SMED30029670

Overview
NameSMED30029670
Smed IDSMED30029670
Length (bp)1574
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 SMED30029670 (SMED30029670) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029670 (SMED30029670) 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 SMED30029670 (SMED30029670) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029670 (SMED30029670) 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



SMED30029670

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30029670h1SMcG0020879 SmedASXL_026868SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30029670h1SMcG0020879 SmedASXL_001869SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30029670h1SMcG0020879 dd_Smed_v4_29431_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029670h1SMcG0020879 dd_Smed_v4_29431_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
SMED30029670 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003380:26839..28412 +7861
Homology
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BLAST of SMED30029670 vs. Planmine SMEST
Match: SMESG000016956.1 (SMESG000016956.1)

HSP 1 Score: 930.243 bits (2403), Expect = 0.000e+0
Identity = 512/513 (99.81%), Postives = 512/513 (99.81%), Query Frame = 2 
Query:   29 MDNETTCLICMEEIDEKNLADVIPCNHEFCVSCIKECIYLSECCPLYRCSVDSILVSNTNRVKVNITVEQIIQEMIVQYIHENKKRFKSFINKLCPAMTNWFQMKKEFEKIIDXXXXXXXXXXXXXXXXXXXXXXXXXAFIKFDYKYFQSIISEFKSLNTTHXXXXXXXXXXXXXXXXXXXXXXXXEKNFAYIVSNLLEKLVDQIKSMSLVFEQTKISFDLKFSKSTELDLFENDIFDDMYPVWTNIIVIETLFWTSIKTCIITDVELINPMAAVFQEIDFSKCIICNSQTRFDAHCRFKNCNHSVCMMCVHKHSIYKGYCPMENHPMNHSLYLHHRNYIDIQDYWIKNFGKTQKFLHWNFSQFIRIFRRSISNHILVLDDFMEKFIVFMSNLNETCAFHNLEQAFERLILHFGLNLFNDSTENDIYDALQLRKSQFLDLENEIYDVPQSDKIFVNHKENYLSCSGMKDVLVEAQYSAIKYMNERVFHNPTINDHLKNTFADYIAVKMLHGIK 1567
            MDNETTCLICMEEIDEKNLA VIPCNHEFCVSCIKECIYLSECCPLYRCSVDSILVSNTNRVKVNITVEQIIQEMIVQYIHENKKRFKSFINKLCPAMTNWFQMKKEFEKIIDQDNISLIQNQLNQNQIQNRFQLLNQAFIKFDYKYFQSIISEFKSLNTTHHGIIGKLLKYKILNLNLNHLSSGNEKNFAYIVSNLLEKLVDQIKSMSLVFEQTKISFDLKFSKSTELDLFENDIFDDMYPVWTNIIVIETLFWTSIKTCIITDVELINPMAAVFQEIDFSKCIICNSQTRFDAHCRFKNCNHSVCMMCVHKHSIYKGYCPMENHPMNHSLYLHHRNYIDIQDYWIKNFGKTQKFLHWNFSQFIRIFRRSISNHILVLDDFMEKFIVFMSNLNETCAFHNLEQAFERLILHFGLNLFNDSTENDIYDALQLRKSQFLDLENEIYDVPQSDKIFVNHKENYLSCSGMKDVLVEAQYSAIKYMNERVFHNPTINDHLKNTFADYIAVKMLHGIK
Sbjct:    1 MDNETTCLICMEEIDEKNLAVVIPCNHEFCVSCIKECIYLSECCPLYRCSVDSILVSNTNRVKVNITVEQIIQEMIVQYIHENKKRFKSFINKLCPAMTNWFQMKKEFEKIIDQDNISLIQNQLNQNQIQNRFQLLNQAFIKFDYKYFQSIISEFKSLNTTHHGIIGKLLKYKILNLNLNHLSSGNEKNFAYIVSNLLEKLVDQIKSMSLVFEQTKISFDLKFSKSTELDLFENDIFDDMYPVWTNIIVIETLFWTSIKTCIITDVELINPMAAVFQEIDFSKCIICNSQTRFDAHCRFKNCNHSVCMMCVHKHSIYKGYCPMENHPMNHSLYLHHRNYIDIQDYWIKNFGKTQKFLHWNFSQFIRIFRRSISNHILVLDDFMEKFIVFMSNLNETCAFHNLEQAFERLILHFGLNLFNDSTENDIYDALQLRKSQFLDLENEIYDVPQSDKIFVNHKENYLSCSGMKDVLVEAQYSAIKYMNERVFHNPTINDHLKNTFADYIAVKMLHGIK 513
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BLAST of SMED30029670 vs. Planmine SMEST
Match: SMESG000043150.1 (SMESG000043150.1)

HSP 1 Score: 53.1434 bits (126), Expect = 2.276e-7
Identity = 33/103 (32.04%), Postives = 53/103 (51.46%), Query Frame = 2 
Query:   47 CLICMEEIDEKNLADVIPCNHEFCVSCIKECIYLSECCPLYRCSVDSILVSNTNRVKVNITVEQIIQEMIVQYIHENKKRFKSFINKLCPAMTNWFQMKKEFE 355
            C IC++   +   A V+PC H FC+SCI+  +  + CCPL R  + +IL+ N +   V       + +++V  I +NK   +  +    P + N F   KEFE
Sbjct:    8 CSICLDYNSDNEYAIVLPCQHRFCLSCIRSWVTENPCCPLDRSDITNILIHNNSFDHVQSVT---VSDILVDQISKNK---QILLENHLPLIINLF---KEFE 101
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BLAST of SMED30029670 vs. Planmine SMEST
Match: SMESG000067072.1 (SMESG000067072.1)

HSP 1 Score: 53.5286 bits (127), Expect = 2.676e-7
Identity = 33/120 (27.50%), Postives = 60/120 (50.00%), Query Frame = 2 
Query:  653 SLVFEQTKISFDLKFSKSTEL--DLFEND--IFDDMYPVWTNIIVIETLFWTSIKTCIITDVELINPMAAVFQEIDFSKCIICNSQTRFDAHCRFKNCNHSVCMMCVHKHSIYKGYCPME 1000
            +L+ ++    F  KF   ++L   + EN   I +D+  +    +  + +F  +IK     D++L     +  ++ D  KC+IC      +++C+F NCNH +C+ CV K  I  G CP +
Sbjct:  178 TLLMKKNITYFPFKFQSESQLLPSILENQFIIKNDLIDLNDIYLFGKYIFIQNIKG----DLDLYQSFQSGIEKADIDKCLICTRLISKESYCKFLNCNHKLCITCVDKFMITHGSCPFD 293
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BLAST of SMED30029670 vs. Planmine SMEST
Match: SMESG000012758.1 (SMESG000012758.1)

HSP 1 Score: 51.9878 bits (123), Expect = 7.483e-7
Identity = 34/113 (30.09%), Postives = 61/113 (53.98%), Query Frame = 2 
Query:   35 NETT--CLICMEEIDEKNLADVIPCNHEFCVSCIKECIYLSECCPLYRCSVDSILVSNTNRVKVNITVEQIIQEMIVQYIHENKKRFKSFINKLCPAMTNWFQMKKEFEKIID 367
            NET   C IC+++   ++L+ ++PC+H+FC  CIK  +  S CCPL R  + +I V N+     + T+   + ++++++I +NK+                FQ+K    KI+D
Sbjct:    2 NETNEVCNICLDDNRNEHLSVILPCHHKFCFPCIKTWVIESPCCPLDRSDIVNISV-NSGHATPSQTI--FVADILIEHILQNKQ----------------FQIKNHLPKILD 95
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BLAST of SMED30029670 vs. Planmine SMEST
Match: SMESG000065437.1 (SMESG000065437.1)

HSP 1 Score: 49.2914 bits (116), Expect = 5.335e-6
Identity = 27/69 (39.13%), Postives = 39/69 (56.52%), Query Frame = 2 
Query:   41 TTCLICMEEIDEKNLADVIPCNHEFCVSCIKECIYLSECCPLYRCSVDSILV-SNTNRVKVNITVEQII 244
              C IC++   E   A V+PC H+FCV CIK+ I  +  CPL R  +  IL+ SN +    N++V  I+
Sbjct:    2 NVCSICIDNNLENECATVLPCRHKFCVKCIKKWISENPNCPLDRYDISEILINSNQSESITNLSVTDIL 70
The following BLAST results are available for this feature:
BLAST of SMED30029670 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 SMED30029670 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 SMED30029670 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 SMED30029670 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 SMED30029670 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 SMED30029670 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 SMED30029670 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 SMED30029670 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 SMED30029670 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 SMED30029670 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 SMED30029670 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 SMED30029670 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 SMED30029670 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 SMED30029670 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000016956.10.000e+099.81SMESG000016956.1[more]
SMESG000043150.12.276e-732.04SMESG000043150.1[more]
SMESG000067072.12.676e-727.50SMESG000067072.1[more]
SMESG000012758.17.483e-730.09SMESG000012758.1[more]
SMESG000065437.15.335e-639.13SMESG000065437.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029670 ID=SMED30029670|Name=SMED30029670|organism=Schmidtea mediterranea sexual|type=transcript|length=1574bp
CGAAAGTTAAAATAATTTAAAACACAAAATGGATAACGAAACGACTTGTT
TAATATGCATGGAAGAAATTGACGAGAAAAATTTGGCAGATGTAATACCA
TGCAATCATGAATTCTGTGTAAGTTGCATCAAGGAATGCATCTATCTCTC
TGAATGCTGTCCATTGTATCGGTGCTCAGTGGATTCCATCTTGGTGAGCA
ACACCAACAGGGTTAAAGTGAACATTACAGTCGAACAAATCATTCAGGAA
ATGATTGTACAGTACATCCATGAAAACAAAAAAAGGTTCAAATCTTTTAT
CAATAAACTTTGTCCAGCAATGACAAATTGGTTTCAAATGAAGAAAGAAT
TCGAAAAAATCATTGATCAAGACAACATAAGCCTTATCCAAAATCAATTG
AACCAGAATCAAATACAAAACAGATTTCAATTATTAAATCAAGCGTTTAT
TAAGTTTGATTACAAATATTTCCAAAGCATAATATCGGAATTTAAGTCAC
TGAATACCACTCACCATGGTATCATTGGGAAGTTATTAAAATACAAGATT
CTCAATCTGAATTTGAACCATTTGTCCTCGGGAAATGAAAAAAACTTTGC
TTATATTGTAAGCAATCTCCTGGAAAAATTAGTGGATCAAATTAAATCCA
TGAGTTTGGTTTTTGAACAGACGAAAATATCGTTTGATTTAAAATTTTCT
AAATCGACTGAACTAGATCTTTTTGAAAATGACATATTCGATGACATGTA
TCCGGTTTGGACGAATATTATAGTAATCGAAACACTTTTTTGGACATCTA
TCAAAACGTGTATAATCACAGATGTTGAACTAATCAATCCAATGGCAGCT
GTCTTTCAGGAAATCGATTTTTCAAAATGTATTATTTGCAATAGTCAAAC
CCGATTCGACGCACACTGTCGATTTAAGAATTGCAATCATTCGGTGTGCA
TGATGTGTGTGCATAAGCATTCGATTTATAAGGGATATTGTCCAATGGAA
AACCATCCAATGAACCATTCGCTATATTTACATCATCGCAATTATATTGA
CATTCAAGACTACTGGATAAAAAATTTCGGAAAAACCCAGAAATTTTTGC
ATTGGAATTTCTCTCAATTTATTCGAATTTTCCGGAGATCTATTTCAAAT
CATATTTTGGTTTTGGATGATTTTATGGAGAAATTTATTGTATTCATGTC
TAACTTAAATGAAACTTGCGCATTTCACAACCTAGAACAGGCCTTTGAAA
GACTAATTTTACATTTCGGATTGAATTTGTTCAATGATTCGACAGAAAAT
GACATTTATGATGCTCTTCAACTCAGAAAGTCGCAATTTTTAGATTTAGA
AAATGAAATTTATGATGTTCCTCAAAGCGATAAAATTTTTGTAAACCATA
AGGAAAATTATTTGAGTTGCAGCGGGATGAAAGATGTGCTCGTTGAAGCG
CAATATTCAGCGATAAAGTATATGAATGAAAGGGTTTTCCATAACCCCAC
CATCAACGATCACTTGAAAAATACATTTGCAGATTATATAGCAGTCAAAA
TGTTACATGGAATTAAATAAAAAA
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protein sequence of SMED30029670-orf-1

>SMED30029670-orf-1 ID=SMED30029670-orf-1|Name=SMED30029670-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=514bp
MDNETTCLICMEEIDEKNLADVIPCNHEFCVSCIKECIYLSECCPLYRCS
VDSILVSNTNRVKVNITVEQIIQEMIVQYIHENKKRFKSFINKLCPAMTN
WFQMKKEFEKIIDQDNISLIQNQLNQNQIQNRFQLLNQAFIKFDYKYFQS
IISEFKSLNTTHHGIIGKLLKYKILNLNLNHLSSGNEKNFAYIVSNLLEK
LVDQIKSMSLVFEQTKISFDLKFSKSTELDLFENDIFDDMYPVWTNIIVI
ETLFWTSIKTCIITDVELINPMAAVFQEIDFSKCIICNSQTRFDAHCRFK
NCNHSVCMMCVHKHSIYKGYCPMENHPMNHSLYLHHRNYIDIQDYWIKNF
GKTQKFLHWNFSQFIRIFRRSISNHILVLDDFMEKFIVFMSNLNETCAFH
NLEQAFERLILHFGLNLFNDSTENDIYDALQLRKSQFLDLENEIYDVPQS
DKIFVNHKENYLSCSGMKDVLVEAQYSAIKYMNERVFHNPTINDHLKNTF
ADYIAVKMLHGIK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR001841Znf_RING
IPR013083Znf_RING/FYVE/PHD
IPR018957Znf_C3HC4_RING-type
IPR017907Znf_RING_CS
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0008270zinc ion binding
GO:0046872metal ion binding
GO:0004842ubiquitin-protein transferase activity
GO:0016740transferase activity
GO:0061630ubiquitin protein ligase activity
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0005654nucleoplasm
GO:0036126sperm flagellum
Vocabulary: biological process
TermDefinition
GO:0008584male gonad development
GO:0016567protein ubiquitination
GO:0043161proteasome-mediated ubiquitin-dependent protein catabolic process