SMED30024850
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., 2020SMED30024850 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 9
Alignments
SMED30024850 aligns in the following genomic locations:
Homology
BLAST of SMED30024850 vs. Planmine SMEST
Match: SMESG000013745.1 (SMESG000013745.1) HSP 1 Score: 253.832 bits (647), Expect = 6.809e-88 Identity = 122/122 (100.00%), Postives = 122/122 (100.00%), Query Frame = 3 Query: 99 INCEYLVFTTWPKVMKNINEIVNTYDQRLSSPEFIPIVNCPQKIELATTISSECGETYYLEIDPHQNPPSIITVENCKCQPINNKIKFRKYNLFSKGHTKYLFVEDDLKDLVVNCKSNLYRT 464 INCEYLVFTTWPKVMKNINEIVNTYDQRLSSPEFIPIVNCPQKIELATTISSECGETYYLEIDPHQNPPSIITVENCKCQPINNKIKFRKYNLFSKGHTKYLFVEDDLKDLVVNCKSNLYRT Sbjct: 14 INCEYLVFTTWPKVMKNINEIVNTYDQRLSSPEFIPIVNCPQKIELATTISSECGETYYLEIDPHQNPPSIITVENCKCQPINNKIKFRKYNLFSKGHTKYLFVEDDLKDLVVNCKSNLYRT 135
BLAST of SMED30024850 vs. Planmine SMEST
Match: SMESG000081054.1 (SMESG000081054.1) HSP 1 Score: 71.2478 bits (173), Expect = 2.672e-16 Identity = 39/116 (33.62%), Postives = 62/116 (53.45%), Query Frame = 3 Query: 99 INCEYLVFTTWPKVMKNINEIVNTYDQRLSSPEFIPIVNCPQKIELATTISSECGETYYLEIDPHQNPPSIITVENCKCQPINNKIKFRKYNLFSKGHTKYLFVEDDLKDLVVNCK 446 I Y+ +WP++ + ++ + + +FI I N Q ++L TI ++C E+YYLEI+P+ PP I VENCKC I F+KY + +YL +E+ + V CK Sbjct: 7 IRDHYVQKRSWPEIFEFVDLQLKNHSAHPKLLDFISIKNFKQILKLQITIPTKCKESYYLEIEPYLEPPVKIFVENCKCTNIYKTETFKKYKIIKWPEDEYLLIEEFQEKYVSQCK 122
BLAST of SMED30024850 vs. Planmine SMEST
Match: SMESG000013744.1 (SMESG000013744.1) HSP 1 Score: 68.5514 bits (166), Expect = 5.459e-15 Identity = 32/108 (29.63%), Postives = 60/108 (55.56%), Query Frame = 3 Query: 126 TWPKVMKNINEIVNTYDQRLSSPEFIPIVNCPQKIELATTISSECGETYYLEIDPHQNPPSIITVENC-KCQPINNKIKFRKYNLFSKGHTKYLFVEDDLKDLVVNCK 446 +WP++++ I+ IV ++ + P I + N Q I+L+T++ ++C E Y++ I PH +PP++I +ENC C K F+ + + +YL V + +V C Sbjct: 32 SWPEIIEYIHSIVTDHNANIEIPANIQVTNVTQTIQLSTSLPTKCHEKYFIRISPHFDPPAVIYIENCFNCHQEIQKKVFKIFQIEKYASNQYLVVNEISDQFIVQCS 139
BLAST of SMED30024850 vs. Planmine SMEST
Match: SMESG000023071.1 (SMESG000023071.1) HSP 1 Score: 53.5286 bits (127), Expect = 2.487e-9 Identity = 35/101 (34.65%), Postives = 52/101 (51.49%), Query Frame = 3 Query: 102 NCEYLVFTTWPKVMKNINEIVNTYDQRLSSPEFIPIVNCPQKIELATTISSECGETYYLEIDPHQNPPSIITVENCK--CQPINNKIKFRKYN-LFSKGHT 395 N EYL W VM I++++ ++ + P++I + Q IEL + C YYL+I+P Q+PP+ I NCK C +N F+K LF K T Sbjct: 31 NREYLPPRLWSDVMSYIDDMLRSHPSQPIFPDYIRMFEKDQTIELIVKNPNICVGCYYLKINPLQDPPAYIIASNCKYECIEVNKVYGFKKLQILFGKLLT 131
BLAST of SMED30024850 vs. Planmine SMEST
Match: SMESG000023071.1 (SMESG000023071.1) HSP 1 Score: 53.5286 bits (127), Expect = 3.137e-9 Identity = 34/98 (34.69%), Postives = 51/98 (52.04%), Query Frame = 3 Query: 102 NCEYLVFTTWPKVMKNINEIVNTYDQRLSSPEFIPIVNCPQKIELATTISSECGETYYLEIDPHQNPPSIITVENCK--CQPINNKIKFRKYN-LFSK 386 N EYL W VM I++++ ++ + P++I + Q IEL + C YYL+I+P Q+PP+ I NCK C +N F+K LF K Sbjct: 38 NREYLPPRLWSDVMSYIDDMLRSHPSQPIFPDYIRMFEKDQTIELIVKNPNICVGCYYLKINPLQDPPAYIIASNCKYECIEVNKVYGFKKLQILFGK 135 The following BLAST results are available for this feature:
BLAST of SMED30024850 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30024850 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30024850 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30024850 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30024850 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30024850 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30024850 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30024850 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30024850 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30024850 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30024850 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30024850 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30024850 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30024850 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 >SMED30024850 ID=SMED30024850|Name=SMED30024850|organism=Schmidtea mediterranea sexual|type=transcript|length=528bpback to top protein sequence of SMED30024850-orf-1 >SMED30024850-orf-1 ID=SMED30024850-orf-1|Name=SMED30024850-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=137bp MMLVKIMILMMAAMINCEYLVFTTWPKVMKNINEIVNTYDQRLSSPEFIPback 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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