SMED30020900
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., 2020SMED30020900 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 9
Alignments
SMED30020900 aligns in the following genomic locations:
Homology
BLAST of SMED30020900 vs. Planmine SMEST
Match: SMESG000022353.1 (SMESG000022353.1) HSP 1 Score: 248.44 bits (633), Expect = 1.535e-76 Identity = 167/228 (73.25%), Postives = 179/228 (78.51%), Query Frame = 1 Query: 1342 CLTLFN*LS*EIRIGGL*DINMDFQICFLLNLRSR----LKFQNNFRTFCKTVLEFFENNYGKIFEIRESLPKSKTSWLSVENSLPTVINSLSALYKERVEMKNFQSIPITTESDIVIVKLGFT*MVSSSIINIL*VNKESQWKPIQTIESTNFAEPSSRKRKRKFKVLAATENVSTLVDNVPDFDVGVXXXXXXXXXXXXXXXXXXEEKQFLKNNKKRKIGESALNF 2013 C++LF L+ ++ G ++R+R + F + TFCKTVLEFFENNYGKI+EIRESLPKSKTSWLSVENSLPTVINSLSALYKERVEMKNFQSIPITTESDIVI VNKESQWKPIQTIESTN AEPSS+KRKRK KVLAATENVSTLVDNVPDFDVGVSKKQKKKMKQEMNSKIKKEEKQFLKNNKKRKIGESALNF Sbjct: 134 CISLFELLTATMKTG---------------HIRARCALGITFTSIIGTFCKTVLEFFENNYGKIYEIRESLPKSKTSWLSVENSLPTVINSLSALYKERVEMKNFQSIPITTESDIVI------------------VNKESQWKPIQTIESTNVAEPSSKKRKRKSKVLAATENVSTLVDNVPDFDVGVSKKQKKKMKQEMNSKIKKEEKQFLKNNKKRKIGESALNF 328
BLAST of SMED30020900 vs. Planmine SMEST
Match: SMESG000022827.1 (SMESG000022827.1) HSP 1 Score: 152.91 bits (385), Expect = 1.962e-42 Identity = 80/86 (93.02%), Postives = 84/86 (97.67%), Query Frame = 2 Query: 56 MLGRSXXXXXYVCDNNTRDKIKLRLLDIQGVLDLNNIDCQFPDKNIEIASISLKEAQFRLDIYANISKLSIYLMNDYEFFTAASLQ 313 MLGRSDDDDDYVCDNNTRDKIKLRLLDIQGVLDLNNIDCQFP+KNIEIASISLKEAQ+RLDIYANISKLSIYLMNDY+FF+ SLQ Sbjct: 1 MLGRSDDDDDYVCDNNTRDKIKLRLLDIQGVLDLNNIDCQFPEKNIEIASISLKEAQYRLDIYANISKLSIYLMNDYDFFSKISLQ 86
BLAST of SMED30020900 vs. Planmine SMEST
Match: SMESG000022827.1 (SMESG000022827.1) HSP 1 Score: 152.91 bits (385), Expect = 4.435e-41 Identity = 80/86 (93.02%), Postives = 84/86 (97.67%), Query Frame = 2 Query: 56 MLGRSXXXXXYVCDNNTRDKIKLRLLDIQGVLDLNNIDCQFPDKNIEIASISLKEAQFRLDIYANISKLSIYLMNDYEFFTAASLQ 313 MLGRSDDDDDYVCDNNTRDKIKLRLLDIQGVLDLNNIDCQFP+KNIEIASISLKEAQ+RLDIYANISKLSIYLMNDY+FF+ SLQ Sbjct: 1 MLGRSDDDDDYVCDNNTRDKIKLRLLDIQGVLDLNNIDCQFPEKNIEIASISLKEAQYRLDIYANISKLSIYLMNDYDFFSKISLQ 86
BLAST of SMED30020900 vs. Planmine SMEST
Match: SMESG000022832.1 (SMESG000022832.1) HSP 1 Score: 104.375 bits (259), Expect = 4.543e-23 Identity = 52/84 (61.90%), Postives = 67/84 (79.76%), Query Frame = 2 Query: 89 VCDNNTRDKIKLRLLDIQGVLDLNNIDCQFPDKNIEIASISLKEAQFRLDIYANISKLSIYLMNDYEFFTAASLQVFNLYILYK 340 VCD NTR IKL+LLD++ LD N+DC F ++N++I SI+L+EA+ RL IYANISKLSIYLMND+EFFTAASLQ + + Y+ Sbjct: 13 VCDYNTRISIKLKLLDLKNGLDFTNVDCGFTERNLDIDSITLEEAETRLKIYANISKLSIYLMNDFEFFTAASLQSAFICLTYE 96 The following BLAST results are available for this feature:
BLAST of SMED30020900 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30020900 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30020900 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30020900 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30020900 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30020900 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30020900 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30020900 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30020900 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30020900 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30020900 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30020900 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30020900 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30020900 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 4
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30020900 ID=SMED30020900|Name=SMED30020900|organism=Schmidtea mediterranea sexual|type=transcript|length=2013bpback to top protein sequence of SMED30020900-orf-1 >SMED30020900-orf-1 ID=SMED30020900-orf-1|Name=SMED30020900-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp MDFQICFLLNLRSRLKFQNNFRTFCKTVLEFFENNYGKIFEIRESLPKSKback to top protein sequence of SMED30020900-orf-2 >SMED30020900-orf-2 ID=SMED30020900-orf-2|Name=SMED30020900-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp MLGRSDDDDDYVCDNNTRDKIKLRLLDIQGVLDLNNIDCQFPDKNIEIASback to top Annotated Terms
The following terms have been associated with this transcript:
|