SMED30021579
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., 2020SMED30021579 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30021579 aligns in the following genomic locations:
Homology
BLAST of SMED30021579 vs. Planmine SMEST
Match: SMESG000072336.1 (SMESG000072336.1) HSP 1 Score: 541.191 bits (1393), Expect = 5.781e-176 Identity = 292/299 (97.66%), Postives = 294/299 (98.33%), Query Frame = 1 Query: 22 MTDIEKYNFFDVISILTGRPKLVQCLKLCKFRSILDFINFNDKSIDNVQEYVRIICSIMSVEERKMYLDEDDILNPQDYFITPGIRNRLLKAVTVILASIGINKVKSNDLFNHKTPPKRFELETNDFPNSNALEFXXXXXXXXXXQVKYRKRLISKSIESKEIGYEHRLSKASSNCVESTTEDPIDEFRGFFKHVRNNLLGFYNEHKMESKHKPKIHFDLEFHIENDTKKSFGYFIXXXXXXXXXXXXXXXXMVISFGSIKSHLKTHHDYVA--NNIPQKRKNAINGEQTKSKRNKFSK 912 MTDIEKYNFFDVISILTGRPKLVQCLKLCKFRSILDFINFNDKSIDNVQEYVRIICSIMSVEERKMYLDEDDI NPQDYFITPGIRNRLLKAVTVILASIGINKVKSNDLFNHKTPPKRFELE NDFPNSNALEFSPSKKPS SPQVKYRKRLISKSIESKEIGYEHRLSKASSNCVESTTEDPIDEFRGFFKHVRNNLLGFYNEHKMESKHKPKIHFDLEFHIENDTKKSFGYFICFNCNKKKLKFSFSSKMVISFGSIKSHLKTHHDYVA NNIPQKRKNAINGEQTKSKRNKF++ Sbjct: 1 MTDIEKYNFFDVISILTGRPKLVQCLKLCKFRSILDFINFNDKSIDNVQEYVRIICSIMSVEERKMYLDEDDIPNPQDYFITPGIRNRLLKAVTVILASIGINKVKSNDLFNHKTPPKRFELENNDFPNSNALEFSPSKKPSSSPQVKYRKRLISKSIESKEIGYEHRLSKASSNCVESTTEDPIDEFRGFFKHVRNNLLGFYNEHKMESKHKPKIHFDLEFHIENDTKKSFGYFICFNCNKKKLKFSFSSKMVISFGSIKSHLKTHHDYVANNNNIPQKRKNAINGEQTKSKRNKFNR 299
BLAST of SMED30021579 vs. Planmine SMEST
Match: SMESG000072330.1 (SMESG000072330.1) HSP 1 Score: 113.62 bits (283), Expect = 3.306e-29 Identity = 87/270 (32.22%), Postives = 156/270 (57.78%), Query Frame = 1 Query: 52 DVISILTGRPKLVQCLKLCKFRSILDFINFNDKSIDNVQEYVRIICSIMSVEERKMYLDEDDILNPQDYFITPGIRNRLLKAVTVILASIGINKVKSNDLFNHKT-------PPKRFELETNDFPNSNALEFXXXXXXXXXXQVKYRKRLISKSIESKEIGYEHRLSKASSN----CVESTTED-PIDEFRGFFKHVRNNLLGFYNEHKMESKHKPKIHFDLEFHIENDT-KKSFGYFIXXXXXXXXXXXXXXXXMVISFGSIKSHLKTH 822 + I+ L PK+ L+LCKF + DF+NFN+ ++D +++Y++I CS+M + R++YL+E D+L+P + I+PG+RNRLLKAV ++++ IN + ++ HK+ K E ++ + N+N + + S + + + S+ +GYE L ++N C+ + ++D + EF+ + + + +++ PK +FDLEFH +D+ S+G +IC+ CNKKKLKF F++ + + +G+IKSHLK H Sbjct: 7 NAIAYLCEFPKVANWLELCKFELMDDFLNFNNNTVDKIEKYIQIQCSLMPINVRQLYLNESDLLSPTKFLISPGLRNRLLKAVDILVSYFEINSLNNSI---HKSFCMENMLYQKLSETDSGNNTNNNLMFSANILDISENDSRISAPKHYESTNSSQTLGYESTLEVINNNDSEICLANQSKDLQVGEFKINIDQYFEDFVEVL-KRELDFNLVPKENFDLEFHFNSDSISNSYGNYICYYCNKKKLKFKFTAMLKVVYGNIKSHLKKH 272
BLAST of SMED30021579 vs. Planmine SMEST
Match: SMESG000072339.1 (SMESG000072339.1) HSP 1 Score: 104.76 bits (260), Expect = 9.441e-26 Identity = 50/107 (46.73%), Postives = 72/107 (67.29%), Query Frame = 1 Query: 43 NFFDVISILTGRPKLVQCLKLCKFRSILDFINFNDKSIDNVQEYVRIICSIMSVEERKMYLDEDDILNPQDYFITPGIRNRLLKAVTVILASI-GINKVKSNDLFNH 360 N FD ++ LTG K KLC F +I D ++FND SID ++EY+++ CS+M + ER +YLD DDI NP+ + I+PG+RNR+ KAV+ I+ S+ G + S L NH Sbjct: 4 NIFDALNYLTGSSKTSARFKLCDFNTITDLLSFNDTSIDKMEEYIQLQCSLMDLAERSIYLDGDDIQNPKCFMISPGLRNRICKAVSTIVNSMNGASLSLSQKLLNH 110
BLAST of SMED30021579 vs. Planmine SMEST
Match: SMESG000036851.1 (SMESG000036851.1) HSP 1 Score: 68.9366 bits (167), Expect = 2.263e-13 Identity = 31/85 (36.47%), Postives = 54/85 (63.53%), Query Frame = 1 Query: 55 VISILTGRPKLVQCLKLCKFRSILDFINFNDKSIDNVQEYVRIICSIMSVEERKMYLDEDDILNPQDYFITPGIRNRLLKAVTVI 309 +I +TG K++ CL+LC + +D IN +DK ID ++ + + C +M ++ + Y+DE NP + I+PGIR +LL++V +I Sbjct: 8 IILEVTGSEKIIACLELCDIKEDVDVINIDDKVIDRIENFTKECCLLMLPDQMQFYIDERFYNNPSRFLISPGIRIKLLRSVKII 92
BLAST of SMED30021579 vs. Planmine SMEST
Match: SMESG000047524.1 (SMESG000047524.1) HSP 1 Score: 68.9366 bits (167), Expect = 4.394e-13 Identity = 67/283 (23.67%), Postives = 122/283 (43.11%), Query Frame = 1 Query: 52 DVISILTGRPKLVQCLKLCKFRSILDFINFNDKSIDNVQEYVRIICSIMSVEERKMYLDEDDILNPQDYFITPGIRNRLLKAVTVI--------LASIGINKVKSNDLF-----NHKTPPKRFELETNDFPNSNALEFXXXXXXXXXXQVKYRKRL-ISKSIESKEIGYEHRLSKASSNCVESTTEDPIDEFRGFFKHVRNNLLGFYNEHKMESKHKPKIHFDLEFHIENDTKKSFGYFIXXXXXXXXXXXXXXXXMVISFGSIKSHLKTHHDYVANNIPQKR 858 + I+ + P ++ CL++ + DFINF+ ++D ++ Y+R S+M + +R YL + I P+ + TPG+RNRLLKA +I S + +SN++ N TP + + + N ++ +E P S +K + S+ +++ E Y + A+ N +E + +D ++ +L+G+Y+ H + K F N + + +I SHLKTH+ YV N +KR Sbjct: 7 ETIANVVESPLVLSCLEIAELLEPDDFINFSHTNVDILENYIRCRTSVMEINDRIPYLSGEFIHFPEKFMFTPGMRNRLLKAAKLISKDVYAAVFESNQTSDCESNEMSCDSNNNSTTPMNKLQPQNNISIENSLIENQFLLSPLNSSIIKQELDMNRSRHLQNMEKYYNDIVKNAAKNFIECSLIPDVDFHLSIPENDSTDLIGYYHCHLCTDRKKAMTKIKFRFSKYNS---------------------------VIYTNINSHLKTHYQYVLENNDRKR 262 The following BLAST results are available for this feature:
BLAST of SMED30021579 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30021579 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30021579 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30021579 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30021579 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30021579 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30021579 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30021579 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30021579 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30021579 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30021579 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30021579 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30021579 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30021579 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 >SMED30021579 ID=SMED30021579|Name=SMED30021579|organism=Schmidtea mediterranea sexual|type=transcript|length=980bpback to top protein sequence of SMED30021579-orf-1 >SMED30021579-orf-1 ID=SMED30021579-orf-1|Name=SMED30021579-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=305bp VLLIICNMTDIEKYNFFDVISILTGRPKLVQCLKLCKFRSILDFINFNDKback 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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