SMED30001949

Overview
NameSMED30001949
Smed IDSMED30001949
Length (bp)1044
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 SMED30001949 (SMED30001949) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001949 (SMED30001949) 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 SMED30001949 (SMED30001949) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001949 (SMED30001949) 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




SMED30001949

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
reproductive organSMED30001949SMESG000079507.1 SMESG000029374.1 Contig43588newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30001949SMESG000079507.1 SMESG000029374.1 Contig43588uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30001949SMESG000029374.1 Contig52544newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30001949SMESG000029374.1 Contig52544uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
testis primordiumSMED30001949SMESG000029360.1 Contig3193_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001949 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000080:32861..39976 -4854
Homology
BLAST of SMED30001949 vs. Planmine SMEST
Match: SMESG000029374.1 (SMESG000029374.1)

HSP 1 Score: 290.041 bits (741), Expect = 3.264e-98
Identity = 144/151 (95.36%), Postives = 146/151 (96.69%), Query Frame = 2
Query:   56 MSAIQNLALILTFGLKLVASAQYNEKKITTLNCLNGAKITTSCIFAIEIKPIITTPLICNLLFDSNNVKVLLTVTNITITGQVGNKCPKINFAVFSSGNPEQISTTCGKSTPLINKTVDGFSRAIIYYDNKGLNDTNTVVFITISNQNCKT 508
            MSAIQNLALILTFGLKLVASA+YNEKKITTLNCLNGAKITTSCIFAIEIKP+IT PLICNLLFDSNN KVLLTVTNITITGQVGNKCPKINFAVF SGNPEQISTTCGKSTPLINKT DGFSRAIIYYDNKGLNDTNTVVFITISNQNC T
Sbjct:    1 MSAIQNLALILTFGLKLVASAKYNEKKITTLNCLNGAKITTSCIFAIEIKPVITAPLICNLLFDSNNAKVLLTVTNITITGQVGNKCPKINFAVFFSGNPEQISTTCGKSTPLINKTFDGFSRAIIYYDNKGLNDTNTVVFITISNQNCNT 151          
BLAST of SMED30001949 vs. Planmine SMEST
Match: SMESG000029371.1 (SMESG000029371.1)

HSP 1 Score: 240.736 bits (613), Expect = 3.398e-79
Identity = 124/157 (78.98%), Postives = 132/157 (84.08%), Query Frame = 2
Query:   56 MSAIQNLALILTFGLKLVASAQYNEKKITTLNCLNGAKITTSCIFAIEIKPIITTPLICNLLFDSNNVKVLLTVTNITITGQVGNKCPKINFAVFSSGNPEQISTTCGKSTPLINKTVDGFSRAIIYYDNKGLNDTNTVVFITIS-----NQNCKTD 511
            MSAIQNLALILTF LKLVASAQYNE+K TTLNCLNG  I TSCIF+IEIKP IT PLIC L FDSNN KVLLTVTNIT+TGQV   CPK NF VFSSGNPE+ISTTCGKSTPLINKTV+GF+ AII+YDNKGLNDT TV FI IS     N+NC TD
Sbjct:    1 MSAIQNLALILTFELKLVASAQYNEQKTTTLNCLNGDLILTSCIFSIEIKPAITAPLICTLEFDSNNAKVLLTVTNITVTGQVDKICPKFNFEVFSSGNPEKISTTCGKSTPLINKTVEGFTSAIIFYDNKGLNDTTTVAFIKISKTNLGNENCNTD 157          
BLAST of SMED30001949 vs. Planmine SMEST
Match: SMESG000029371.1 (SMESG000029371.1)

HSP 1 Score: 236.884 bits (603), Expect = 4.791e-78
Identity = 123/156 (78.85%), Postives = 131/156 (83.97%), Query Frame = 2
Query:   56 MSAIQNLALILTFGLKLVASAQYNEKKITTLNCLNGAKITTSCIFAIEIKPIITTPLICNLLFDSNNVKVLLTVTNITITGQVGNKCPKINFAVFSSGNPEQISTTCGKSTPLINKTVDGFSRAIIYYDNKGLNDTNTVVFITIS-----NQNCKT 508
            MSAIQNLALILTF LKLVASAQYNE+K TTLNCLNG  I TSCIF+IEIKP IT PLIC L FDSNN KVLLTVTNIT+TGQV   CPK NF VFSSGNPE+ISTTCGKSTPLINKTV+GF+ AII+YDNKGLNDT TV FI IS     N+NC T
Sbjct:    1 MSAIQNLALILTFELKLVASAQYNEQKTTTLNCLNGDLILTSCIFSIEIKPAITAPLICTLEFDSNNAKVLLTVTNITVTGQVDKICPKFNFEVFSSGNPEKISTTCGKSTPLINKTVEGFTSAIIFYDNKGLNDTTTVAFIKISKTNLGNENCNT 156          
BLAST of SMED30001949 vs. Planmine SMEST
Match: SMESG000029364.1 (SMESG000029364.1)

HSP 1 Score: 184.496 bits (467), Expect = 2.433e-57
Identity = 96/155 (61.94%), Postives = 114/155 (73.55%), Query Frame = 2
Query:   56 MSAIQNLALILTFGLKLVASAQYNEKKITTLNCLNGAKITTSCIFAIEIKPIITTPLICNLLFDSNNVKVLLTVTNITITGQVGNKCPKINFAVFSSGNPEQISTTCGKSTPLINKTVDGFSRAIIYYDNKGLNDTNTVVFITIS-----NQNCK 505
            MSAIQNLAL+LT GL LV SA + EKKITTLNCL+GAKITTSCIFAIEI P+I+ PL C L F S++ +V+LT  NITI  Q+ NKCP  N  VFSSG  ++ISTTCG     I KTV+GF+ A++ YDNKGL D+ TV FI IS      QNC+
Sbjct:    1 MSAIQNLALVLTLGLNLVVSAPHYEKKITTLNCLDGAKITTSCIFAIEINPVISAPLSCTLQFISSSAQVILTAFNITIKSQIDNKCPMFNMNVFSSGKTQKISTTCGGEISGIKKTVEGFTSAVLNYDNKGLTDSTTVAFIKISKTNLEKQNCE 155          
BLAST of SMED30001949 vs. Planmine SMEST
Match: SMESG000036641.1 (SMESG000036641.1)

HSP 1 Score: 182.57 bits (462), Expect = 4.456e-55
Identity = 92/116 (79.31%), Postives = 102/116 (87.93%), Query Frame = 3
Query:  576 HRLIQISREMQKILVT*IEPSRAKILYQRLTAAQRGWAEEKQLVQNQKTQIRSLEVELSACQEGN*VTYQLVFTPAQIAYRDASSTTKPVAAKRPQRRPGKAKRAKHRAQQVTERD 923
            ++LIQ+SRE+QKI  T IEP+RAK + QRLTAAQRGWAEEKQLVQNQ+TQ RSLEV L ACQEGN VTYQLV  PAQIAYRDASSTTKPV AKRPQ+RPGK +RAKHRAQQ T+RD
Sbjct:  179 NQLIQMSREIQKIRATWIEPARAKAINQRLTAAQRGWAEEKQLVQNQRTQNRSLEVALLACQEGNAVTYQLVIAPAQIAYRDASSTTKPVTAKRPQQRPGKTERAKHRAQQATDRD 294          
The following BLAST results are available for this feature:
BLAST of SMED30001949 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 SMED30001949 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 SMED30001949 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 SMED30001949 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 SMED30001949 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 SMED30001949 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 SMED30001949 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 SMED30001949 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 SMED30001949 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 SMED30001949 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 SMED30001949 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 SMED30001949 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 SMED30001949 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 SMED30001949 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000029374.13.264e-9895.36SMESG000029374.1[more]
SMESG000029371.13.398e-7978.98SMESG000029371.1[more]
SMESG000029371.14.791e-7878.85SMESG000029371.1[more]
SMESG000029364.12.433e-5761.94SMESG000029364.1[more]
SMESG000036641.14.456e-5579.31SMESG000036641.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001949 ID=SMED30001949|Name=SMED30001949|organism=Schmidtea mediterranea sexual|type=transcript|length=1044bp
CGAATACTTATTTCGAATATCAAATTAATATTTGAACTTGTTGGATATTT
TCTACATGTCAGCCATTCAGAATTTGGCATTGATTTTGACTTTTGGGTTG
AAATTGGTCGCCTCTGCTCAATACAATGAGAAAAAAATCACCACTTTGAA
TTGTCTGAATGGCGCTAAGATAACGACTTCATGCATATTTGCAATAGAAA
TCAAGCCCATAATTACTACTCCATTGATTTGCAATCTCCTATTCGATTCG
AACAATGTGAAAGTGTTATTGACAGTTACTAACATCACAATTACAGGTCA
AGTTGGTAATAAATGTCCTAAAATCAACTTTGCAGTGTTCTCCTCTGGAA
ATCCAGAACAAATTTCGACAACTTGTGGTAAATCAACACCTCTGATTAAC
AAAACGGTTGATGGATTTTCTAGAGCAATTATATATTACGATAATAAAGG
TTTGAATGATACAAATACCGTTGTATTCATAACGATTTCAAATCAAAATT
GTAAAACAGATATGCAATCACTCAGAATTCTGAGTAAGGAGTTGGTAAAT
CTCGGAGAGAAAACGCAGAACTCCACACCGACTTATCCAGATAAGTCGCG
AAATGCAGAAGATTCTTGTGACTTAGATCGAACCCTCCAGAGCGAAAATT
CTATATCAGCGATTGACCGCCGCTCAACGAGGATGGGCGGAGGAGAAGCA
ACTGGTCCAGAACCAGAAAACTCAGATTAGGAGCTTGGAGGTAGAACTGT
CGGCTTGCCAGGAGGGCAACTAAGTGACCTACCAGCTAGTATTCACACCA
GCCCAGATAGCCTACCGGGATGCAAGTAGCACCACTAAACCGGTAGCTGC
TAAACGCCCTCAGCGACGACCAGGGAAGGCGAAACGAGCAAAACATCGCG
CACAACAAGTAACGGAGCGCGATTAACAATCAAAATACATCAGTAGTTTA
GCTCGGAAATATGTAGTTCGTATTACAAAAATAAATGTTTTATTGTTCAT
CTTGTAAATTTAATAATCTAAATTGAAAATTAATAAGTTGAAAT
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protein sequence of SMED30001949-orf-1

>SMED30001949-orf-1 ID=SMED30001949-orf-1|Name=SMED30001949-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=225bp
MSAIQNLALILTFGLKLVASAQYNEKKITTLNCLNGAKITTSCIFAIEIK
PIITTPLICNLLFDSNNVKVLLTVTNITITGQVGNKCPKINFAVFSSGNP
EQISTTCGKSTPLINKTVDGFSRAIIYYDNKGLNDTNTVVFITISNQNCK
TDMQSLRILSKELVNLGEKTQNSTPTYPDKSRNAEDSCDLDRTLQSENSI
SAIDRRSTRMGGGEATGPEPENSD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
PLANA:0003304testis primordium
Vocabulary: INTERPRO
TermDefinition
IPR014010REJ_dom
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..11
score: 0.517