SMED30028226
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., 2020SMED30028226 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 15Note: Hover over icons to view figure legend
Alignments
SMED30028226 aligns in the following genomic locations:
Homology
BLAST of SMED30028226 vs. Planmine SMEST
Match: SMESG000030745.1 (SMESG000030745.1) HSP 1 Score: 173.711 bits (439), Expect = 1.399e-56 Identity = 100/103 (97.09%), Postives = 100/103 (97.09%), Query Frame = 1 Query: 229 MNLIIVFGVLIVSCQCWAAQIEGLXXXXXXXXXXXXXKDIGKLDDENEISEN--EPSMKNGCNYIIKKCPKRMRSECKTCIFNRDKRMGYCRETGKVKCFHKH 531 MNLIIVFGV IVSCQCWAAQIEGLAEEVEGAEDMVEEKDIGKLDDENEISEN EPSMKNGCNYIIKKCPKRMRSECKTCIFNRDKRMGYCRETGKVKCFHKH Sbjct: 1 MNLIIVFGVFIVSCQCWAAQIEGLAEEVEGAEDMVEEKDIGKLDDENEISENVLEPSMKNGCNYIIKKCPKRMRSECKTCIFNRDKRMGYCRETGKVKCFHKH 103
BLAST of SMED30028226 vs. Planmine SMEST
Match: SMESG000030634.1 (SMESG000030634.1) HSP 1 Score: 158.303 bits (399), Expect = 2.054e-50 Identity = 93/108 (86.11%), Postives = 99/108 (91.67%), Query Frame = 1 Query: 214 MKIEKMNLIIVFGVLIVSCQCWAAQIEGLXXXXXXXXXXXXXKDIGKLDDENEISEN--EPSMKNGCNYIIKKCPKRMRSECKTCIFNRDKRMGYCRETGKVKCFHKH 531 MKIEKMNLIIVFGVLIVSCQCWAAQIEGLAEEVEGAED+VEEKDI KLD+ENEISEN E SMK+ CNY+IKKCPK MRSECKTCIF R K+M +CRETGKVKCFHKH Sbjct: 1 MKIEKMNLIIVFGVLIVSCQCWAAQIEGLAEEVEGAEDIVEEKDIRKLDEENEISENVLEDSMKDSCNYLIKKCPKSMRSECKTCIFYRKKKMFFCRETGKVKCFHKH 108
BLAST of SMED30028226 vs. Planmine SMEST
Match: SMESG000030634.1 (SMESG000030634.1) HSP 1 Score: 149.828 bits (377), Expect = 3.578e-47 Identity = 88/103 (85.44%), Postives = 94/103 (91.26%), Query Frame = 1 Query: 229 MNLIIVFGVLIVSCQCWAAQIEGLXXXXXXXXXXXXXKDIGKLDDENEISEN--EPSMKNGCNYIIKKCPKRMRSECKTCIFNRDKRMGYCRETGKVKCFHKH 531 MNLIIVFGVLIVSCQCWAAQIEGLAEEVEGAED+VEEKDI KLD+ENEISEN E SMK+ CNY+IKKCPK MRSECKTCIF R K+M +CRETGKVKCFHKH Sbjct: 1 MNLIIVFGVLIVSCQCWAAQIEGLAEEVEGAEDIVEEKDIRKLDEENEISENVLEDSMKDSCNYLIKKCPKSMRSECKTCIFYRKKKMFFCRETGKVKCFHKH 103
BLAST of SMED30028226 vs. Planmine SMEST
Match: SMESG000030767.1 (SMESG000030767.1) HSP 1 Score: 88.5817 bits (218), Expect = 4.714e-23 Identity = 58/60 (96.67%), Postives = 59/60 (98.33%), Query Frame = 1 Query: 214 MKIEKMNLIIVFGVLIVSCQCWAAQIEGLXXXXXXXXXXXXXKDIGKLDDENEISENEPS 393 MKIEKMNLIIVFGVLIVSCQCWAAQIEGLAEEVEGAEDMVEEKDIGKLDDENEISEN P+ Sbjct: 1 MKIEKMNLIIVFGVLIVSCQCWAAQIEGLAEEVEGAEDMVEEKDIGKLDDENEISENGPT 60
BLAST of SMED30028226 vs. Planmine SMEST
Match: SMESG000030767.1 (SMESG000030767.1) HSP 1 Score: 79.7221 bits (195), Expect = 1.158e-19 Identity = 53/55 (96.36%), Postives = 54/55 (98.18%), Query Frame = 1 Query: 229 MNLIIVFGVLIVSCQCWAAQIEGLXXXXXXXXXXXXXKDIGKLDDENEISENEPS 393 MNLIIVFGVLIVSCQCWAAQIEGLAEEVEGAEDMVEEKDIGKLDDENEISEN P+ Sbjct: 1 MNLIIVFGVLIVSCQCWAAQIEGLAEEVEGAEDMVEEKDIGKLDDENEISENGPT 55 The following BLAST results are available for this feature:
BLAST of SMED30028226 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30028226 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30028226 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30028226 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30028226 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30028226 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30028226 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30028226 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30028226 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30028226 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30028226 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30028226 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30028226 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30028226 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 >SMED30028226 ID=SMED30028226|Name=SMED30028226|organism=Schmidtea mediterranea sexual|type=transcript|length=534bpback to top protein sequence of SMED30028226-orf-1 >SMED30028226-orf-1 ID=SMED30028226-orf-1|Name=SMED30028226-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp MKIEKMNLIIVFGVLIVSCQCWAAQIEGLAEEVEGAEDMVEEKDIGKLDDback 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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