SMED30015125
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., 2020SMED30015125 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 15
Alignments
SMED30015125 aligns in the following genomic locations:
Homology
BLAST of SMED30015125 vs. TrEMBL
Match: A0A0R3XAL7 (Uncharacterized protein OS=Hydatigena taeniaeformis OX=6205 GN=TTAC_LOCUS10577 PE=4 SV=1) HSP 1 Score: 55.8398 bits (133), Expect = 9.033e-7 Identity = 36/98 (36.73%), Postives = 57/98 (58.16%), Query Frame = 2 Query: 62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISG---CVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNE 346 ML G+P+LF LFA ++ LIGG ++GSG + N K ++G+I+ G CVLF I F++ I++R+ K+ ++ Q F N+ Q D+E Sbjct: 1 MLLFEGEPILFILFALFILSFLIGGCMWGSGEEANDRTKHIVGIIIFFFGVTCCVLFFILFIYKKIRQRRREKKDFEELMRMQNEFAANEGFQ--DDE 96
BLAST of SMED30015125 vs. TrEMBL
Match: A0A0R3SPF6 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS6841 PE=4 SV=1) HSP 1 Score: 55.8398 bits (133), Expect = 1.001e-6 Identity = 35/102 (34.31%), Postives = 59/102 (57.84%), Query Frame = 2 Query: 62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISG---CVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNEALNV 358 ML G+P+LF LFA ++ LIGG ++GSG + K ++G+I+ G CVLF + F + I++++ +E K E Q M N+ T Q++ ++ +V Sbjct: 1 MLLFEGEPVLFILFALFILSFLIGGCMWGSGEEAQDEPKYIVGIIIFFFGVTCCVLFFVLFTYKKIRQKR--REEKEFE-QLMRMQNEFATNQAFHDDEYSV 99
BLAST of SMED30015125 vs. TrEMBL
Match: A0A0R3UN72 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS9232 PE=4 SV=1) HSP 1 Score: 54.6842 bits (130), Expect = 3.276e-6 Identity = 33/99 (33.33%), Postives = 55/99 (55.56%), Query Frame = 2 Query: 62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISG---CVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQS--YDN 343 ML G+P LF LF+++++ LIGG L+GSG D K +G+++ G CV F + F + IK+++ K+ ++ Q F N+ Q+ YD+ Sbjct: 1 MLLFEGEPALFLLFSASILSFLIGGCLWGSGEDAGNQAKRTVGIVIFFCGVTCCVAFFMLFTYKTIKRKRREKQDFEELMRMQNEFAANEGFQNDEYDD 99
BLAST of SMED30015125 vs. TrEMBL
Match: A0A3P6PVJ9 (Uncharacterized protein OS=Dibothriocephalus latus OX=60516 GN=DILT_LOCUS1233 PE=4 SV=1) HSP 1 Score: 53.5286 bits (127), Expect = 5.611e-6 Identity = 34/90 (37.78%), Postives = 49/90 (54.44%), Query Frame = 2 Query: 62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISG---CVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNK 322 ML G+PLLF LF +++ LIGG ++G G D N + V G+ + G CV F I FV+ IKK + K A ++ Q F +N+ Sbjct: 1 MLLFEGEPLLFTLFGLSVLSLLIGGCMWGVGTDTNDHPRYVAGISVFFFGTGCCVCFIIVFVYKHIKKMRIRKRDLAEVVRLQNEFAENE 90
BLAST of SMED30015125 vs. Planmine SMEST
Match: SMESG000061766.1 (SMESG000061766.1) HSP 1 Score: 201.06 bits (510), Expect = 7.249e-67 Identity = 101/103 (98.06%), Postives = 101/103 (98.06%), Query Frame = 2 Query: 62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISGCVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNEALNVTVPL 370 MLFCNGDPLLFG FASAMI TLIGGMLYGSGVDNNILEKTVIGLILLISGCVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNEALNVTVPL Sbjct: 1 MLFCNGDPLLFGFFASAMISTLIGGMLYGSGVDNNILEKTVIGLILLISGCVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNEALNVTVPL 103
BLAST of SMED30015125 vs. Planmine SMEST
Match: SMESG000061777.1 (SMESG000061777.1) HSP 1 Score: 80.8777 bits (198), Expect = 8.229e-20 Identity = 48/98 (48.98%), Postives = 68/98 (69.39%), Query Frame = 2 Query: 62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISGCVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNEALN 355 ML CNGDP+LFGLFA ++ TLIGGML+G G I K + GL+LL SGC L IG ++IKK++ +K+ K +E+++Q MF K +T + N+AL+ Sbjct: 1 MLLCNGDPVLFGLFAFGILSTLIGGMLFGQGEYYLIKVKRIAGLVLLCSGCALLIIGIFVIVIKKQQKIKQVKNLEIERQNMFRKKETGTGFTNDALD 98
BLAST of SMED30015125 vs. Planmine SMEST
Match: SMESG000008768.1 (SMESG000008768.1) HSP 1 Score: 49.6766 bits (117), Expect = 3.162e-7 Identity = 38/103 (36.89%), Postives = 53/103 (51.46%), Query Frame = 2 Query: 62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISGCVLFAIGFVFLIIKKRKTLKESKAIELQKQE---MFN----KNKTTQSYDNEA 349 ML C GD LLFGL++ A+I LIGG L+G G D N K G+++ I G + I + I K K + + + I +E +FN KN Q+ N A Sbjct: 1 MLLCGGDQLLFGLYSVAIICLLIGGCLWGQGQDKNDSAKLTAGIVVFIIGGSIAIIAVIVNIFKSLKKMNKRRKIARMSKEKPLVFNKEQLKNPNIQNIQNHA 103 The following BLAST results are available for this feature:
BLAST of SMED30015125 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30015125 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30015125 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30015125 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30015125 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30015125 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30015125 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30015125 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 4
BLAST of SMED30015125 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30015125 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30015125 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30015125 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30015125 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30015125 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 3
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30015125 ID=SMED30015125|Name=SMED30015125|organism=Schmidtea mediterranea sexual|type=transcript|length=635bpback to top protein sequence of SMED30015125-orf-1 >SMED30015125-orf-1 ID=SMED30015125-orf-1|Name=SMED30015125-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISGback 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
|