SMED30025512

Overview
NameSMED30025512
Smed IDSMED30025512
Length (bp)773
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 SMED30025512 (SMED30025512) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30025512 (SMED30025512) 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.
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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



SMED30025512

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
reproductive organSMED30025512h1SMcG0000373 Contig21514newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30025512h1SMcG0000373 Contig21514uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30025512 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008814:24371..25343 +3770
Homology
[Close]
BLAST of SMED30025512 vs. TrEMBL
Match: A0A2Z4EM42 (Tspan1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 80.4925 bits (197), Expect = 2.479e-14
Identity = 55/231 (23.81%), Postives = 119/231 (51.52%), Query Frame = 2 
Query:   50 MICAIILLGPSLYVLITVGMMTKLTFTRTLILVPTIIMMHALFMILNSSLVFLAIKRRXXXXXXXXXXXXXXXXXXXVTIGSIYLIKSPLMKPNIESFLHDSIIDRTSYRGYSIIRPIDIVQNMYQCCGKINYNDYKVLESDLPTSCCRAMNSCQHSI-EFIHKDKKTGCVDPIYQNIFQKPNKWILIGLLLNVVLETIVLAVSLALRFRY---NRIQDQNFQDINMLNGM 730
            +I  + ++  S Y ++T+G+  ++  +  L++   I++    ++++ SSLVF  +++R+   LK   +++ + +  ++   S+ ++    M   ++  + D++ D   Y+    IR +D++Q    CCG+I+Y +Y +   DLP SCCR  ++C +++      D  TGC++ I   I   P    LI L+   V+E ++  +   + F +    +   QN + +N +  M
Sbjct:   17 LIIGLFIIFSSSYFIVTLGLSNQIELSSYLVIFTFILLGCGTYIVIYSSLVFHGLRKRNSRYLKTFSALVVLFLILQIGSLSLGILFRKSMIEKLDFLMDDAVTDEIEYKYTKHIRYMDLIQYSLSCCGRISYREYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGI--SPTMICLIVLIF--VVEILMALLGWLIEFNFISIGKFIHQNARGMNTMMSM 243
[Close]
BLAST of SMED30025512 vs. Planmine SMEST
Match: SMESG000070572.1 (SMESG000070572.1)

HSP 1 Score: 294.278 bits (752), Expect = 1.891e-102
Identity = 139/139 (100.00%), Postives = 139/139 (100.00%), Query Frame = 2 
Query:  320 MKPNIESFLHDSIIDRTSYRGYSIIRPIDIVQNMYQCCGKINYNDYKVLESDLPTSCCRAMNSCQHSIEFIHKDKKTGCVDPIYQNIFQKPNKWILIGLLLNVVLETIVLAVSLALRFRYNRIQDQNFQDINMLNGMTA 736
            MKPNIESFLHDSIIDRTSYRGYSIIRPIDIVQNMYQCCGKINYNDYKVLESDLPTSCCRAMNSCQHSIEFIHKDKKTGCVDPIYQNIFQKPNKWILIGLLLNVVLETIVLAVSLALRFRYNRIQDQNFQDINMLNGMTA
Sbjct:    1 MKPNIESFLHDSIIDRTSYRGYSIIRPIDIVQNMYQCCGKINYNDYKVLESDLPTSCCRAMNSCQHSIEFIHKDKKTGCVDPIYQNIFQKPNKWILIGLLLNVVLETIVLAVSLALRFRYNRIQDQNFQDINMLNGMTA 139
[Close]
BLAST of SMED30025512 vs. Planmine SMEST
Match: SMESG000011084.1 (SMESG000011084.1)

HSP 1 Score: 294.278 bits (752), Expect = 1.891e-102
Identity = 139/139 (100.00%), Postives = 139/139 (100.00%), Query Frame = 2 
Query:  320 MKPNIESFLHDSIIDRTSYRGYSIIRPIDIVQNMYQCCGKINYNDYKVLESDLPTSCCRAMNSCQHSIEFIHKDKKTGCVDPIYQNIFQKPNKWILIGLLLNVVLETIVLAVSLALRFRYNRIQDQNFQDINMLNGMTA 736
            MKPNIESFLHDSIIDRTSYRGYSIIRPIDIVQNMYQCCGKINYNDYKVLESDLPTSCCRAMNSCQHSIEFIHKDKKTGCVDPIYQNIFQKPNKWILIGLLLNVVLETIVLAVSLALRFRYNRIQDQNFQDINMLNGMTA
Sbjct:    1 MKPNIESFLHDSIIDRTSYRGYSIIRPIDIVQNMYQCCGKINYNDYKVLESDLPTSCCRAMNSCQHSIEFIHKDKKTGCVDPIYQNIFQKPNKWILIGLLLNVVLETIVLAVSLALRFRYNRIQDQNFQDINMLNGMTA 139
[Close]
BLAST of SMED30025512 vs. Planmine SMEST
Match: SMESG000066703.1 (SMESG000066703.1)

HSP 1 Score: 80.4925 bits (197), Expect = 6.893e-18
Identity = 55/231 (23.81%), Postives = 119/231 (51.52%), Query Frame = 2 
Query:   50 MICAIILLGPSLYVLITVGMMTKLTFTRTLILVPTIIMMHALFMILNSSLVFLAIKRRXXXXXXXXXXXXXXXXXXXVTIGSIYLIKSPLMKPNIESFLHDSIIDRTSYRGYSIIRPIDIVQNMYQCCGKINYNDYKVLESDLPTSCCRAMNSCQHSI-EFIHKDKKTGCVDPIYQNIFQKPNKWILIGLLLNVVLETIVLAVSLALRFRY---NRIQDQNFQDINMLNGM 730
            +I  + ++  S Y ++T+G+  ++  +  L++   I++    ++++ SSLVF  +++R+   LK   +++ + +  ++   S+ ++    M   ++  + D++ D   Y+    IR +D++Q    CCG+I+Y +Y +   DLP SCCR  ++C +++      D  TGC++ I   I   P    LI L+   V+E ++  +   + F +    +   QN + +N +  M
Sbjct:   17 LIIGLFIIFSSSYFIVTLGLSNQIELSSYLVIFTFILLGCGTYIVIYSSLVFHGLRKRNSRYLKTFSALVVLFLILQIGSLSLGILFRKSMIEKLDFLMDDAVTDEIEYKYTKHIRYMDLIQYSLSCCGRISYREYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGI--SPTMICLIVLIF--VVEILMALLGWLIEFNFISIGKFIHQNARGMNTMMSM 243
[Close]
BLAST of SMED30025512 vs. Planmine SMEST
Match: SMESG000044356.1 (SMESG000044356.1)

HSP 1 Score: 47.3654 bits (111), Expect = 3.760e-6
Identity = 32/117 (27.35%), Postives = 59/117 (50.43%), Query Frame = 2 
Query:  386 SIIRPIDIVQNMYQCCGKINYNDYKVLESDLPTSCCRAM------NSCQHSIE-FIHKDKKTGCVDPIYQNIFQKPNKWILIGLLLNVVLETIVLAVSLALRFRYNRIQDQNFQDIN 715
            S+ + ID +Q+  QCCG  NY D+++  + +P SCCR M      +S Q +I    ++    GC + + + + Q    +I++ L+  + L+ I L  S  +  R+      ++Q  N
Sbjct:  129 SLRKEIDYIQSTLQCCGVQNYTDWEMYNNSIPDSCCRNMKCKPVLSSTQTTISPDAYEPYIIGCSETV-EKLIQHKFVYIILILISVIALQVISLVASCCI-IRHRSSSSSDYQPFN 243
The following BLAST results are available for this feature:
BLAST of SMED30025512 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 SMED30025512 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 SMED30025512 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 SMED30025512 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 SMED30025512 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 SMED30025512 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 SMED30025512 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 SMED30025512 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A2Z4EM422.479e-1423.81Tspan1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=... [more]
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BLAST of SMED30025512 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 SMED30025512 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 SMED30025512 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 SMED30025512 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 SMED30025512 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 SMED30025512 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000070572.11.891e-102100.00SMESG000070572.1[more]
SMESG000011084.11.891e-102100.00SMESG000011084.1[more]
SMESG000066703.16.893e-1823.81SMESG000066703.1[more]
SMESG000044356.13.760e-627.35SMESG000044356.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025512 ID=SMED30025512|Name=SMED30025512|organism=Schmidtea mediterranea sexual|type=transcript|length=773bp
AATGCGTCGGTTTTTTGCTATACTATTAACATTATTTGCCACATTGGAAA
TGATTTGTGCCATAATTTTACTTGGACCCTCTCTTTACGTATTGATAACC
GTCGGAATGATGACTAAGCTTACGTTTACAAGAACTTTAATTTTGGTACC
GACAATTATTATGATGCACGCTCTTTTTATGATCCTTAATTCATCTCTCG
TATTCCTTGCAATCAAACGTAGAAGCGGCATAATTCTGAAAATTTCTGGA
TCAATTTTAGCAATTTTAATTGCCTCAAAAGTGACAATAGGATCAATTTA
TTTAATCAAATCACCTCTCATGAAACCAAATATTGAAAGCTTTCTCCACG
ATTCCATCATCGACCGAACCTCATATAGAGGTTATTCAATAATTCGTCCA
ATTGACATCGTTCAGAACATGTATCAATGTTGCGGAAAAATCAATTACAA
TGACTACAAAGTATTAGAAAGTGACCTCCCGACTTCTTGTTGTCGAGCAA
TGAACAGCTGCCAGCATTCAATTGAATTTATTCATAAAGACAAAAAAACT
GGCTGTGTTGATCCGATCTATCAAAACATTTTCCAAAAGCCAAATAAATG
GATCTTGATTGGATTGCTTTTGAATGTCGTGCTTGAAACAATCGTATTAG
CGGTGAGTCTAGCACTGAGATTCAGATACAATAGAATCCAGGACCAAAAT
TTCCAGGATATCAACATGTTGAACGGAATGACAGCATAATGAGTTAAATT
ATGTTTCTCATACAGATTTCTGC
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protein sequence of SMED30025512-orf-1

>SMED30025512-orf-1 ID=SMED30025512-orf-1|Name=SMED30025512-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=246bp
MRRFFAILLTLFATLEMICAIILLGPSLYVLITVGMMTKLTFTRTLILVP
TIIMMHALFMILNSSLVFLAIKRRSGIILKISGSILAILIASKVTIGSIY
LIKSPLMKPNIESFLHDSIIDRTSYRGYSIIRPIDIVQNMYQCCGKINYN
DYKVLESDLPTSCCRAMNSCQHSIEFIHKDKKTGCVDPIYQNIFQKPNKW
ILIGLLLNVVLETIVLAVSLALRFRYNRIQDQNFQDINMLNGMTA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR018499Tetraspanin/Peripherin
IPR008952Tetraspanin_EC2_sf
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
IPR018499Tetraspanin/PeripherinPFAMPF00335Tetraspanincoord: 7..222
e-value: 5.0E-16
score: 59.1
IPR008952Tetraspanin, EC2 domain superfamilyGENE3DG3DSA:1.10.1450.10coord: 105..183
e-value: 1.7E-6
score: 29.7
IPR008952Tetraspanin, EC2 domain superfamilySUPERFAMILYSSF48652Tetraspanincoord: 114..189
NoneNo IPR availableCDDcd03127tetraspanin_LELcoord: 134..190
e-value: 2.56414E-11
score: 56.3587
NoneNo IPR availableTMHMMTMhelixcoord: 49..71
NoneNo IPR availableTMHMMTMhelixcoord: 200..222
NoneNo IPR availableTMHMMTMhelixcoord: 7..29
NoneNo IPR availableTMHMMTMhelixcoord: 78..100