SMED30032378

Overview
NameSMED30032378
Smed IDSMED30032378
Length (bp)379
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30032378

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30032378 SmedASXL_005087SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
secretory systemSMED30032378 dd_Smed_v6_8133_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30032378h1SMcG0004836 Contig23027newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30032378 Contig31113newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30032378 Contig31113uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30032378 Contig28711uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30032378 Contig28711newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
cement glandSMED30032378 GDAG01026281.1SmedSxl_ww_GDAG01.fsa_ntPMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30032378 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007328:6156..6534 -1859
v31.051052:1831..2209 -1607
v31.007328:3934..4312 +1589
Homology
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BLAST of SMED30032378 vs. Planmine SMEST
Match: SMESG000005261.1 (SMESG000005261.1)

HSP 1 Score: 228.409 bits (581), Expect = 5.039e-79
Identity = 111/111 (100.00%), Postives = 111/111 (100.00%), Query Frame = 3 
Query:   12 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKNNKADYIKVVKTLNSDHSLFSGMDKGIVRAVMENIKKSQAS 344
            MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKNNKADYIKVVKTLNSDHSLFSGMDKGIVRAVMENIKKSQAS
Sbjct:    1 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKNNKADYIKVVKTLNSDHSLFSGMDKGIVRAVMENIKKSQAS 111
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BLAST of SMED30032378 vs. Planmine SMEST
Match: SMESG000005262.1 (SMESG000005262.1)

HSP 1 Score: 204.142 bits (518), Expect = 2.186e-69
Identity = 98/111 (88.29%), Postives = 104/111 (93.69%), Query Frame = 3 
Query:   12 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKNNKADYIKVVKTLNSDHSLFSGMDKGIVRAVMENIKKSQAS 344
            MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIK NKA YI V+KTL+SDH LF GMDK +++ VMENIKK+QAS
Sbjct:    1 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKKNKAKYINVMKTLSSDHVLFHGMDKKMLKIVMENIKKAQAS 111
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BLAST of SMED30032378 vs. Planmine SMEST
Match: SMESG000057760.1 (SMESG000057760.1)

HSP 1 Score: 70.8626 bits (172), Expect = 1.015e-16
Identity = 42/108 (38.89%), Postives = 64/108 (59.26%), Query Frame = 3 
Query:   12 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKNNKADYIKVVKTLNSDHSLFSGMDKGIVRAVMENIKKS 335
            MK  + FL VVI+ F  LL      C ++F D DIPF   KD  +A+  +KK + + ++D+L+CD+N++K  KA+Y+     LNS H     M+K    AV +++KKS
Sbjct:   17 MKQLVIFLLVVISEFSPLLADPDNLCKNEFSDNDIPFLTAKDVKDALRKAKKEISEPEFDQLLCDLNKVKGKKAEYL---PELNSPH-----MNKFFAVAVDKDVKKS 116
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BLAST of SMED30032378 vs. Planmine SMEST
Match: SMESG000057736.1 (SMESG000057736.1)

HSP 1 Score: 64.3142 bits (155), Expect = 3.238e-14
Identity = 29/81 (35.80%), Postives = 47/81 (58.02%), Query Frame = 3 
Query:   12 MKHQINFLGVVIAIFI-SLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKNNKADYIKVV 251
            M  Q  FL +VI++ + S       GC ++F+DGD+P  PI     A++  K   P+ +YD++VC +NR+K NK   +K +
Sbjct:    1 MNRQRTFLSIVISVLLFSKTRSAESGCNENFEDGDVPLYPIDRVRLALSKFKNAFPQSEYDRIVCILNRVKENKELVLKAM 81
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BLAST of SMED30032378 vs. Planmine SMEST
Match: SMESG000048474.1 (SMESG000048474.1)

HSP 1 Score: 63.5438 bits (153), Expect = 9.516e-14
Identity = 37/104 (35.58%), Postives = 57/104 (54.81%), Query Frame = 3 
Query:   12 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKNNKADYIKVVKTLNSDH---SLFSGMDKGIVRAV 314
            MK  + FL V I++F  L  + +  C D F D +IPF   KD   A+  + K + K +++ L+CD+N IK  K +Y+     LNS H    L + +DKG+  +V
Sbjct:   17 MKQFVIFLLVAISVFSPLFAKPSNLCNDKFADNEIPFLSEKDVKVALIKTMKQMTKTEFNTLLCDLNEIKEKKPEYM---AELNSPHFKKFLSAAIDKGVEESV 117
The following BLAST results are available for this feature:
BLAST of SMED30032378 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 SMED30032378 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 SMED30032378 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 SMED30032378 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 SMED30032378 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 SMED30032378 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 SMED30032378 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 SMED30032378 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 SMED30032378 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 SMED30032378 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 SMED30032378 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 SMED30032378 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 SMED30032378 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 SMED30032378 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000005261.15.039e-79100.00SMESG000005261.1[more]
SMESG000005262.12.186e-6988.29SMESG000005262.1[more]
SMESG000057760.11.015e-1638.89SMESG000057760.1[more]
SMESG000057736.13.238e-1435.80SMESG000057736.1[more]
SMESG000048474.19.516e-1435.58SMESG000048474.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032378 ID=SMED30032378|Name=SMED30032378|organism=Schmidtea mediterranea sexual|type=transcript|length=379bp
TTTAGTTTAGCATGAAACATCAAATAAACTTTCTAGGAGTTGTCATTGCA
ATATTTATATCACTTTTGTTGCAATTCACAGAGGGATGCCCAGATGATTT
CAAGGATGGCGACATTCCCTTTACGCCAATTAAAGATTTCAATGAAGCCA
TGGCGAATTCAAAGAAAACCTTACCGAAAGAGCAGTATGATAAATTGGTA
TGCGATATGAACCGAATCAAAAATAACAAAGCCGATTACATCAAGGTCGT
AAAGACACTCAATAGTGACCACTCGTTGTTCAGTGGAATGGACAAAGGCA
TAGTGAGGGCAGTTATGGAAAATATTAAGAAGTCACAAGCCTCGTAACTG
TTAAACTCGTTTAATAAACTTTTAGATTA
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protein sequence of SMED30032378-orf-1

>SMED30032378-orf-1 ID=SMED30032378-orf-1|Name=SMED30032378-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=112bp
MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANS
KKTLPKEQYDKLVCDMNRIKNNKADYIKVVKTLNSDHSLFSGMDKGIVRA
VMENIKKSQAS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000224cement gland
PLANA:0000418head
PLANA:0000484secretory system
PLANA:0002089reproductive organ
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..25
score: 0.861
NoneNo IPR availableTMHMMTMhelixcoord: 5..22