SMED30012783

Overview
NameSMED30012783
Smed IDSMED30012783
Length (bp)994
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 SMED30012783 (SMED30012783) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012783 (SMED30012783) 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 SMED30012783 (SMED30012783) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30012783 (SMED30012783) 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



SMED30012783

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 regionSMED30012783h1SMcG0010054 SmedASXL_013600SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30012783h1SMcG0010054 dd_Smed_v4_16605_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30012783h1SMcG0010054 dd_Smed_v4_16605_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30012783 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005002:22909..30427 -4740
Homology
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BLAST of SMED30012783 vs. Planmine SMEST
Match: SMESG000064443.1 (SMESG000064443.1)

HSP 1 Score: 511.531 bits (1316), Expect = 0.000e+0
Identity = 296/298 (99.33%), Postives = 296/298 (99.33%), Query Frame = 3 
Query:   27 MNREKKLFCVKLLLIFGFTLAFLSCVLAVISYIIPQWMVYVAYSSDVPSKWIEYNRTRGIFQECMESTLKQDPAVQLPYVMNKQQCITNDVGQYNSDSGDGNYEIIIRMRQXXXXXXXXXXXXXXXXXXXXXXXXXKWCCMTDDTIYYLKWRITXXXXXXXXXXXXXXXXXXXTVLYYEVEVNMKYKTNLLPFSQFNLNNIKRFGPIYYIAWISAGLAFLSSIFFTVSSCLGKEMEIEKFYPENWKKTNDAFLNDEFPKSNQFYEQFTHPIKRNLPSAPESLQRYDLSNNPVPSEIDI 920
            MNREKKLFCVKLLLIFGFTLAFLSCVLAVISYIIPQWMVYVAYSSDVPSKWIEYNRTRGIFQECMESTLKQDPAVQLPYVMNKQQCITNDVGQYNSDSGDGNYEIIIRMRQSHI LHSVSILLLLIMLIFGIGVFIKWCCMTDDTIYYLKWRITLSIFSIIICLCLSASCSIATVLYYEVEVNMKYKTNLLPFSQFNLNNIKRFGPIYYIAWISAGLAFLSSIFFTVSSCLGKEMEIEKFYPENWKKTNDAFLNDEFPKSNQFYEQF HPIKRNLPSAPESLQRYDLSNNPVPSEIDI
Sbjct:    1 MNREKKLFCVKLLLIFGFTLAFLSCVLAVISYIIPQWMVYVAYSSDVPSKWIEYNRTRGIFQECMESTLKQDPAVQLPYVMNKQQCITNDVGQYNSDSGDGNYEIIIRMRQSHIALHSVSILLLLIMLIFGIGVFIKWCCMTDDTIYYLKWRITLSIFSIIICLCLSASCSIATVLYYEVEVNMKYKTNLLPFSQFNLNNIKRFGPIYYIAWISAGLAFLSSIFFTVSSCLGKEMEIEKFYPENWKKTNDAFLNDEFPKSNQFYEQFPHPIKRNLPSAPESLQRYDLSNNPVPSEIDI 298
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BLAST of SMED30012783 vs. Planmine SMEST
Match: SMESG000064443.1 (SMESG000064443.1)

HSP 1 Score: 436.802 bits (1122), Expect = 1.335e-155
Identity = 259/261 (99.23%), Postives = 259/261 (99.23%), Query Frame = 3 
Query:  138 MVYVAYSSDVPSKWIEYNRTRGIFQECMESTLKQDPAVQLPYVMNKQQCITNDVGQYNSDSGDGNYEIIIRMRQXXXXXXXXXXXXXXXXXXXXXXXXXKWCCMTDDTIYYLKWRITXXXXXXXXXXXXXXXXXXXTVLYYEVEVNMKYKTNLLPFSQFNLNNIKRFGPIYYIAWISAGLAFLSSIFFTVSSCLGKEMEIEKFYPENWKKTNDAFLNDEFPKSNQFYEQFTHPIKRNLPSAPESLQRYDLSNNPVPSEIDI 920
            MVYVAYSSDVPSKWIEYNRTRGIFQECMESTLKQDPAVQLPYVMNKQQCITNDVGQYNSDSGDGNYEIIIRMRQSHI LHSVSILLLLIMLIFGIGVFIKWCCMTDDTIYYLKWRITLSIFSIIICLCLSASCSIATVLYYEVEVNMKYKTNLLPFSQFNLNNIKRFGPIYYIAWISAGLAFLSSIFFTVSSCLGKEMEIEKFYPENWKKTNDAFLNDEFPKSNQFYEQF HPIKRNLPSAPESLQRYDLSNNPVPSEIDI
Sbjct:    1 MVYVAYSSDVPSKWIEYNRTRGIFQECMESTLKQDPAVQLPYVMNKQQCITNDVGQYNSDSGDGNYEIIIRMRQSHIALHSVSILLLLIMLIFGIGVFIKWCCMTDDTIYYLKWRITLSIFSIIICLCLSASCSIATVLYYEVEVNMKYKTNLLPFSQFNLNNIKRFGPIYYIAWISAGLAFLSSIFFTVSSCLGKEMEIEKFYPENWKKTNDAFLNDEFPKSNQFYEQFPHPIKRNLPSAPESLQRYDLSNNPVPSEIDI 261
[Close]
BLAST of SMED30012783 vs. Planmine SMEST
Match: SMESG000075916.1 (SMESG000075916.1)

HSP 1 Score: 129.798 bits (325), Expect = 3.693e-35
Identity = 113/299 (37.79%), Postives = 170/299 (56.86%), Query Frame = 3 
Query:   27 MNREKKLFCVKLLLIFGFTLAFLSCVLAVISYIIPQWMVYVAYSSDVPSKWIEYNRTRGIFQECMESTLKQDPAVQLPYVMNKQQCITNDVGQYNSDSGDGNYEIIIRMRQXXXXXXXXXXXXXXXXXXXXXXXXXKWCCMTDDTIYYLKWRITXXXXXXXXXXXXXXXXXXXTVLYYEVEVNMKYKTNLLPFSQFNLNNIKRFGPIYYIAWISAGLAFLSSIFFTVSSCLGKEMEIEKFYPENWKKTNDAFLNDEFPKSNQFYEQFTHPIKRNLPSA---------PESLQRYDLSNN 896
            MN E++  C+K+L+I GF     S  LA+ +Y IP W+  ++ SS++ S W  Y+R+ GIFQEC+ + +    ++  PY++ K  C  ND+GQY   S +  Y  IIRMRQS IGLH  +ILLLL +L+ GIG+F+KWCC   D+++Y+KWR  L   S++  LC SAS SI T  +Y +  N  Y+ + L    F   ++   G ++Y+AW     + L+SI F +SS  GK +E+ K+ P      N AF +D++  +   + Q    I RN  S          P  L RY+++ N
Sbjct:    1 MNIEQRFSCIKILVIIGFAFVSFSFTLAIATYSIPYWLT-LSSSSNISSDWRSYSRSIGIFQECLITQITSTISIPAPYII-KNNCTDNDIGQYGVTSSNSYYLTIIRMRQSQIGLHGATILLLLFVLLTGIGIFMKWCCGFMDSLFYIKWRNALGCLSLLSFLCFSASSSIGTA-FYLMYGNTTYQVSELSLISFQQGSVT-VGFMFYLAWTGCLTSLLASICFFISSHYGKSLEMSKYKPHVISVDNPAFDSDDYKIAEPIFLQ--PSIGRNDFSKLSLTANVNNPGPLPRYNINVN 293
The following BLAST results are available for this feature:
BLAST of SMED30012783 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 SMED30012783 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 SMED30012783 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 SMED30012783 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 SMED30012783 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 SMED30012783 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 SMED30012783 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 SMED30012783 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 SMED30012783 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 SMED30012783 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 SMED30012783 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 SMED30012783 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 SMED30012783 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 SMED30012783 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000064443.10.000e+099.33SMESG000064443.1[more]
SMESG000064443.11.335e-15599.23SMESG000064443.1[more]
SMESG000075916.13.693e-3537.79SMESG000075916.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012783 ID=SMED30012783|Name=SMED30012783|organism=Schmidtea mediterranea sexual|type=transcript|length=994bp
TTTCAGTTTGACATTTTCAGGAGTTTATGAACCGAGAAAAAAAATTATTT
TGTGTTAAATTATTGTTAATTTTTGGCTTTACGTTGGCATTTCTTTCATG
TGTATTGGCTGTGATATCTTACATTATTCCTCAGTGGATGGTTTATGTGG
CTTATAGTTCAGATGTTCCATCGAAATGGATTGAATACAATAGAACAAGA
GGAATATTTCAGGAATGCATGGAGAGTACGTTAAAACAAGATCCGGCTGT
ACAATTACCGTATGTAATGAACAAGCAGCAGTGTATTACTAATGACGTTG
GTCAGTATAATTCGGATTCCGGTGATGGAAACTATGAAATAATCATCAGA
ATGCGTCAGAGTCACATTGGCCTCCACAGCGTGTCTATTCTCCTTTTATT
AATTATGCTAATTTTCGGAATTGGAGTTTTCATAAAGTGGTGCTGTATGA
CTGACGATACTATATACTATTTGAAATGGAGAATTACCCTATCAATTTTT
TCTATTATTATTTGTCTATGTTTGAGTGCTTCATGCTCAATCGCAACTGT
ATTGTATTACGAAGTAGAAGTCAATATGAAATATAAGACAAATTTATTAC
CATTCAGCCAATTTAATTTGAATAATATAAAACGATTCGGACCAATTTAT
TATATTGCCTGGATTTCCGCTGGACTTGCATTTCTCTCTTCGATCTTTTT
CACAGTTAGCAGTTGTTTGGGTAAAGAAATGGAAATAGAAAAGTTTTATC
CGGAAAACTGGAAAAAGACCAACGACGCATTTTTAAATGATGAATTTCCA
AAATCTAACCAATTCTACGAACAATTTACTCATCCAATTAAAAGAAATTT
ACCATCGGCACCCGAAAGCTTACAAAGATATGATTTGTCCAACAATCCAG
TGCCAAGCGAAATTGATATTTAAAACAAATTTCAATCAAAGAACCTTGCT
TTCACCATTCTTGGATTTTTATAACAAATCAAACAAATAAATTT
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protein sequence of SMED30012783-orf-1

>SMED30012783-orf-1 ID=SMED30012783-orf-1|Name=SMED30012783-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=299bp
MNREKKLFCVKLLLIFGFTLAFLSCVLAVISYIIPQWMVYVAYSSDVPSK
WIEYNRTRGIFQECMESTLKQDPAVQLPYVMNKQQCITNDVGQYNSDSGD
GNYEIIIRMRQSHIGLHSVSILLLLIMLIFGIGVFIKWCCMTDDTIYYLK
WRITLSIFSIIICLCLSASCSIATVLYYEVEVNMKYKTNLLPFSQFNLNN
IKRFGPIYYIAWISAGLAFLSSIFFTVSSCLGKEMEIEKFYPENWKKTND
AFLNDEFPKSNQFYEQFTHPIKRNLPSAPESLQRYDLSNNPVPSEIDI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000420parapharyngeal region
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR006187Claudin
Vocabulary: cellular component
TermDefinition
GO:0005923bicellular tight junction
Vocabulary: molecular function
TermDefinition
GO:0005198structural molecule activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.20.140.150coord: 10..240
e-value: 3.6E-15
score: 57.9
NoneNo IPR availablePROSITEPS51257PROKAR_LIPOPROTEINcoord: 1..25
score: 7.0
NoneNo IPR availableTMHMMTMhelixcoord: 156..178
NoneNo IPR availableTMHMMTMhelixcoord: 114..136
NoneNo IPR availableTMHMMTMhelixcoord: 209..231
NoneNo IPR availableTMHMMTMhelixcoord: 12..34
IPR006187ClaudinPANTHERPTHR12002CLAUDINcoord: 85..241