SMED30026856
Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ 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 AppSub-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., 2020SMED30026856 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Homology
BLAST of SMED30026856 vs. Planmine SMEST
Match: SMESG000034975.1 (SMESG000034975.1) HSP 1 Score: 293.893 bits (751), Expect = 5.222e-108 Identity = 142/142 (100.00%), Postives = 142/142 (100.00%), Query Frame = -1 Query: 873 MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT 1298 MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT Sbjct: 1 MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT 142 HSP 2 Score: 117.472 bits (293), Expect = 5.222e-108 Identity = 56/56 (100.00%), Postives = 56/56 (100.00%), Query Frame = -3 Query: 685 KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR 852 KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR Sbjct: 168 KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR 223
BLAST of SMED30026856 vs. Planmine SMEST
Match: SMESG000034973.1 (SMESG000034973.1) HSP 1 Score: 293.893 bits (751), Expect = 5.222e-108 Identity = 142/142 (100.00%), Postives = 142/142 (100.00%), Query Frame = -1 Query: 873 MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT 1298 MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT Sbjct: 1 MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT 142 HSP 2 Score: 117.472 bits (293), Expect = 5.222e-108 Identity = 56/56 (100.00%), Postives = 56/56 (100.00%), Query Frame = -3 Query: 685 KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR 852 KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR Sbjct: 168 KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR 223
BLAST of SMED30026856 vs. Planmine SMEST
Match: SMESG000034972.1 (SMESG000034972.1) HSP 1 Score: 317.005 bits (811), Expect = 8.255e-108 Identity = 170/170 (100.00%), Postives = 170/170 (100.00%), Query Frame = 2 Query: 176 MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWXXXXXXXXXXXXXXDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQKKVHSNGEPTNKGLWHSYAENSTVIDSNSLSVANCQNVTNLC 685 MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWLAVILLILILWTIIDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQKKVHSNGEPTNKGLWHSYAENSTVIDSNSLSVANCQNVTNLC Sbjct: 1 MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWLAVILLILILWTIIDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQKKVHSNGEPTNKGLWHSYAENSTVIDSNSLSVANCQNVTNLC 170
BLAST of SMED30026856 vs. Planmine SMEST
Match: SMESG000034972.1 (SMESG000034972.1) HSP 1 Score: 232.646 bits (592), Expect = 3.217e-75 Identity = 129/129 (100.00%), Postives = 129/129 (100.00%), Query Frame = 2 Query: 176 MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWXXXXXXXXXXXXXXDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQK 562 MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWLAVILLILILWTIIDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQK Sbjct: 1 MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWLAVILLILILWTIIDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQK 129
BLAST of SMED30026856 vs. Planmine SMEST
Match: SMESG000006125.1 (SMESG000006125.1) HSP 1 Score: 74.7146 bits (182), Expect = 6.239e-15 Identity = 37/123 (30.08%), Postives = 66/123 (53.66%), Query Frame = -1 Query: 918 ELTKVFTFDPI--CELCRQRLT-TELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHS 1277 +L + ++ PI C +C++ + E + C H YH+ CL HN + + C C + Y+K + + I +RVV+K+ Y +G + Y + KGY F++G+Y +P + + +N T HS Sbjct: 7 KLPEEYSHVPITTCHVCQKNINPNERLRLPNCNHEYHFSCLFIHNFDKKSTCPICHKPYDKAEFILNEKIHSRVVVKNYIYDYRIGLTHYVNDERKGYSFMIGLYRPVYPFVFTISVNSTKHS 129 The following BLAST results are available for this feature:
BLAST of SMED30026856 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30026856 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30026856 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30026856 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30026856 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30026856 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30026856 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30026856 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30026856 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30026856 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30026856 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30026856 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30026856 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30026856 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 >SMED30026856 ID=SMED30026856|Name=SMED30026856|organism=Schmidtea mediterranea sexual|type=transcript|length=1385bpback to top protein sequence of SMED30026856-orf-1 >SMED30026856-orf-1 ID=SMED30026856-orf-1|Name=SMED30026856-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=153bp MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLback to top protein sequence of SMED30026856-orf-2 >SMED30026856-orf-2 ID=SMED30026856-orf-2|Name=SMED30026856-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=201bp MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNback 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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