SMED30033765
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., 2020SMED30033765 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 6
Alignments
SMED30033765 aligns in the following genomic locations:
Homology
BLAST of SMED30033765 vs. Planmine SMEST
Match: SMESG000017154.1 (SMESG000017154.1) HSP 1 Score: 445.662 bits (1145), Expect = 4.890e-158 Identity = 236/238 (99.16%), Postives = 236/238 (99.16%), Query Frame = 2 Query: 134 MEVLVIFLLLLRNALGHSIISERTDIRCANGACYNVVYELYQDSSGYRMNVVTKSDCPPINCNNCVYKGDWTLIASSGAYYLTRNTFLCLADSFRNFTEIFPDPSSSNMVDIACNSYQCTRYHYIIKEPFLYTYNLGKCSDFSCEGCNMCNYWQLNKTQSYTFLQRQTSSCQALTRIRMEDFFPPSGTPQVYQQHDFISSEILYKSSWNTPRXXXXXXXXXXXXXXXXXXXTFWCRNL 847 MEVLVIFLLLLRNALGHSIISERTDIRCANGACYNVVYELYQDSSGYRMNVVTKSDCPPINCNNCVYKGDWTLIASSGAYYLTRNTFLCLADSFRNFTEIFPDPSSSNMVDIACNSYQCT YHYIIKEPFLYTYNLGKCSDFSCEGCNMCNYWQLNKTQSYTFLQRQTSSCQALTRIRMEDFFPPSG PQVYQQHDFISSEILYKSSWNTPRILALIISSIMIIILFIILITFWCRNL Sbjct: 1 MEVLVIFLLLLRNALGHSIISERTDIRCANGACYNVVYELYQDSSGYRMNVVTKSDCPPINCNNCVYKGDWTLIASSGAYYLTRNTFLCLADSFRNFTEIFPDPSSSNMVDIACNSYQCTIYHYIIKEPFLYTYNLGKCSDFSCEGCNMCNYWQLNKTQSYTFLQRQTSSCQALTRIRMEDFFPPSGIPQVYQQHDFISSEILYKSSWNTPRILALIISSIMIIILFIILITFWCRNL 238
BLAST of SMED30033765 vs. Planmine SMEST
Match: SMESG000017181.1 (SMESG000017181.1) HSP 1 Score: 196.823 bits (499), Expect = 1.274e-60 Identity = 103/185 (55.68%), Postives = 121/185 (65.41%), Query Frame = 2 Query: 134 MEVLVIFLLLLRNALGHSIISERTDIRCANGACYNVVYELYQDSSGYR--MNVVTKSDCPPINCNNCVYKGDWTLIASSGAYYLTRNTFLCLADSFRNFTEIFPDPSSSNMVDIACNSYQCTRYHYIIKEPFLYTYNLGKCSDFSCEGCNMCNYWQLNKTQSYTFLQRQTSSCQALTRIRMEDFF 682 M LVIFLLLLRNALG S I+ER DI CAN C NV Y LY D Y +NV +S CP +NCNNC YKG+W L +SG Y+L R+T C DS RNFTEIFP S N+ DIAC++Y C++Y+Y+ + LYT LG CS SCEGC WQ SY LQR SSC ++TRI MEDFF Sbjct: 1 MAFLVIFLLLLRNALGCSFINERNDITCANRTCNNVRYRLYYDDQSYHYYVNVAGESVCPSVNCNNCSYKGNWMLGKASGTYFLYRSTNSCSTDSIRNFTEIFPSSSPLNVTDIACSNYGCSKYNYLFESSKLYTKYLGNCSYPSCEGCKTLTPWQYVNGNSYNLLQRNVSSCPSITRINMEDFF 185
BLAST of SMED30033765 vs. Planmine SMEST
Match: SMESG000017240.1 (SMESG000017240.1) HSP 1 Score: 123.25 bits (308), Expect = 1.868e-32 Identity = 61/183 (33.33%), Postives = 99/183 (54.10%), Query Frame = 2 Query: 134 MEVLVIFLLLLRNALGHSIISERTDIRCANGACYNVVYELYQDSSGYRMNVVTKSDCPPINCNNCVYKGDWTLIASSGAYYLTRNTFLCLADSFRNFTEIFPDPSSSNMVDIACNSYQCTRYHYIIKEPFLYTYNLGKCSDFSCEGCNMCNYWQLNKTQSYTFLQRQTSSCQALTRIRMEDFF 682 + +++ FLL + + G II+ER D+ C G C + Y++ S Y ++ S C P C NC +K DW+L+ G Y+ RNT CL+++ + EIFP S ++DI CNSY C + Y ++ ++ G CSD C+ C + W K L R+T+ C+A ++I++ D+F Sbjct: 8 ISMIIHFLLFIHLSAGCKIINERNDVSCNKGKCSIIRYQISGAKSNYELSSRLISSCDPTKCKNCAHKSDWSLLKIQGVSYVVRNTNSCLSENAKEPKEIFPR-KYSKVLDIRCNSYSCWKDIYQVRTNYMKITPQGPCSDDYCKKCYFSDKWNFTKFAGSPILTRKTTLCEASSKIKITDYF 189
BLAST of SMED30033765 vs. Planmine SMEST
Match: SMESG000017240.1 (SMESG000017240.1) HSP 1 Score: 122.479 bits (306), Expect = 2.930e-32 Identity = 61/181 (33.70%), Postives = 98/181 (54.14%), Query Frame = 2 Query: 140 VLVIFLLLLRNALGHSIISERTDIRCANGACYNVVYELYQDSSGYRMNVVTKSDCPPINCNNCVYKGDWTLIASSGAYYLTRNTFLCLADSFRNFTEIFPDPSSSNMVDIACNSYQCTRYHYIIKEPFLYTYNLGKCSDFSCEGCNMCNYWQLNKTQSYTFLQRQTSSCQALTRIRMEDFF 682 +++ FLL + + G II+ER D+ C G C + Y++ S Y ++ S C P C NC +K DW+L+ G Y+ RNT CL+++ + EIFP S ++DI CNSY C + Y ++ ++ G CSD C+ C + W K L R+T+ C+A ++I++ D+F Sbjct: 1 MIIHFLLFIHLSAGCKIINERNDVSCNKGKCSIIRYQISGAKSNYELSSRLISSCDPTKCKNCAHKSDWSLLKIQGVSYVVRNTNSCLSENAKEPKEIFPR-KYSKVLDIRCNSYSCWKDIYQVRTNYMKITPQGPCSDDYCKKCYFSDKWNFTKFAGSPILTRKTTLCEASSKIKITDYF 180
BLAST of SMED30033765 vs. Planmine SMEST
Match: SMESG000017134.1 (SMESG000017134.1) HSP 1 Score: 116.316 bits (290), Expect = 6.292e-30 Identity = 62/177 (35.03%), Postives = 94/177 (53.11%), Query Frame = 2 Query: 152 FLLLLRNALGHSIISERTDIRCANGACYNVVYELYQDSSGYRMNVVTKSDCPPINCNNCVYKGDWTLIASSGAYYLTRNTFLCLADSFRNFTEIFPDPSSSNMVDIACNSYQCTRYHYIIKEPFLYTYNLGKCSDFSCEGCNMCNYWQLNKTQSYTFLQRQTSSCQALTRIRMEDFF 682 F+ L G +I+ER D+ C G C + Y+L Q+ S Y + ++C C NC YK +W++ S+ Y+L R+T C A++ RN +IFP SSS ++D+ C C++++Y ++ NLG C+ C+ C W L S L RQT SC T I+MED+F Sbjct: 7 FIFLFSICQGFQVINERNDVTCLFGYCQRIKYQLLQEISSYSIRPTFIANCDSRVCENCSYKSNWSMGMSNEGYFLVRSTSNCHAENERNSADIFPSNSSS-VLDLVCVENTCSKFNYSFTNGVFFSENLGSCNISGCQNCVTSTKWNLKSFSSRLILVRQTESCSLPTFIKMEDYF 182 The following BLAST results are available for this feature:
BLAST of SMED30033765 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30033765 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30033765 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30033765 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30033765 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30033765 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30033765 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30033765 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30033765 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30033765 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30033765 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30033765 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30033765 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30033765 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 >SMED30033765 ID=SMED30033765|Name=SMED30033765|organism=Schmidtea mediterranea sexual|type=transcript|length=1277bpback to top protein sequence of SMED30033765-orf-1 >SMED30033765-orf-1 ID=SMED30033765-orf-1|Name=SMED30033765-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=239bp MEVLVIFLLLLRNALGHSIISERTDIRCANGACYNVVYELYQDSSGYRMNback to top protein sequence of SMED30033765-orf-2 >SMED30033765-orf-2 ID=SMED30033765-orf-2|Name=SMED30033765-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=132bp RNPYIFILDYLYLYLHLSFGYYLSLWVSSIVSPSTIFSFCGFQKDFQTKPback 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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