SMED30006229

Overview
NameSMED30006229
Smed IDSMED30006229
Length (bp)381
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30006229 (SMED30006229) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30006229 (SMED30006229) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30006229

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30006229h1SMcG0001277 Contig30265newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30006229h1SMcG0001277 Contig30265uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30006229h1SMcG0001277 Contig25475newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30006229h1SMcG0001277 Contig25475uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30006229h1SMcG0001277 dd_Smed_v4_12403_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30006229h1SMcG0001277 dd_Smed_v4_12403_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30006229h1SMcG0001277 dd_Smed_v4_12403_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30006229h1SMcG0001277 dd_Smed_v4_12403_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30006229h1SMcG0001277 dd_Smed_v4_12403_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
SMED30006229 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.041411:1662..2042 +1905
Homology
BLAST of SMED30006229 vs. TrEMBL
Match: A0A369SK48 (Exostosin-2 OS=Trichoplax sp. H2 OX=287889 GN=TrispH2_001503 PE=3 SV=1)

HSP 1 Score: 48.521 bits (114), Expect = 1.711e-6
Identity = 21/41 (51.22%), Postives = 29/41 (70.73%), Query Frame = 1
Query:  232 FSDKYVLPFSEVLDWNRCAIILRHYQIENASMILSRISPET 354
             SD+Y+LPFSEVLDW R A++ R  Q+ +   +LS IS +T
Sbjct:  345 LSDEYILPFSEVLDWKRAALVFREDQLLSLPAVLSSISTKT 385          

HSP 2 Score: 31.187 bits (69), Expect = 1.711e-6
Identity = 15/40 (37.50%), Postives = 20/40 (50.00%), Query Frame = 2
Query:  140 QDSIFCLVFNIGISMGFHFFNAISKNCIPVVFPTNTCCPF 259
            QDS FCL+      +  +F +A+   CIPVV       PF
Sbjct:  314 QDSTFCLMLRGYRLIQSNFLDALKFGCIPVVLSDEYILPF 353          
BLAST of SMED30006229 vs. TrEMBL
Match: B3RVD9 (Uncharacterized protein OS=Trichoplax adhaerens OX=10228 GN=TRIADDRAFT_24279 PE=3 SV=1)

HSP 1 Score: 48.521 bits (114), Expect = 1.906e-6
Identity = 21/41 (51.22%), Postives = 29/41 (70.73%), Query Frame = 1
Query:  232 FSDKYVLPFSEVLDWNRCAIILRHYQIENASMILSRISPET 354
             SD+Y+LPFSEVLDW R A++ R  Q+ +   +LS IS +T
Sbjct:  287 LSDEYILPFSEVLDWKRAALVFREDQLLSLPAVLSSISTKT 327          

HSP 2 Score: 30.8018 bits (68), Expect = 1.906e-6
Identity = 15/40 (37.50%), Postives = 20/40 (50.00%), Query Frame = 2
Query:  140 QDSIFCLVFNIGISMGFHFFNAISKNCIPVVFPTNTCCPF 259
            QDS FCL+      +  +F +A+   CIPVV       PF
Sbjct:  256 QDSTFCLMLRGYRLIQSNFLDALKFGCIPVVLSDEYILPF 295          
BLAST of SMED30006229 vs. TrEMBL
Match: A0A075AEM6 (Uncharacterized protein OS=Opisthorchis viverrini OX=6198 GN=T265_05932 PE=3 SV=1)

HSP 1 Score: 42.3578 bits (98), Expect = 7.517e-6
Identity = 17/47 (36.17%), Postives = 28/47 (59.57%), Query Frame = 1
Query:  238 DKYVLPFSEVLDWNRCAIILRHYQIENASMILSRISPETVTHHQHHC 378
            D ++LPFSEVLDW++ AI +RH ++      L+ +S + +   Q   
Sbjct:  161 DNFILPFSEVLDWSKIAIRVRHSELHKIVTTLTSLSSQEIAQFQRQV 207          

HSP 2 Score: 35.039 bits (79), Expect = 7.517e-6
Identity = 18/46 (39.13%), Postives = 24/46 (52.17%), Query Frame = 2
Query:  128 DYFEQ--DSIFCLVFNIGISMGFHFFNAISKNCIPVVFPTNTCCPF 259
            DY E    S+FCL+  I     F  F+++S  CIPV+   N   PF
Sbjct:  122 DYGEALVGSLFCLIIQIPPVGQFALFDSMSAGCIPVIADDNFILPF 167          
BLAST of SMED30006229 vs. Ensembl Sea Lamprey
Match: ext2 (exostosin glycosyltransferase 2 [Source:ZFIN;Acc:ZDB-GENE-041124-3])

HSP 1 Score: 38.891 bits (89), Expect = 5.747e-6
Identity = 19/50 (38.00%), Postives = 29/50 (58.00%), Query Frame = 1
Query:  232 FSDKYVLPFSEVLDW-NRCAIILRHYQIENASMILSRISPETVTHHQHHC 378
            F+D YVLPFS+VLDW +R +++L   +I +   IL  I  + +   Q   
Sbjct:  251 FADSYVLPFSDVLDWKSRASVVLPEDKIPDMYNILKTIPHKQIVDMQRQV 300          

HSP 2 Score: 25.409 bits (54), Expect = 5.747e-6
Identity = 11/40 (27.50%), Postives = 18/40 (45.00%), Query Frame = 2
Query:  140 QDSIFCLVFNIGISMGFHFFNAISKNCIPVVFPTNTCCPF 259
            Q++ FC+V            + +   CIPV+F  +   PF
Sbjct:  220 QEATFCVVLRRARLGQSALSDTMQAGCIPVIFADSYVLPF 259          
BLAST of SMED30006229 vs. Ensembl Nematostella
Match: EDO39195 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SAR9])

HSP 1 Score: 43.5134 bits (101), Expect = 5.321e-6
Identity = 18/37 (48.65%), Postives = 25/37 (67.57%), Query Frame = 1
Query:  235 SDKYVLPFSEVLDWNRCAIILRHYQIENASMILSRIS 345
            SD Y+LPFSEVLDW R A+++   +I+   +IL   S
Sbjct:  267 SDDYILPFSEVLDWKRAAVVVSENEIDRIPLILKDYS 303          
BLAST of SMED30006229 vs. Planmine SMEST
Match: SMESG000019033.1 (SMESG000019033.1)

HSP 1 Score: 141.739 bits (356), Expect = 2.338e-40
Identity = 74/99 (74.75%), Postives = 76/99 (76.77%), Query Frame = 2
Query:   41 VRQQCSETSKKFCIKLIETGKLKSEIVPNDYFEQDSIFCLVFNIGISMGFHFFNAISKNCIPVVFPTNTCCPFL------RCSIGIVVLSFYAIIKLKM 319
            VRQQCSETSKKFCIKLIETGKLKSEIVPNDYFEQDSIFCLVFNIGISMGFHFFNAISKNCIPVVF      PF       RC+I   +L  Y I    M
Sbjct:  254 VRQQCSETSKKFCIKLIETGKLKSEIVPNDYFEQDSIFCLVFNIGISMGFHFFNAISKNCIPVVFSDKYVLPFSEVLDWNRCAI---ILRHYQIENASM 349          

HSP 2 Score: 109.768 bits (273), Expect = 7.700e-29
Identity = 50/50 (100.00%), Postives = 50/50 (100.00%), Query Frame = 1
Query:  232 FSDKYVLPFSEVLDWNRCAIILRHYQIENASMILSRISPETVTHHQHHCS 381
            FSDKYVLPFSEVLDWNRCAIILRHYQIENASMILSRISPETVTHHQHHCS
Sbjct:  318 FSDKYVLPFSEVLDWNRCAIILRHYQIENASMILSRISPETVTHHQHHCS 367          
The following BLAST results are available for this feature:
BLAST of SMED30006229 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 SMED30006229 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 SMED30006229 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 SMED30006229 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 SMED30006229 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 SMED30006229 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 SMED30006229 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 SMED30006229 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A369SK481.711e-651.22Exostosin-2 OS=Trichoplax sp. H2 OX=287889 GN=Tris... [more]
B3RVD91.906e-651.22Uncharacterized protein OS=Trichoplax adhaerens OX... [more]
A0A075AEM67.517e-636.17Uncharacterized protein OS=Opisthorchis viverrini ... [more]
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BLAST of SMED30006229 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 SMED30006229 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ext25.747e-638.00exostosin glycosyltransferase 2 [Source:ZFIN;Acc:Z... [more]
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BLAST of SMED30006229 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 SMED30006229 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO391955.321e-648.65Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30006229 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 SMED30006229 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000019033.12.338e-4074.75SMESG000019033.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006229 ID=SMED30006229|Name=SMED30006229|organism=Schmidtea mediterranea sexual|type=transcript|length=381bp
AGAAAATTTAATAAAGAATTCTAATAATATTAAAATTATCGTTCGCCAGC
AGTGCTCAGAAACTTCAAAGAAATTTTGTATTAAATTAATTGAAACAGGA
AAACTAAAATCTGAGATCGTCCCAAATGATTACTTCGAACAAGACTCCAT
ATTCTGTCTCGTATTTAATATAGGCATTTCCATGGGGTTTCATTTCTTCA
ATGCTATTAGTAAGAATTGCATTCCGGTAGTTTTTCCGACAAATACGTGT
TGCCCTTTTCTGAGGTGCTCGATTGGAATCGTTGTGCTATCATTTTACGC
CATTATCAAATTGAAAATGCATCGATGATTTTATCCAGGATTTCACCTGA
AACTGTTACACATCATCAGCATCACTGTTCT
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protein sequence of SMED30006229-orf-1

>SMED30006229-orf-1 ID=SMED30006229-orf-1|Name=SMED30006229-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
ENLIKNSNNIKIIVRQQCSETSKKFCIKLIETGKLKSEIVPNDYFEQDSI
FCLVFNIGISMGFHFFNAISKNCIPVVFPTNTCCPFLRCSIGIVVLSFYA
IIKLKMHR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
Vocabulary: INTERPRO
TermDefinition
IPR040911Exostosin_GT47
IPR027673Exostosin-2
IPR004263Exostosin
Vocabulary: biological process
TermDefinition
GO:0015012heparan sulfate proteoglycan biosynthetic process
GO:0006024glycosaminoglycan biosynthetic process
GO:0006486protein glycosylation
Vocabulary: molecular function
TermDefinition
GO:0015020glucuronosyltransferase activity
GO:0016757transferase activity, transferring glycosyl groups
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR040911Exostosin, GT47 domainPFAMPF03016Exostosincoord: 8..106
e-value: 4.2E-15
score: 55.7
IPR027673Exostosin-2PANTHERPTHR11062:SF128EXOSTOSIN-2coord: 47..104
IPR004263Exostosin-likePANTHERPTHR11062EXOSTOSIN HEPARAN SULFATE GLYCOSYLTRANSFERASE -RELATEDcoord: 47..104