SMED30007558
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., 2020SMED30007558 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 8
Alignments
SMED30007558 aligns in the following genomic locations:
Homology
BLAST of SMED30007558 vs. TrEMBL
Match: I1ZID3 (Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1) HSP 1 Score: 67.0106 bits (162), Expect = 1.046e-8 Identity = 57/197 (28.93%), Postives = 90/197 (45.69%), Query Frame = 2 Query: 311 DTTLGIYQCKICPKHNDDYRICKFRFTKY------GSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYK----DSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHF-------SMADSRRTKRGRKGKHSK 850 +T G + C I +HN+ IC F K+ SI ILVH++ H + + + + L + +K + I+ D L + H + A +KF C L + DF++Y+ DS G ++C +C +T N ++ KF FT S+ FTNI HL HF + A SR+ + KHS+ Sbjct: 169 ETKNGFFACSI-NQHNE---ICG-EFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSE 360
BLAST of SMED30007558 vs. Planmine SMEST
Match: SMESG000071865.1 (SMESG000071865.1) HSP 1 Score: 503.056 bits (1294), Expect = 0.000e+0 Identity = 244/244 (100.00%), Postives = 244/244 (100.00%), Query Frame = 2 Query: 122 MCVNEECIDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHLKVNEDFNVFTNSFDTTLGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYKDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHFSMADSRRTKRGRKGKHSKV 853 MCVNEECIDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHLKVNEDFNVFTNSFDTTLGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYKDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHFSMADSRRTKRGRKGKHSKV Sbjct: 1 MCVNEECIDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHLKVNEDFNVFTNSFDTTLGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYKDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHFSMADSRRTKRGRKGKHSKV 244
BLAST of SMED30007558 vs. Planmine SMEST
Match: SMESG000071713.1 (SMESG000071713.1) HSP 1 Score: 188.734 bits (478), Expect = 5.506e-57 Identity = 104/233 (44.64%), Postives = 142/233 (60.94%), Query Frame = 2 Query: 143 IDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHLKVNEDFNVFTNSFDTTLGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYKDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHFSMADSRRTKRGRKGK 841 ID S + S+ N LA+ SIH++++K A+LKF DC+LK +E FN+F + + G +QCKICPK +D ++ KF F+ YGS+ FMNI VHL HFS ES PL+RGRR + V+ T L LCD+ Y + V D+A F SC+LK + DF++YKD+ + L+GY++CK+C +Q KF FT Y SLNF+NI+ HL SHF RGRK K Sbjct: 146 IDVSNDISMELSFSNNDDSYLANDSIHEYVMKTASLKFKDCNLKKHEHFNIFKLNSNKLTGYFQCKICPKVHDKFKTYKFSFSNYGSLNFMNIKVHLLTHFSTKESEPLKRGRRSS-------------VLNQTQLELCDDSYSKNVIDLAANCFASCQLKTD-DFAIYKDTSNVLVGYFICKICPNDSQ--KHLKFSFTNYQSLNFSNIKTHLTSHFKKKKPIENTRGRKRK 362
BLAST of SMED30007558 vs. Planmine SMEST
Match: SMESG000044230.1 (SMESG000044230.1) HSP 1 Score: 67.0106 bits (162), Expect = 2.910e-12 Identity = 57/197 (28.93%), Postives = 90/197 (45.69%), Query Frame = 2 Query: 311 DTTLGIYQCKICPKHNDDYRICKFRFTKY------GSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYK----DSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHF-------SMADSRRTKRGRKGKHSK 850 +T G + C I +HN+ IC F K+ SI ILVH++ H + + + + L + +K + I+ D L + H + A +KF C L + DF++Y+ DS G ++C +C +T N ++ KF FT S+ FTNI HL HF + A SR+ + KHS+ Sbjct: 169 ETKNGFFACSI-NQHNE---ICG-EFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSE 360 HSP 2 Score: 56.6102 bits (135), Expect = 7.180e-9 Identity = 49/154 (31.82%), Postives = 68/154 (44.16%), Query Frame = 2 Query: 74 NES*KIIDLTNESFSKMCVNEECIDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHLKVNEDFNVFT----NSFDTTLGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHF-SLAESAPLRRGRRKTLFKTTKNTSK 520 N+S + IDL + S ++ E I F+E KFIDCHL + DFNV+ +S T G + C IC K + KF FT S+ F NI+ HL+ HF S+A A R++T KT K++ K Sbjct: 238 NKSSRSIDLADAKLSNNFIHNEIIKFAEQ------------------------------KFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSEK 361
BLAST of SMED30007558 vs. Planmine SMEST
Match: SMESG000047524.1 (SMESG000047524.1) HSP 1 Score: 56.6102 bits (135), Expect = 6.586e-9 Identity = 33/81 (40.74%), Postives = 47/81 (58.02%), Query Frame = 2 Query: 563 EKYHQYVSDMALEKFDSCRLKMNKDFSLY---KDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHF 796 EKY+ + A + F C L + DF L DS D L+GYY C LC + + + KFRF+KY+S+ +TNI HL +H+ Sbjct: 172 EKYYNDIVKNAAKNFIECSLIPDVDFHLSIPENDSTD-LIGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHY 251 HSP 2 Score: 54.6842 bits (130), Expect = 2.256e-8 Identity = 30/74 (40.54%), Postives = 41/74 (55.41%), Query Frame = 2 Query: 230 IVKRAALKFIDCHLKVNEDFNVFTNSFDTT--LGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHF 445 IVK AA FI+C L + DF++ D+T +G Y C +C KFRF+KY S+ + NI HLK H+ Sbjct: 178 IVKNAAKNFIECSLIPDVDFHLSIPENDSTDLIGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHY 251
BLAST of SMED30007558 vs. Planmine SMEST
Match: SMESG000047524.1 (SMESG000047524.1) HSP 1 Score: 56.6102 bits (135), Expect = 7.078e-9 Identity = 33/81 (40.74%), Postives = 47/81 (58.02%), Query Frame = 2 Query: 563 EKYHQYVSDMALEKFDSCRLKMNKDFSLY---KDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHF 796 EKY+ + A + F C L + DF L DS D L+GYY C LC + + + KFRF+KY+S+ +TNI HL +H+ Sbjct: 184 EKYYNDIVKNAAKNFIECSLIPDVDFHLSIPENDSTD-LIGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHY 263 HSP 2 Score: 54.6842 bits (130), Expect = 2.459e-8 Identity = 30/74 (40.54%), Postives = 41/74 (55.41%), Query Frame = 2 Query: 230 IVKRAALKFIDCHLKVNEDFNVFTNSFDTT--LGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHF 445 IVK AA FI+C L + DF++ D+T +G Y C +C KFRF+KY S+ + NI HLK H+ Sbjct: 190 IVKNAAKNFIECSLIPDVDFHLSIPENDSTDLIGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHY 263 The following BLAST results are available for this feature:
BLAST of SMED30007558 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30007558 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30007558 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30007558 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30007558 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30007558 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30007558 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30007558 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of SMED30007558 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30007558 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30007558 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30007558 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30007558 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30007558 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 >SMED30007558 ID=SMED30007558|Name=SMED30007558|organism=Schmidtea mediterranea sexual|type=transcript|length=956bpback to top protein sequence of SMED30007558-orf-1 >SMED30007558-orf-1 ID=SMED30007558-orf-1|Name=SMED30007558-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=245bp MCVNEECIDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHLback to top Annotated Terms
The following terms have been associated with this transcript:
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