMED30035419-orf-1 ID=SMED30035419-orf-1|Name=SMED30035419-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=209bp
MNDSFQKHVENIHFNVQMAFIEKFRDESEKFLELNSSLLRDNVLVFQFLR
QNPRKSIKLPASMIGNSISDSIFVCYNYARICGLLKKIVLNFECTTIVDF
PNGKVQNFINDDFWFLVWGEIDSFSDMISSVLPSNDCGHEYRIYKICVYL
IKLSRHFSLFYDKVKILIKMRGDEENFRLAMCYQLLVGLRNIYEFCFNIL
GMSFLNVI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
Vocabulary: INTERPRO
TermDefinition
IPR008909DALR_anticod-bd
IPR009080tRNAsynth_Ia_anticodon-bd
Vocabulary: biological process
TermDefinition
GO:0006420arginyl-tRNA aminoacylation
GO:0006418tRNA aminoacylation for protein translation
Vocabulary: molecular function
TermDefinition
GO:0005524ATP binding
GO:0004814arginine-tRNA ligase activity
GO:0000166nucleotide binding
GO:0004812aminoacyl-tRNA ligase activity