SMED30035879

Overview
NameSMED30035879
Smed IDSMED30035879
Length (bp)1359
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30035879 (SMED30035879) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035879 (SMED30035879) 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.
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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



SMED30035879

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30035879h1SMcG0019887 SmedASXL_009261SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30035879h1SMcG0019887 dd_Smed_v4_9070_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30035879h1SMcG0019887 dd_Smed_v6_9070_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
SMED30035879 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007219:4890..14470 -6633
Homology
[Close]
BLAST of SMED30035879 vs. Planmine SMEST
Match: SMESG000072342.1 (SMESG000072342.1)

HSP 1 Score: 832.017 bits (2148), Expect = 0.000e+0
Identity = 421/421 (100.00%), Postives = 421/421 (100.00%), Query Frame = 3 
Query:   15 MLYKCSIIFIVILLKFITSQPIYPKLFKERFQRDRPLLPKVPEIRDVYVIEDCKHQGNNVPVAMPDLEITNDYGLMIWWNRATKFLDPYKLESGNINDSYASTDDVQGIFDCTITIKLGPHDSRISYQEMIFGYLTKLDMKNSPFFNDISNSVSLLNPDNTLANKGLKELIAACKDAEGDCRYVGCIIIEYGDKVIRTCKGSTGNMGDNFKWFTRDNVRIRILAIGTFIGKDRSNKNVTIAYPPYNVDFRLDFTRLYGGPCYNKDQYYCPTHGVCIRYLLACDPRSMWNCPSYSFNPGFDEPSPCSPDQSNNIPKALNLPDASATLNLQIFWIVXXXXXXXXXXXXXXXXXWRPGYLIWRCGRIRNWCAFGNCCYKACHDCSQSCNTPCCKTHGTFDTTETSTVVWSKFPTGDGFHMRENR 1277
            MLYKCSIIFIVILLKFITSQPIYPKLFKERFQRDRPLLPKVPEIRDVYVIEDCKHQGNNVPVAMPDLEITNDYGLMIWWNRATKFLDPYKLESGNINDSYASTDDVQGIFDCTITIKLGPHDSRISYQEMIFGYLTKLDMKNSPFFNDISNSVSLLNPDNTLANKGLKELIAACKDAEGDCRYVGCIIIEYGDKVIRTCKGSTGNMGDNFKWFTRDNVRIRILAIGTFIGKDRSNKNVTIAYPPYNVDFRLDFTRLYGGPCYNKDQYYCPTHGVCIRYLLACDPRSMWNCPSYSFNPGFDEPSPCSPDQSNNIPKALNLPDASATLNLQIFWIVLGIFLSLLGYLLLNYCLWRPGYLIWRCGRIRNWCAFGNCCYKACHDCSQSCNTPCCKTHGTFDTTETSTVVWSKFPTGDGFHMRENR
Sbjct:    1 MLYKCSIIFIVILLKFITSQPIYPKLFKERFQRDRPLLPKVPEIRDVYVIEDCKHQGNNVPVAMPDLEITNDYGLMIWWNRATKFLDPYKLESGNINDSYASTDDVQGIFDCTITIKLGPHDSRISYQEMIFGYLTKLDMKNSPFFNDISNSVSLLNPDNTLANKGLKELIAACKDAEGDCRYVGCIIIEYGDKVIRTCKGSTGNMGDNFKWFTRDNVRIRILAIGTFIGKDRSNKNVTIAYPPYNVDFRLDFTRLYGGPCYNKDQYYCPTHGVCIRYLLACDPRSMWNCPSYSFNPGFDEPSPCSPDQSNNIPKALNLPDASATLNLQIFWIVLGIFLSLLGYLLLNYCLWRPGYLIWRCGRIRNWCAFGNCCYKACHDCSQSCNTPCCKTHGTFDTTETSTVVWSKFPTGDGFHMRENR 421
[Close]
BLAST of SMED30035879 vs. Planmine SMEST
Match: SMESG000018135.1 (SMESG000018135.1)

HSP 1 Score: 56.6102 bits (135), Expect = 1.664e-8
Identity = 75/324 (23.15%), Postives = 122/324 (37.65%), Query Frame = 3 
Query:  474 SLLNPDNTLANKGLKELIAACKDAEGDCRYVGCIII---EYGDKVIRTCKGSTGNMGDNFKWFTRDNVRIRILAIGTFIGKDRSNKNVTIAYPPYNVDFRLDFTRLYGGPCYNK-DQYYCPTHGVCIRYLLACDPRSMWNCPSYSFNPGFDEPSPCSPDQSNNIPKALNLPDASATLNLQ--IFWIVXXXXXXXXXXXXXXXXXWRPGYLIWRCGRIRN--WCAFGNCCYKACHDCSQSC---NTP----CCKTHGTFD-----------------------------------------TTETSTVVWSKFPTGDGFHMRENR 1277
            S L  D+ L N       A  K   GD    GC+ +   EY   V+  C  +     D  ++F++D + +R   +G     +  N+  T+   P  V+  +DF   Y G C +  +++ C     CI   L CD     +C   +        S  S DQS      +    ++A +N+    +W++  +       + L +  +RPG+  WRC R+RN   C   +CC K    CS  C   N+P    CC++    D                                           E +   W+++  GDG+H+RE R
Sbjct:   40 SGLRYDSNLTNLYFPNASANIKAVCGDACKTGCMQLIHPEY-QTVVSLCNSNQLTGTDYTEYFSQDFLMLRFYLLGGIYNYENENRTNTVISRP-TVNLIIDFFSFYFGKCVDSTNEFQCIYTDRCIAMDLKCDYYGGMDCGIVT------GGSSISYDQS------VCTQSSTAVVNITNTSYWLLFLLLCLPFLIMGLIFLFYRPGFCCWRCARLRNCYLCRKSSCCRK----CSLLCVLGNSPKTCLCCRSAANSDDFSDVMTKGLCCCAQNEENSNNALYNNISKNKVFPSNSTSIDDEYANSNWTQYTLGDGYHLRECR 345
[Close]
BLAST of SMED30035879 vs. Planmine SMEST
Match: SMESG000018135.1 (SMESG000018135.1)

HSP 1 Score: 56.6102 bits (135), Expect = 1.976e-8
Identity = 75/324 (23.15%), Postives = 122/324 (37.65%), Query Frame = 3 
Query:  474 SLLNPDNTLANKGLKELIAACKDAEGDCRYVGCIII---EYGDKVIRTCKGSTGNMGDNFKWFTRDNVRIRILAIGTFIGKDRSNKNVTIAYPPYNVDFRLDFTRLYGGPCYNK-DQYYCPTHGVCIRYLLACDPRSMWNCPSYSFNPGFDEPSPCSPDQSNNIPKALNLPDASATLNLQ--IFWIVXXXXXXXXXXXXXXXXXWRPGYLIWRCGRIRN--WCAFGNCCYKACHDCSQSC---NTP----CCKTHGTFD-----------------------------------------TTETSTVVWSKFPTGDGFHMRENR 1277
            S L  D+ L N       A  K   GD    GC+ +   EY   V+  C  +     D  ++F++D + +R   +G     +  N+  T+   P  V+  +DF   Y G C +  +++ C     CI   L CD     +C   +        S  S DQS      +    ++A +N+    +W++  +       + L +  +RPG+  WRC R+RN   C   +CC K    CS  C   N+P    CC++    D                                           E +   W+++  GDG+H+RE R
Sbjct:   87 SGLRYDSNLTNLYFPNASANIKAVCGDACKTGCMQLIHPEY-QTVVSLCNSNQLTGTDYTEYFSQDFLMLRFYLLGGIYNYENENRTNTVISRP-TVNLIIDFFSFYFGKCVDSTNEFQCIYTDRCIAMDLKCDYYGGMDCGIVT------GGSSISYDQS------VCTQSSTAVVNITNTSYWLLFLLLCLPFLIMGLIFLFYRPGFCCWRCARLRNCYLCRKSSCCRK----CSLLCVLGNSPKTCLCCRSAANSDDFSDVMTKGLCCCAQNEENSNNALYNNISKNKVFPSNSTSIDDEYANSNWTQYTLGDGYHLRECR 392
The following BLAST results are available for this feature:
BLAST of SMED30035879 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 SMED30035879 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 SMED30035879 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 SMED30035879 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 SMED30035879 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 SMED30035879 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 SMED30035879 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 SMED30035879 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 SMED30035879 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 SMED30035879 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 SMED30035879 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 SMED30035879 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 SMED30035879 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 SMED30035879 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000072342.10.000e+0100.00SMESG000072342.1[more]
SMESG000018135.11.664e-823.15SMESG000018135.1[more]
SMESG000018135.11.976e-823.15SMESG000018135.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035879 ID=SMED30035879|Name=SMED30035879|organism=Schmidtea mediterranea sexual|type=transcript|length=1359bp
TTACAATATTAAATATGCTGTATAAATGCTCTATAATTTTTATAGTGATT
CTCTTAAAATTCATCACAAGCCAACCGATATATCCCAAATTATTTAAAGA
AAGATTTCAAAGAGATCGGCCTCTTCTTCCTAAGGTTCCTGAAATAAGAG
ATGTTTATGTAATAGAAGATTGTAAGCATCAGGGAAATAATGTACCAGTA
GCGATGCCAGATTTGGAAATTACTAATGACTATGGACTAATGATATGGTG
GAATCGCGCAACGAAATTCTTAGATCCTTATAAACTAGAATCAGGCAATA
TTAATGACAGCTATGCATCTACTGATGACGTCCAAGGAATATTTGACTGC
ACAATAACAATAAAGTTAGGCCCTCATGATTCAAGAATCAGTTATCAAGA
AATGATTTTCGGATATTTGACTAAACTTGATATGAAAAATTCACCATTTT
TCAATGACATTTCAAACAGTGTTTCTTTGTTAAATCCTGACAATACGCTT
GCTAATAAAGGGTTGAAAGAACTGATCGCTGCTTGTAAAGATGCTGAAGG
GGATTGCAGATACGTTGGATGCATCATTATCGAATATGGTGATAAAGTTA
TTCGCACTTGCAAAGGGAGTACAGGAAATATGGGCGATAACTTTAAATGG
TTCACCAGAGATAATGTCCGAATTCGCATTTTGGCAATAGGGACATTTAT
AGGAAAAGATAGATCAAATAAGAATGTGACTATTGCTTACCCTCCATATA
ATGTTGATTTCCGTCTAGACTTCACTAGATTATATGGCGGACCTTGTTAC
AATAAAGACCAATACTACTGTCCAACGCATGGAGTTTGTATAAGGTATTT
GCTAGCATGTGATCCACGATCTATGTGGAACTGTCCCAGTTATTCATTTA
ACCCTGGGTTTGATGAGCCAAGCCCATGCTCCCCCGATCAGAGCAATAAC
ATTCCAAAGGCTCTAAATTTACCAGATGCAAGTGCAACGCTAAATTTACA
AATATTCTGGATTGTCTTAGGAATATTTCTTTCACTTTTGGGGTATTTGT
TGCTTAACTACTGTTTATGGAGGCCAGGTTACTTGATTTGGAGATGCGGG
AGAATCCGAAATTGGTGCGCATTTGGAAACTGTTGTTACAAGGCTTGCCA
TGATTGTTCACAATCATGTAACACACCTTGTTGTAAAACCCACGGAACCT
TTGATACCACTGAAACCTCCACTGTGGTGTGGTCAAAATTTCCAACTGGT
GATGGCTTTCATATGAGAGAAAACAGATAACTTATTTTACAAACTAATGA
ATAATTTATAATTTTTGATTACATTTGTGTTAATATATTTTTGTTTCATT
AAAAAAAAA
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protein sequence of SMED30035879-orf-1

>SMED30035879-orf-1 ID=SMED30035879-orf-1|Name=SMED30035879-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=426bp
TILNMLYKCSIIFIVILLKFITSQPIYPKLFKERFQRDRPLLPKVPEIRD
VYVIEDCKHQGNNVPVAMPDLEITNDYGLMIWWNRATKFLDPYKLESGNI
NDSYASTDDVQGIFDCTITIKLGPHDSRISYQEMIFGYLTKLDMKNSPFF
NDISNSVSLLNPDNTLANKGLKELIAACKDAEGDCRYVGCIIIEYGDKVI
RTCKGSTGNMGDNFKWFTRDNVRIRILAIGTFIGKDRSNKNVTIAYPPYN
VDFRLDFTRLYGGPCYNKDQYYCPTHGVCIRYLLACDPRSMWNCPSYSFN
PGFDEPSPCSPDQSNNIPKALNLPDASATLNLQIFWIVLGIFLSLLGYLL
LNYCLWRPGYLIWRCGRIRNWCAFGNCCYKACHDCSQSCNTPCCKTHGTF
DTTETSTVVWSKFPTGDGFHMRENR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000418head
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR042333LDLRAD2
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR042333Low-density lipoprotein receptor class A domain-containing protein 2PANTHERPTHR24652FAMILY NOT NAMEDcoord: 250..391
NoneNo IPR availableTMHMMTMhelixcoord: 334..356
NoneNo IPR availableTMHMMTMhelixcoord: 5..27