SMED30023043

Overview
NameSMED30023043
Smed IDSMED30023043
Length (bp)1930
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 SMED30023043 (SMED30023043) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023043 (SMED30023043) 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 SMED30023043 (SMED30023043) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023043 (SMED30023043) 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




SMED30023043

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30023043SMESG000019067.1 SmedASXL_016476SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30023043SMESG000019067.1 dd_Smed_v4_13671_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30023043SMESG000019067.1 dd_Smed_v4_13671_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023043SMESG000019067.1 dd_Smed_v4_13671_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023043SMESG000019067.1 dd_Smed_v4_13671_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30023043SMESG000019067.1 dd_Smed_v6_13671_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30023043SMESG000019067.1 dd_Smed_v4_13671_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30023043 vs. Planmine SMEST
Match: SMESG000019067.1 (SMESG000019067.1)

HSP 1 Score: 741.495 bits (1913), Expect = 0.000e+0
Identity = 453/454 (99.78%), Postives = 454/454 (100.00%), Query Frame = 3
Query:    9 MDFRQFCEDEKISLSFLKEYXXXXXXXXXXXXXXXXXXXXXVDNSQCNKGFFGNPNEPVKNDFEKFDIHSHIHFEPYMEKSGPFTFCDKCNGTTSQDYLNNPKYFKKNKTILKKEIPEHLMGRIPCRXXXXXXXXXXXXXXXXXXXXXXLYKIIVKTNCDIKAGTSCPVFIRFVDKLKKSEPIELKKNFGSLKFYFAPNSTENFYIKSIPISDLKNVNIKLQTEKDSDEWFPEWLRVEEMVGEKRKWYCKIDKYLSSTRKDCKLVAQLKAVRITVPLIKYQIKVKVSHESVDECYXXXXXXXXXXXXXTDVLKLNNSKYSKIKCGTTPNFTIEHEEIGIIKAIWLXXXXXXXXXXXXXXXXXXXXXXQNVRKVSETSEAVQKKLNQRKGWEDIKVDSVIIEWVDSEKRTHSVEFICNKWIGLSDKMTQKSVLLKSPVENKKWNKSKQLKSDSLE 1370
            MDFRQFCEDEKISLSFLKEYKQIIENSKKSNNKNIILKKPKVDNSQCNKGFFGNPNEPVKNDFEKFDIHSHIHFEPYMEKSGPFTFCDKCNGTTSQDYLNNPKYFKKNKTILKKEIPEHLMGRIPCRKSVASSSSSESEDEDKKPKESVLYKIIVKTNCDIKAGTSCPVFIRFVDKLKKSEPIELKKNFGSLKFYFAPNSTENFYIKSIPISDLKNVNIKLQTEKDSDEWFPEWLRVEEMVGEKRKWYCKIDKYLSSTRKDCKLVAQLKAVRITVPLIKYQIKVKVSHESVDECYGLLSIKLSGSLLKTDVLKLNNSKYSKIKCGTTPNFTIEHEEIGIIKAIWLSISSSSNLS+PEEEKERKEKNKQNVRKVSETSEAVQKKLNQRKGWEDIKVDSVIIEWVDSEKRTHSVEFICNKWIGLSDKMTQKSVLLKSPVENKKWNKSKQLKSDSLE
Sbjct:    1 MDFRQFCEDEKISLSFLKEYKQIIENSKKSNNKNIILKKPKVDNSQCNKGFFGNPNEPVKNDFEKFDIHSHIHFEPYMEKSGPFTFCDKCNGTTSQDYLNNPKYFKKNKTILKKEIPEHLMGRIPCRKSVASSSSSESEDEDKKPKESVLYKIIVKTNCDIKAGTSCPVFIRFVDKLKKSEPIELKKNFGSLKFYFAPNSTENFYIKSIPISDLKNVNIKLQTEKDSDEWFPEWLRVEEMVGEKRKWYCKIDKYLSSTRKDCKLVAQLKAVRITVPLIKYQIKVKVSHESVDECYGLLSIKLSGSLLKTDVLKLNNSKYSKIKCGTTPNFTIEHEEIGIIKAIWLSISSSSNLSKPEEEKERKEKNKQNVRKVSETSEAVQKKLNQRKGWEDIKVDSVIIEWVDSEKRTHSVEFICNKWIGLSDKMTQKSVLLKSPVENKKWNKSKQLKSDSLE 454          

HSP 2 Score: 303.523 bits (776), Expect = 1.941e-93
Identity = 173/173 (100.00%), Postives = 173/173 (100.00%), Query Frame = 1
Query: 1372 VNGPDVGTVTKINVWHDNKGFASGWNLDKISVIRHLTPTEICETLEQMKKKSQLPKAIKLQNGEMFIDNDVLQKDDSPIRKQTSASSNKKKGQIRDXXXXXXXXXXXXXXXXXXXXEGSSKNKTANKSVTQIFTLPFAEESKFSCDKWLSKDVANDSLNKTFASEGSSYLSST 1890
            VNGPDVGTVTKINVWHDNKGFASGWNLDKISVIRHLTPTEICETLEQMKKKSQLPKAIKLQNGEMFIDNDVLQKDDSPIRKQTSASSNKKKGQIRDPDSEISSSSSSIDKTNPKSSEGSSKNKTANKSVTQIFTLPFAEESKFSCDKWLSKDVANDSLNKTFASEGSSYLSST
Sbjct:  511 VNGPDVGTVTKINVWHDNKGFASGWNLDKISVIRHLTPTEICETLEQMKKKSQLPKAIKLQNGEMFIDNDVLQKDDSPIRKQTSASSNKKKGQIRDPDSEISSSSSSIDKTNPKSSEGSSKNKTANKSVTQIFTLPFAEESKFSCDKWLSKDVANDSLNKTFASEGSSYLSST 683          
The following BLAST results are available for this feature:
BLAST of SMED30023043 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 SMED30023043 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 SMED30023043 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 SMED30023043 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 SMED30023043 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 SMED30023043 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 SMED30023043 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 SMED30023043 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 SMED30023043 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 SMED30023043 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 SMED30023043 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 SMED30023043 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 SMED30023043 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 SMED30023043 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000019067.11.941e-9399.78SMESG000019067.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023043 ID=SMED30023043|Name=SMED30023043|organism=Schmidtea mediterranea sexual|type=transcript|length=1930bp
TTCAAACTATGGATTTCAGACAATTTTGTGAAGACGAAAAGATTTCTCTA
AGCTTTTTGAAAGAATACAAACAAATTATTGAAAATTCAAAGAAATCAAA
TAATAAAAACATTATTCTTAAAAAACCGAAAGTAGATAATAGTCAATGTA
ACAAAGGATTTTTTGGAAATCCCAATGAACCAGTGAAAAATGACTTTGAA
AAATTTGACATTCATTCTCACATACATTTTGAACCTTACATGGAGAAATC
CGGGCCCTTCACATTTTGTGACAAATGTAATGGAACGACTTCCCAAGATT
ACTTAAATAATCCTAAGTATTTCAAGAAGAATAAAACTATTTTAAAGAAA
GAAATCCCGGAACATTTAATGGGTAGAATTCCGTGTCGTAAATCTGTTGC
GTCAAGTTCATCGTCCGAATCTGAAGATGAAGACAAAAAGCCTAAAGAAA
GCGTTTTGTATAAAATCATAGTGAAAACCAATTGTGATATCAAAGCTGGT
ACAAGCTGTCCAGTTTTTATCCGTTTTGTGGATAAACTGAAGAAATCTGA
ACCCATTGAATTGAAAAAAAATTTCGGTTCATTGAAATTTTATTTCGCTC
CGAATTCTACTGAAAATTTTTATATAAAAAGCATTCCAATATCTGATTTG
AAAAATGTTAATATTAAGCTACAAACAGAGAAAGATTCTGATGAATGGTT
TCCAGAATGGTTAAGGGTGGAAGAGATGGTCGGAGAAAAAAGGAAATGGT
ATTGTAAAATTGATAAATATTTGTCATCTACGAGAAAAGATTGTAAATTA
GTAGCTCAGTTAAAAGCTGTCCGAATTACAGTACCTCTCATCAAATATCA
AATCAAAGTGAAAGTCTCACATGAAAGTGTCGATGAATGCTATGGCTTAT
TATCCATTAAATTATCAGGGAGTCTACTAAAGACAGATGTTTTGAAGCTG
AATAATTCCAAATATTCTAAAATAAAATGCGGAACGACCCCGAATTTTAC
AATTGAGCATGAAGAAATAGGAATTATAAAAGCTATTTGGCTTTCAATTT
CTTCCTCTTCAAATCTTTCGGAACCAGAAGAAGAAAAGGAAAGAAAAGAA
AAAAATAAACAAAATGTCAGAAAAGTCTCAGAAACATCAGAAGCTGTTCA
AAAGAAACTAAACCAAAGAAAAGGATGGGAAGACATAAAAGTCGATAGTG
TAATTATCGAATGGGTTGATTCCGAAAAAAGAACTCATTCGGTGGAATTT
ATATGCAATAAATGGATCGGACTCAGTGATAAGATGACGCAAAAATCTGT
TCTTCTCAAAAGTCCAGTTGAAAATAAAAAATGGAATAAATCAAAACAAC
TGAAATCGGATTCTCTTGAAGGTAAATGGACCTGATGTGGGAACCGTCAC
AAAAATTAATGTCTGGCACGATAATAAAGGGTTTGCTTCAGGGTGGAATC
TAGATAAAATAAGTGTAATCCGGCACTTAACTCCGACAGAAATATGTGAG
ACCCTGGAACAAATGAAGAAAAAATCCCAGCTTCCTAAAGCCATTAAACT
GCAAAATGGAGAGATGTTTATTGATAATGATGTTTTACAGAAAGACGATT
CTCCTATTAGAAAACAAACATCTGCCTCTTCTAACAAAAAAAAAGGTCAA
ATACGTGATCCTGATTCAGAGATTTCTAGCAGTTCTAGTTCAATTGATAA
AACCAACCCAAAGAGCTCTGAAGGATCTAGTAAAAATAAAACTGCTAATA
AATCCGTGACACAAATCTTCACACTGCCCTTTGCTGAAGAATCGAAATTT
TCCTGTGACAAATGGCTGTCTAAAGACGTCGCAAACGACTCTCTAAACAA
GACCTTTGCATCGGAAGGCAGTAGTTATTTATCTTCTACAATTAATCTTC
TAATCAATCCAGATAACTGAATTATTTTAA
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protein sequence of SMED30023043-orf-1

>SMED30023043-orf-1 ID=SMED30023043-orf-1|Name=SMED30023043-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=461bp
QTMDFRQFCEDEKISLSFLKEYKQIIENSKKSNNKNIILKKPKVDNSQCN
KGFFGNPNEPVKNDFEKFDIHSHIHFEPYMEKSGPFTFCDKCNGTTSQDY
LNNPKYFKKNKTILKKEIPEHLMGRIPCRKSVASSSSSESEDEDKKPKES
VLYKIIVKTNCDIKAGTSCPVFIRFVDKLKKSEPIELKKNFGSLKFYFAP
NSTENFYIKSIPISDLKNVNIKLQTEKDSDEWFPEWLRVEEMVGEKRKWY
CKIDKYLSSTRKDCKLVAQLKAVRITVPLIKYQIKVKVSHESVDECYGLL
SIKLSGSLLKTDVLKLNNSKYSKIKCGTTPNFTIEHEEIGIIKAIWLSIS
SSSNLSEPEEEKERKEKNKQNVRKVSETSEAVQKKLNQRKGWEDIKVDSV
IIEWVDSEKRTHSVEFICNKWIGLSDKMTQKSVLLKSPVENKKWNKSKQL
KSDSLEGKWT*
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protein sequence of SMED30023043-orf-2

>SMED30023043-orf-2 ID=SMED30023043-orf-2|Name=SMED30023043-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=136bp
MKKKSQLPKAIKLQNGEMFIDNDVLQKDDSPIRKQTSASSNKKKGQIRDP
DSEISSSSSSIDKTNPKSSEGSSKNKTANKSVTQIFTLPFAEESKFSCDK
WLSKDVANDSLNKTFASEGSSYLSSTINLLINPDN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR036392PLAT/LH2_dom_sf
IPR001024PLAT/LH2_dom
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001024PLAT/LH2 domainPFAMPF01477PLATcoord: 153..252
e-value: 3.5E-8
score: 34.0
IPR001024PLAT/LH2 domainPROSITEPS50095PLATcoord: 280..436
score: 10.023
IPR001024PLAT/LH2 domainPROSITEPS50095PLATcoord: 151..271
score: 10.918
NoneNo IPR availableGENE3DG3DSA:2.60.60.20coord: 150..277
e-value: 1.2E-15
score: 59.4
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 357..380
IPR036392PLAT/LH2 domain superfamilySUPERFAMILYSSF49723Lipase/lipooxygenase domain (PLAT/LH2 domain)coord: 149..258