SMED30029044

Overview
NameSMED30029044
Smed IDSMED30029044
Length (bp)1118
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 SMED30029044 (SMED30029044) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029044 (SMED30029044) 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 SMED30029044 (SMED30029044) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029044 (SMED30029044) 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



SMED30029044

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
nervous systemSMED30029044 dd_Smed_v4_30057_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029044 dd_Smed_v4_30057_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30029044 dd_Smed_v4_30057_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
SMED30029044 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000866:73771..74873 -5479
Homology
[Close]
BLAST of SMED30029044 vs. Planmine SMEST
Match: SMESG000013334.1 (SMESG000013334.1)

HSP 1 Score: 77.7962 bits (190), Expect = 1.234e-15
Identity = 88/292 (30.14%), Postives = 139/292 (47.60%), Query Frame = 1 
Query:  166 GFILNFLSAIFFHRIRHKGNFLTLIYILSVIESIYGLTFFINQMFFYQTRLLHRQVSTTILSSIGVNFIAHLIRNISRIF----LTSRNWMIAYIAWIRCLVIRDPLKSQSLNRKTIAKHIIILITS-SCILNIPRMFESRISMSETGKVKFHLNYHTKFAWYTFFYLPFYFIAVSXXXXXXXXXXXXXXXXXXK---------------FRNRQFSHEQNLNNNFSTKTVLILCGIFMICELPKSSTVVVMFIDQYADIIGNKNQLNHFTXXXXXXXXXXXXXNFLVYIYS 981
            GF+LN  +  FFHR   + +F  ++  LS++E I+ L+  + + F++   +L R         + VNFI +L+ N   +     L SRNW+I  IAW R   I  PL S+ L  K + +++I  I + S  L  PR+FE   S S   K      Y    + Y   Y   +FI +SP+P  +I   SI ++  ++                +N   S     N + S KTVL+LC +F  CE P     +   I + +  +  +  L HF  + ++L+S DSI NF++Y  S
Sbjct:   35 GFVLNLWAFSFFHRFEKQSHFCFMLKHLSLVELIFSLSGVVFECFYFTLVVLQRP-----FPKVLVNFIIYLVFNFMWLMYKSSLLSRNWVIVLIAWRRYQAIHRPLSSKQLLSKKLIQYLIFGIYAISLFLVTPRLFEITYSYSNETKNVIITPYLLVNSIYLSTYPILFFILISPVPVCVICFYSIFMLRSLRKPECHELETRSDHFQRQNPTISRRIARNRSSSNKTVLVLCTVFTTCEFPMCLAGIFNQISRESTGVQFQWFLTHFAGVANILTSCDSIFNFVIYFIS 321
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BLAST of SMED30029044 vs. Planmine SMEST
Match: SMESG000061638.1 (SMESG000061638.1)

HSP 1 Score: 63.5438 bits (153), Expect = 6.045e-11
Identity = 71/252 (28.17%), Postives = 117/252 (46.43%), Query Frame = 1 
Query:  154 FVFIGFILNFLSAIFFHRIRHKGNFLTLIYILSVIESIYGLTFFINQMFFYQTRLLHRQVSTTILSSIGVNFIAHLIRNISRIFLTSRNWMIAYIAWIRCLVIRDPLKSQSLNR-KTIAKHIIILITSSCILNIPRMFESRISMSETGKVKFHLN---YHTKFAWYTFFYLPFYFIAVSXXXXXXXXXXXXXXXXXXKFRNRQFSHEQNLNNNFS--------------------TKTVLILCGIFMICELP 837
            F  +G + N +S I+F  +     F  L+  LS +E I+  + FI ++ +Y     H  +S T  +   +  +   +  + +  L +RNW+ A +AW R   I  PL ++     K+I+  + I+     + +IPR FE    + E       +N   Y+T    Y   Y P YF   SP+P ++I +CS+S++IV+K R    ++  +  + FS                     KTV+ILC  F ICELP
Sbjct:    5 FSLLGLMFNIISMIYFATVNRYKIFNLLLLHLSCVEVIFCSSGFIFEVTYYWYAAKHNILSYTWQAKFIIYLVYFWLWVVYKSSLLARNWITAVVAWQRYRAISHPLSTKQYETYKSISMILFIMYFLVILFSIPRAFEKSYYLCEKDVYIITMNNSIYYTDL--YKNIYNPLYFFLSSPLPLLVIIVCSLSMLIVLKKRQENLNNLTSQPSRFSKYKQKSSLGNNSSNSRGQSINKTVIILCAAFTICELP 254
[Close]
BLAST of SMED30029044 vs. Planmine SMEST
Match: SMESG000065943.1 (SMESG000065943.1)

HSP 1 Score: 53.9138 bits (128), Expect = 8.627e-8
Identity = 75/290 (25.86%), Postives = 131/290 (45.17%), Query Frame = 1 
Query:   85 NCSLPENFRDK-SIQTYF------TSIVLVFVFIGFILNFLSAIFFHRIRHKGNFLTLIYILSVIESIYGLTFFINQ-MFFYQTRLLHRQVSTTILSSIGVNFIAHLIRNISRIFLTS----RNWMIAYIAWIRCLVIRDPLKSQSLNRKTIAKHIIILIT---SSCILNIPRMFESRISMSETGKVKFHLNYHTKF--AWY-----TFF--YLPFYFIAVSXXXXXXX-XXXXXXXXXXXKFRNRQFSHEQNLNNNFSTKTVLILCGIFMICELPKSSTVVVMFIDQYA 879
            NC +PE++    S   YF      T I  VF+  G ILN +  I   +         ++  +SV + +  L+  ++     ++TR         I + I +N I   I +I+ IF  S    RNW + Y+A  RC+ I  P+K  ++N  T++K    LIT   +  I+NIP++FE+ +S++  G         + F   WY      FF   +P +   ++ +  +    +   +   +   +++ F  E   N+    KTVL+L  +F+IC+ P  S   ++   Q A
Sbjct:   64 NC-IPEDYEHLLSSNWYFPVAYTLTGINAVFIIKGLILNIICFIIVGKDHSDSVMSGILRFVSVGDELALLSNGVDSFCHVFETR---------INNPISMNKILGYIHSINWIFKASFSASRNWGMMYLAVSRCIYIIYPIK--AVNMITLSKSYKFLITIFVTIMIINIPKVFETMVSITTCGNFTIATIGSSGFMPTWYILITSVFFNSLIPMFITVIANMLLLRKWYMTVANRKTLSSVKSKSFDSEIQKNSTV-IKTVLMLSSLFIICQAPMISYGFIVLSKQTA 340
The following BLAST results are available for this feature:
BLAST of SMED30029044 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 SMED30029044 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 SMED30029044 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 SMED30029044 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 SMED30029044 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 SMED30029044 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 SMED30029044 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 SMED30029044 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 SMED30029044 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 SMED30029044 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 SMED30029044 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 SMED30029044 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 SMED30029044 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 SMED30029044 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000013334.11.234e-1530.14SMESG000013334.1[more]
SMESG000061638.16.045e-1128.17SMESG000061638.1[more]
SMESG000065943.18.627e-825.86SMESG000065943.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029044 ID=SMED30029044|Name=SMED30029044|organism=Schmidtea mediterranea sexual|type=transcript|length=1118bp
AATGATCTAAAATTAATAGCCGACTATTTAACTGTTAAATAACTAAATTG
AACACTCAAAATGTATAACACGACAGAAGATTCCAATTGTTCATTACCCG
AAAACTTCAGAGACAAATCCATCCAAACCTACTTTACCTCCATCGTGCTG
GTATTCGTTTTTATTGGTTTCATCCTCAACTTTCTTTCGGCAATATTTTT
CCATAGAATACGGCATAAAGGTAACTTTCTAACTTTGATTTACATTCTGT
CAGTCATTGAAAGCATCTACGGGTTGACATTTTTTATAAATCAAATGTTT
TTCTATCAAACCAGGCTTCTCCATCGACAAGTGTCCACGACTATTCTTTC
ATCGATTGGCGTAAACTTCATCGCTCACCTGATCCGGAACATTTCCAGAA
TATTCTTAACGAGCCGCAATTGGATGATTGCGTATATTGCGTGGATCCGA
TGTCTAGTGATCAGGGATCCATTGAAATCTCAATCACTTAACCGGAAAAC
AATTGCAAAACATATAATAATACTTATAACATCGAGCTGTATTTTAAACA
TTCCGAGGATGTTTGAATCTCGAATATCCATGAGTGAGACTGGCAAAGTG
AAATTCCATTTAAACTATCATACCAAATTTGCGTGGTATACGTTTTTCTA
CCTACCTTTTTATTTTATTGCTGTTAGTCCAATACCGGCAGTAATAATAA
CGATATGTAGCATCTCTATTATAATAGTAATAAAATTTCGAAACAGACAA
TTTTCTCATGAACAAAATTTAAATAATAACTTTTCTACAAAGACTGTTTT
GATTTTGTGCGGAATTTTCATGATTTGCGAACTGCCGAAGAGTAGCACAG
TTGTAGTAATGTTCATTGATCAATATGCCGACATAATCGGCAACAAGAAC
CAATTAAATCACTTTACCGATATCGGAAGTTTGCTCTCGTCATTGGATTC
GATATTAAACTTTCTCGTTTATATCTATTCGGGAATGAAAAATAGATTAT
TCGACAATTTTTCAATGTGTAATTTTGTGTAGTTGATATTGATAATTGAT
AATTCTCATTGAGCTTGTTAATTATTTAAATTTTTTTATTTATTTATTGT
AAATCTTCAACCTCTTAT
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protein sequence of SMED30029044-orf-1

>SMED30029044-orf-1 ID=SMED30029044-orf-1|Name=SMED30029044-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=324bp
MYNTTEDSNCSLPENFRDKSIQTYFTSIVLVFVFIGFILNFLSAIFFHRI
RHKGNFLTLIYILSVIESIYGLTFFINQMFFYQTRLLHRQVSTTILSSIG
VNFIAHLIRNISRIFLTSRNWMIAYIAWIRCLVIRDPLKSQSLNRKTIAK
HIIILITSSCILNIPRMFESRISMSETGKVKFHLNYHTKFAWYTFFYLPF
YFIAVSPIPAVIITICSISIIIVIKFRNRQFSHEQNLNNNFSTKTVLILC
GIFMICELPKSSTVVVMFIDQYADIIGNKNQLNHFTDIGSLLSSLDSILN
FLVYIYSGMKNRLFDNFSMCNFV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR017452GPCR_Rhodpsn_7TM
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
NoneNo IPR availableGENE3DG3DSA:1.20.1070.10coord: 10..320
e-value: 7.6E-25
score: 89.4
NoneNo IPR availablePANTHERPTHR46641FAMILY NOT NAMEDcoord: 6..309
NoneNo IPR availableCDDcd149787tmA_FMRFamide_R-likecoord: 28..304
e-value: 3.42014E-8
score: 51.8648
NoneNo IPR availableSUPERFAMILYSSF81321Family A G protein-coupled receptor-likecoord: 6..308
NoneNo IPR availableTMHMMTMhelixcoord: 25..47
NoneNo IPR availableTMHMMTMhelixcoord: 200..222
NoneNo IPR availableTMHMMTMhelixcoord: 115..134
NoneNo IPR availableTMHMMTMhelixcoord: 86..108
NoneNo IPR availableTMHMMTMhelixcoord: 247..269
NoneNo IPR availableTMHMMTMhelixcoord: 54..76
NoneNo IPR availableTMHMMTMhelixcoord: 284..306
IPR017452GPCR, rhodopsin-like, 7TMPROSITEPS50262G_PROTEIN_RECEP_F1_2coord: 36..304
score: 14.093