SMED30029023
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., 2020SMED30029023 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Homology
BLAST of SMED30029023 vs. TrEMBL
Match: A0A0C2JKS9 (Uncharacterized protein OS=Thelohanellus kitauei OX=669202 GN=RF11_02307 PE=4 SV=1) HSP 1 Score: 60.8474 bits (146), Expect = 5.137e-8 Identity = 37/104 (35.58%), Postives = 54/104 (51.92%), Query Frame = -2 Query: 2 ITEEAKMFIRSKIESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRYLGYDEDKVIFLNEFSLSCSTRQKYGR 313 +T+E +I ++ D S+TL LK+KL I TTI ++ D YSF RV ++ +R N I RF+ DE K+IF++E + S R YGR Sbjct: 7 LTQEQNDYILDLVDEDCSITLKELKIKLHERFGIQVCITTISKSLGDFLYSFKRVHMIPKRRNGVQTINSRFD-------IDESKIIFMDETGFNISMRSIYGR 103
BLAST of SMED30029023 vs. TrEMBL
Match: A0A4Q9LYZ4 (Putative DDE endonuclease OS=Hamiltosporidium tvaerminnensis OX=1176355 GN=CWI38_0380p0040 PE=4 SV=1) HSP 1 Score: 57.3806 bits (137), Expect = 1.393e-7 Identity = 38/122 (31.15%), Postives = 65/122 (53.28%), Query Frame = -2 Query: 17 FINTGRVNAMTQRRPRESIITEEAKMFIRSKIESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRY----LGYDEDKVIFLNEFSLSCSTR 370 ++ TG V R S ++ E K +++ ++ + + TL L ++ + N+ ST+TID A+R+ +Y+ RV LV ER N + IE R NYA + + D+ +FL+E + TR Sbjct: 100 YLKTGLVFVEKGGGDRRSKLSLEIKESLQAYVDLECTKTLYELAEWVKCTFNVYGSTSTIDRALREFHYTLKRVTLVPERRNTLSTIELRTNYATSFRELEVDNDDKNFVFLDEVGFAVVTR 221 HSP 2 Score: 26.1794 bits (56), Expect = 1.393e-7 Identity = 15/42 (35.71%), Postives = 24/42 (57.14%), Query Frame = -1 Query: 366 RKITDNERSLIIRKYEDQKSIQLISEELGINVKMVTSIIRLY 491 +K++ N+R II K + S+ I+ IN + V SI+R Y Sbjct: 59 QKVSINDRERIIEKKLESYSMSAIASMYRINYQTVNSIVRRY 100
BLAST of SMED30029023 vs. TrEMBL
Match: A0A0C2MJ68 (Uncharacterized protein OS=Thelohanellus kitauei OX=669202 GN=RF11_11236 PE=4 SV=1) HSP 1 Score: 57.3806 bits (137), Expect = 5.473e-7 Identity = 34/122 (27.87%), Postives = 63/122 (51.64%), Query Frame = -2 Query: 2 TGRVNAMTQRRPRESIITEEAKMFIRSKIESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRYLGYDEDK--VIFLNEFSLSCSTRQKYGR 361 +G++ + R R + + + +E D S+TL L + + NI S T+ +++ NYSF ++ + ER N+A+ I R +Y +YL Y ++F++E ++ S R+ YGR Sbjct: 19 SGKITKAPKGRDRAKSLNNSQESILCYIVEDDCSLTLENLSDRFFNAKNIRISKNTVARYLKEYNYSFKKIKFIPERRNIASTIRERHDYVIKYLEYSASNRFILFIDETGVNVSMRRNYGR 140
BLAST of SMED30029023 vs. TrEMBL
Match: A0A0C2JI12 (DDE_3 domain-containing protein OS=Thelohanellus kitauei OX=669202 GN=RF11_01522 PE=4 SV=1) HSP 1 Score: 59.3066 bits (142), Expect = 8.160e-7 Identity = 35/127 (27.56%), Postives = 68/127 (53.54%), Query Frame = -2 Query: 2 FINTGRVNAMTQRRPRESIITEEAKMFIRSKIESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRYL----GYDEDKVIFLNEFSLSCSTRQKYGR 370 F +GR+++ + + + E+ K I+S ++ + + L + K+Q ++I +TID ++ +YS+ RV ++ ER N + + R YA RYL + E + IF++E ++ S R +GR Sbjct: 45 FHQSGRIDSNKRGYIQPEKLNEDQKERIKSWVDDNAGIPLRTIVTKVQEEMDISVGKSTIDRILQRFHYSWKRVSIIPERRNNESTLNIRERYATRYLELLQSFREHQFIFIDECGVNISMRTSHGR 171
BLAST of SMED30029023 vs. TrEMBL
Match: A0A4Q9M1Z3 (DDE-like endonuclease OS=Hamiltosporidium tvaerminnensis OX=1176355 GN=CWI38_0243p0030 PE=4 SV=1) HSP 1 Score: 59.3066 bits (142), Expect = 8.531e-7 Identity = 35/96 (36.46%), Postives = 54/96 (56.25%), Query Frame = -2 Query: 2 IESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRY----LGYDEDKVIFLNEFSLSCSTRQKYGR 277 ++ + + TL L ++ + NI ST+TID A+R+ +Y+ RV LV ER N+ + IE R NYA + + D+ +FL+E S TR GR Sbjct: 107 VDLECTKTLYKLAEWVKCTFNIDVSTSTIDRALREFHYTLKRVTLVHERRNILSTIELRTNYATSFRELEVDNDDKNFVFLDEVGFSVVTRPSRGR 202
BLAST of SMED30029023 vs. Planmine SMEST
Match: SMESG000045086.1 (SMESG000045086.1) HSP 1 Score: 77.411 bits (189), Expect = 6.000e-18 Identity = 42/111 (37.84%), Postives = 66/111 (59.46%), Query Frame = -2 Query: 38 FINTGRVNAMTQRRPRESIITEEAKMFIRSKIESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRYLGYDEDKVIFLNEF 370 FI TGR++A+T R P+ I+E+ I++KI+ DVS+TL +L+ L ++ S +TI I+ N+S V LV N NI+ RF Y YL +E++ IF+++F Sbjct: 50 FIKTGRIDAITNRLPKIKKISEDIDRVIKTKIDEDVSITLKSLQRCLSLEKGLVVSVSTIKRTIKSFNFSLKGVVLVPVARNSEVNIKKRFGYTNDYLLLNEERCIFVDDF 160 The following BLAST results are available for this feature:
BLAST of SMED30029023 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30029023 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30029023 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30029023 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30029023 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30029023 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30029023 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30029023 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 5
BLAST of SMED30029023 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30029023 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30029023 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30029023 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30029023 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30029023 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 1
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30029023 ID=SMED30029023|Name=SMED30029023|organism=Schmidtea mediterranea sexual|type=transcript|length=608bpback to top protein sequence of SMED30029023-orf-1 >SMED30029023-orf-1 ID=SMED30029023-orf-1|Name=SMED30029023-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=112bp PINSILCKHISINSKFIPINSKYILIPKLHMQTAEANLHRKITDNERSLIback to top Annotated Terms
The following terms have been associated with this transcript:
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