SMED30021131

Overview
NameSMED30021131
Smed IDSMED30021131
Length (bp)1373
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 SMED30021131 (SMED30021131) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021131 (SMED30021131) 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 SMED30021131 (SMED30021131) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021131 (SMED30021131) 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



SMED30021131

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
Smed sexual biotypeSMED30021131h1SMcG0010654 Contig46573uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30021131h1SMcG0010654 Contig46573newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
gutSMED30021131h1SMcG0010654 dd_Smed_v4_5937_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30021131h1SMcG0010654 dd_Smed_v6_5937_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021131 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000937:960..4616 -5107
Homology
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BLAST of SMED30021131 vs. TrEMBL
Match: Q5DCS9 (SJCHGC04329 protein OS=Schistosoma japonicum OX=6182 PE=2 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 1.845e-7
Identity = 67/228 (29.39%), Postives = 106/228 (46.49%), Query Frame = 1 
Query:   97 NIPSKVYVIVYKCENLPDLRTXXXXXXXXXSLWQVIFPDAKESLASN-LQEGTSEVIWMVESFLTIKNSSNSFSMSVIDDKSRKAGTVSISLNDI-LIGDKDILKPGRKYEGAREAYRNMEPIQTAKLNFKSIIISFWMWAIAFREPKKESSNLAKLKTFSKSATNLFKPSNIPFFIPETNTNVNSYTNPFESEYQATEGNSST--------NPF---GNSDSFDGKL 741
            NIP KV +IV + ENL  + + K+  KN++  W+VIF    E  A+  + E      W  E  L + + S+  S+ VID      G V+I LN I   G+ +       ++ +R  Y  +EP  T K +     + +W+WAI +  P  +++ +   K+   S TNL   S I       + + +   N   + YQ++E N ST        NPF   GN+  F G +
Sbjct:    4 NIPKKVNIIVKRGENLEYISSLKKASKNRR--WRVIFIGGSERSATEFVDEENGCPTWDCEVTLDLVSPSDPVSLRVIDGDEHHVGQVNIPLNQIPQTGNPN-------FDLSRLCYSELEP--TRKNSHPHGRLVYWIWAIDYWPPGTQANTIRHSKSLRGSLTNLS--SKI------RSKSKHKSKNDHANGYQSSELNGSTLQVPGMSYNPFENDGNASEFSGPM 212
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BLAST of SMED30021131 vs. TrEMBL
Match: A0A4Z2DDJ8 (tRNA-splicing endonuclease subunit Sen2 OS=Schistosoma japonicum OX=6182 GN=EWB00_002055 PE=4 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 1.914e-6
Identity = 67/228 (29.39%), Postives = 106/228 (46.49%), Query Frame = 1 
Query:   97 NIPSKVYVIVYKCENLPDLRTXXXXXXXXXSLWQVIFPDAKESLASN-LQEGTSEVIWMVESFLTIKNSSNSFSMSVIDDKSRKAGTVSISLNDI-LIGDKDILKPGRKYEGAREAYRNMEPIQTAKLNFKSIIISFWMWAIAFREPKKESSNLAKLKTFSKSATNLFKPSNIPFFIPETNTNVNSYTNPFESEYQATEGNSST--------NPF---GNSDSFDGKL 741
            NIP KV +IV + ENL  + + K+  KN++  W+VIF    E  A+  + E      W  E  L + + S+  S+ VID      G V+I LN I   G+ +       ++ +R  Y  +EP  T K +     + +W+WAI +  P  +++ +   K+   S TNL   S I       + + +   N   + YQ++E N ST        NPF   GN+  F G +
Sbjct:    4 NIPKKVNIIVKRGENLEYISSLKKASKNRR--WRVIFIGGSERSATEFVDEENGCPTWDCEVTLDLVSPSDPVSLRVIDGDEHHVGQVNIPLNQIPQTGNPN-------FDLSRLCYSELEP--TRKNSHPHGRLVYWIWAIDYWPPGTQANTIRHSKSLRGSLTNL--SSKI------RSKSKHKSKNDHANGYQSSELNGSTLQVPGMSYNPFENDGNASEFSGPM 212
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BLAST of SMED30021131 vs. Planmine SMEST
Match: SMESG000040206.1 (SMESG000040206.1)

HSP 1 Score: 773.467 bits (1996), Expect = 0.000e+0
Identity = 390/393 (99.24%), Postives = 392/393 (99.75%), Query Frame = 1 
Query:   76 MKNPDPENIPSKVYVIVYKCENLPDLRTXXXXXXXXXSLWQVIFPDAKESLASNLQEGTSEVIWMVESFLTIKNSSNSFSMSVIDDKSRKAGTVSISLNDILIGDKDILKPGRKYEGAREAYRNMEPIQTAKLNFKSIIISFWMWAIAFREPKKESSNLAKLKTFSKSATNLFKPSNIPFFIPETNTNVNSYTNPFESEYQATEGNSSTNPFGNSDSFDGKLTDQVGNSTFTNTELPKFRSSIWLPQNTNDAYSNPFAVPHRSSSLPGLAEHSKQLIHEMNSEIEEFKKNIMDQKLSFGVSEHDLQNLNALSEIYETRKTGPKNSEMIKVLDEEFFTLLNDLRRQFANNIIKIKSLEMENKDLTDELSELRKRFYTVKKKLIENGMSNFLQDN 1254
            MKNPDPENIPSKVYVIVYKCENLPDLRTEKEKKKNKKSLWQVIFPDAKESLASNLQEGTSEVIWMVESFLTIKNSS+SFSMSVIDDKSRKAGTVSISLNDILIGDKDILKPGRKYEG+REAYRNMEPIQTAKLNFKSIIISFWMWAIAFREPKKESSNLAKLKTFSKSATNLFKPSNIPFFIPETNTNVNSYTNPFESEYQATEGNSSTNPF NSDSFDGKLTDQVGNSTFTNTELPKFRSSIWLPQNTNDAYSNPFAVPHRSSSLPGLAEHSKQLIHEMNSEIEEFKKNIMDQKLSFGVSEHDLQNLNALSEIYETRKTGPKNSEMIKVLDEEFFTLLNDLRRQFANNIIKIKSLEMENKDLTDELSELRKRFYTVKKKLIENGMSNFLQDN
Sbjct:    1 MKNPDPENIPSKVYVIVYKCENLPDLRTEKEKKKNKKSLWQVIFPDAKESLASNLQEGTSEVIWMVESFLTIKNSSSSFSMSVIDDKSRKAGTVSISLNDILIGDKDILKPGRKYEGSREAYRNMEPIQTAKLNFKSIIISFWMWAIAFREPKKESSNLAKLKTFSKSATNLFKPSNIPFFIPETNTNVNSYTNPFESEYQATEGNSSTNPFENSDSFDGKLTDQVGNSTFTNTELPKFRSSIWLPQNTNDAYSNPFAVPHRSSSLPGLAEHSKQLIHEMNSEIEEFKKNIMDQKLSFGVSEHDLQNLNALSEIYETRKTGPKNSEMIKVLDEEFFTLLNDLRRQFANNIIKIKSLEMENKDLTDELSELRKRFYTVKKKLIENGMSNFLQDN 393
The following BLAST results are available for this feature:
BLAST of SMED30021131 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 SMED30021131 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 SMED30021131 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 SMED30021131 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 SMED30021131 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 SMED30021131 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 SMED30021131 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 SMED30021131 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
Q5DCS91.845e-729.39SJCHGC04329 protein OS=Schistosoma japonicum OX=61... [more]
A0A4Z2DDJ81.914e-629.39tRNA-splicing endonuclease subunit Sen2 OS=Schisto... [more]
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BLAST of SMED30021131 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 SMED30021131 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 SMED30021131 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 SMED30021131 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 SMED30021131 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 SMED30021131 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000040206.10.000e+099.24SMESG000040206.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021131 ID=SMED30021131|Name=SMED30021131|organism=Schmidtea mediterranea sexual|type=transcript|length=1373bp
GGCACAAGTTGAAATAAATTTACTTAAAATCGAACTATTTTCAAATTTCT
ATCTATTAAACATAATAAATTTTAAATGAAGAATCCTGATCCAGAAAATA
TTCCTTCAAAAGTTTATGTGATAGTCTATAAATGTGAAAATCTGCCAGAT
TTAAGAACGGAAAAAGAAAAGAAAAAAAACAAAAAATCATTATGGCAAGT
TATTTTTCCAGATGCTAAAGAATCTTTAGCAAGCAACCTGCAAGAGGGGA
CATCCGAAGTTATTTGGATGGTTGAAAGTTTCTTGACAATCAAGAATTCT
TCTAACTCATTTTCAATGTCCGTTATCGATGATAAATCCCGTAAGGCTGG
TACGGTCTCTATTAGTTTGAATGACATTCTCATTGGTGACAAGGATATTC
TCAAACCTGGTAGAAAATATGAAGGAGCTCGAGAGGCTTATCGAAACATG
GAACCTATTCAAACAGCAAAATTAAATTTCAAAAGCATTATCATTAGTTT
TTGGATGTGGGCTATTGCATTTCGAGAACCGAAGAAGGAGAGTTCAAATT
TAGCAAAATTGAAAACCTTTTCAAAGTCTGCCACAAATCTTTTTAAACCT
TCCAACATTCCTTTTTTCATCCCCGAAACTAATACAAATGTAAATTCATA
CACAAATCCATTTGAATCTGAATATCAGGCTACAGAAGGAAATAGTTCCA
CAAATCCCTTCGGAAATTCAGACAGTTTCGATGGAAAACTAACCGATCAA
GTGGGTAACTCCACGTTCACAAATACGGAGCTTCCTAAATTTAGAAGCTC
AATTTGGCTTCCACAAAATACAAATGACGCCTACTCTAATCCATTCGCTG
TTCCACATCGTTCTTCGTCGCTACCAGGACTGGCTGAACATTCGAAACAA
TTGATTCATGAGATGAATTCTGAGATTGAAGAGTTCAAAAAAAATATCAT
GGACCAAAAGTTATCATTTGGGGTATCAGAACATGACTTACAAAATTTAA
ATGCGCTAAGTGAAATATACGAAACCAGAAAAACAGGGCCGAAAAATTCT
GAAATGATCAAGGTTTTGGACGAGGAATTTTTCACGTTATTAAATGACTT
AAGAAGGCAGTTTGCGAACAATATTATCAAAATAAAATCTCTCGAAATGG
AAAATAAAGATTTGACAGATGAATTGAGTGAATTGAGGAAAAGATTTTAC
ACAGTAAAGAAAAAACTTATTGAAAACGGAATGAGTAATTTCCTGCAAGA
CAATTAGATGAGAGACTCGTTAAATAAATAACCTAACTACATTTTGAAAT
ATTTTTATATTGAAATATCAATTTTTTCTATAATTGATTTGGTTTTCATA
ATAAAAAATTGTTTATATTAAAA
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protein sequence of SMED30021131-orf-1

>SMED30021131-orf-1 ID=SMED30021131-orf-1|Name=SMED30021131-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=394bp
MKNPDPENIPSKVYVIVYKCENLPDLRTEKEKKKNKKSLWQVIFPDAKES
LASNLQEGTSEVIWMVESFLTIKNSSNSFSMSVIDDKSRKAGTVSISLND
ILIGDKDILKPGRKYEGAREAYRNMEPIQTAKLNFKSIIISFWMWAIAFR
EPKKESSNLAKLKTFSKSATNLFKPSNIPFFIPETNTNVNSYTNPFESEY
QATEGNSSTNPFGNSDSFDGKLTDQVGNSTFTNTELPKFRSSIWLPQNTN
DAYSNPFAVPHRSSSLPGLAEHSKQLIHEMNSEIEEFKKNIMDQKLSFGV
SEHDLQNLNALSEIYETRKTGPKNSEMIKVLDEEFFTLLNDLRRQFANNI
IKIKSLEMENKDLTDELSELRKRFYTVKKKLIENGMSNFLQDN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR012317Poly(ADP-ribose)pol_cat_dom
Vocabulary: molecular function
TermDefinition
GO:0003950NAD+ ADP-ribosyltransferase activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 339..373
NoneNo IPR availableCOILSCoilCoilcoord: 270..297