SMED30034619
Overview
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 progeniesWe 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
Sub-lethal Irradiated Surviving X1 and X2 Cell Population
Embryonic Expression
Davies et. al., 2017
Hover the mouse over a column in the graph to view average RPKM values per sample. Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult. back to top Anatomical Expression
PAGE et. al., 2020SMED30034619 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 7Note: Hover over icons to view figure legend
Alignments
SMED30034619 aligns in the following genomic locations:
Homology
BLAST of SMED30034619 vs. Planmine SMEST
Match: SMESG000029095.1 (SMESG000029095.1) HSP 1 Score: 230.72 bits (587), Expect = 4.749e-79 Identity = 112/113 (99.12%), Postives = 112/113 (99.12%), Query Frame = 1 Query: 127 MSRISLFAIVYLVAYCHCSEQCDRELVPAAKDCDRKYAEIDNFCNGGYAKINKVCKGVDTIECALKYKKFGEACRERQDYFWKNCGPVYKIYQTLCSGVKERAAENKEIAEGN 465 MSRISLFAIVYLVAYCHCSEQCDRELVPAAKDCDRKYAE DNFCNGGYAKINKVCKGVDTIECALKYKKFGEACRERQDYFWKNCGPVYKIYQTLCSGVKERAAENKEIAEGN Sbjct: 1 MSRISLFAIVYLVAYCHCSEQCDRELVPAAKDCDRKYAETDNFCNGGYAKINKVCKGVDTIECALKYKKFGEACRERQDYFWKNCGPVYKIYQTLCSGVKERAAENKEIAEGN 113
BLAST of SMED30034619 vs. Planmine SMEST
Match: SMESG000020501.1 (SMESG000020501.1) HSP 1 Score: 161.384 bits (407), Expect = 1.205e-51 Identity = 72/113 (63.72%), Postives = 92/113 (81.42%), Query Frame = 1 Query: 127 MSRISLFAIVYLVAYCHCSEQCDRELVPAAKDCDRKYAEIDNFCNGGYAKINKVCKGVDTIECALKYKKFGEACRERQDYFWKNCGPVYKIYQTLCSGVKERAAENKEIAEGN 465 MS++S+FA+++++AYCHCS +CD EL PAAK CD+KYAE D FCNGGYA INKVCKGVDTIEC L+YK+F C+ERQ+ FW +C VYK YQT+C+ KER E+KEI +G+ Sbjct: 1 MSKLSIFALLFVIAYCHCSPRCDLELAPAAKRCDKKYAETDAFCNGGYAAINKVCKGVDTIECGLEYKRFAVKCKERQNNFWNDCDQVYKTYQTVCASGKERVEEHKEIVQGD 113
BLAST of SMED30034619 vs. Planmine SMEST
Match: SMESG000028420.1 (SMESG000028420.1) HSP 1 Score: 115.546 bits (288), Expect = 1.521e-33 Identity = 57/117 (48.72%), Postives = 76/117 (64.96%), Query Frame = 1 Query: 124 KMSRISLFAIVYLV---AYCHCSEQCDRELVPAAKDCDRKYAEIDNFCNGGYAKINKVCKGVDTIECALKYKKFGEACRERQDYFWKNCGPVYKIYQTLCSGVKERAAENKEIAEGN 465 K+S +LFA+V +V + E+C + L PAAK CD +Y E D FC+ GY I+K CKG D++EC ++Y K + C E+QDYFWK CGPVYK Y C+ +ER E+ EI EGN Sbjct: 3 KISVYALFAVVVIVNSTKWVPSPEKCLKILTPAAKGCDSRYTETDLFCSVGYKHIDKSCKGHDSVECGVQYAKHKDDCTEKQDYFWKVCGPVYKTYSDECASNEERKEESAEIKEGN 119
BLAST of SMED30034619 vs. Planmine SMEST
Match: SMESG000022139.1 (SMESG000022139.1) HSP 1 Score: 107.457 bits (267), Expect = 2.368e-30 Identity = 54/117 (46.15%), Postives = 69/117 (58.97%), Query Frame = 1 Query: 127 MSRISLFAIVYLVA------YCHCSEQCDRELVPAAKDCDRKYAEIDNFCNGGYAKINKVCKGVDTIECALKYKKFGEACRERQDYFWKNCGPVYKIYQTLCSGVKERAAENKEIAE 459 M + S+ A V + S +C LVPA+K CD+ Y E D FCNGG+AK+NKVC G DT+EC YK F C+E+QD FW C PVY Y+ C+ +E EN+EIAE Sbjct: 1 MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTTLCKEKQDNFWDECDPVYTAYRKECATPEEIKEENQEIAE 117
BLAST of SMED30034619 vs. Planmine SMEST
Match: SMESG000061767.1 (SMESG000061767.1) HSP 1 Score: 98.9821 bits (245), Expect = 8.365e-27 Identity = 49/119 (41.18%), Postives = 70/119 (58.82%), Query Frame = 1 Query: 127 MSRISLF------AIVYLVAYCHCSEQCDRELVPAAKDCDRKYAEIDNFCNGGYAKINKVCKGVDTIECALKYKKFGEACRERQDYFWKNCGPVYKIYQTLCSGVKERAAENKEIAEGN 465 M +S+F A+V+ + S +C + L PAA+ CDRKY E DNFC+ GY INK CKG +TI+C ++ + C+E+QD FW C VY Y+ C+ KE E +EIA+ + Sbjct: 1 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASPKEIKEELQEIADDS 119 The following BLAST results are available for this feature:
BLAST of SMED30034619 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30034619 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30034619 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30034619 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30034619 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30034619 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30034619 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30034619 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30034619 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30034619 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30034619 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30034619 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30034619 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30034619 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 5
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30034619 ID=SMED30034619|Name=SMED30034619|organism=Schmidtea mediterranea sexual|type=transcript|length=530bpback to top protein sequence of SMED30034619-orf-1 >SMED30034619-orf-1 ID=SMED30034619-orf-1|Name=SMED30034619-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp MSRISLFAIVYLVAYCHCSEQCDRELVPAAKDCDRKYAEIDNFCNGGYAKback to top Annotated Terms
The following terms have been associated with this transcript:
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
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