SMED30015077
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., 2020SMED30015077 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30015077 aligns in the following genomic locations:
Homology
BLAST of SMED30015077 vs. Planmine SMEST
Match: SMESG000063966.1 (SMESG000063966.1) HSP 1 Score: 97.4413 bits (241), Expect = 2.812e-35 Identity = 52/81 (64.20%), Postives = 58/81 (71.60%), Query Frame = 1 Query: 400 GRQPILKFASKYSVSVKMGRMKTTQKSVRRCSC*RPAE*RTKKHYM*WQLFVITWSKILHITS-TMQLQIRSRKTHSKIAS 639 G +LKFASKYSV+ KMG M QKS+RR SC RPAE +KHYM WQLFV+T SKIL T+ MQLQIRSR H KI S Sbjct: 105 GTSTMLKFASKYSVNAKMGMMTIKQKSLRRYSCRRPAEKHARKHYMRWQLFVVTLSKILQNTTIIMQLQIRSRNKHPKIES 185 HSP 2 Score: 70.8626 bits (172), Expect = 2.812e-35 Identity = 31/38 (81.58%), Postives = 33/38 (86.84%), Query Frame = 3 Query: 297 DVLPIPAVTAKLGEAVKQEDFEAFAGCNNEVACRGTST 410 DVLPIPAVTA+LGEAV Q DFEA C+NEVACRGTST Sbjct: 71 DVLPIPAVTAELGEAVTQNDFEALVDCDNEVACRGTST 108
BLAST of SMED30015077 vs. Planmine SMEST
Match: SMESG000036624.1 (SMESG000036624.1) HSP 1 Score: 77.7962 bits (190), Expect = 1.202e-25 Identity = 37/62 (59.68%), Postives = 47/62 (75.81%), Query Frame = 3 Query: 294 DDVLPIPAVTAKLGEAVKQEDFEAFAGCNNEVACRGTSTNSEICEQVQRKRQNGADENDTEE 479 DD+L IPAVT +LGEA QE F C+N+V+C TST++EICEQV+R RQN D+NDTE+ Sbjct: 134 DDLLQIPAVTVELGEAATQE---TFVDCDNKVSCHDTSTDAEICEQVRRNRQNWDDDNDTED 192 HSP 2 Score: 58.151 bits (139), Expect = 1.202e-25 Identity = 33/40 (82.50%), Postives = 33/40 (82.50%), Query Frame = 2 Query: 488 DAVVEGPQSNAQRSITCDGNCSSLLGAKSY-ILRVLCSCR 604 DAVV G QSNAQ SITC GNCSSLLGAKSY I RVLCS R Sbjct: 192 DAVVRGLQSNAQISITCAGNCSSLLGAKSYRIQRVLCSGR 231
BLAST of SMED30015077 vs. Planmine SMEST
Match: SMESG000013207.1 (SMESG000013207.1) HSP 1 Score: 67.3958 bits (163), Expect = 1.089e-18 Identity = 33/59 (55.93%), Postives = 40/59 (67.80%), Query Frame = 1 Query: 1138 KNIYQKLNET*RWFCEERQLVQALRTQIRSLETALLLSQEDNAVTYPVIFTQVQFAYRE 1314 K YQ+L R + EE+QL Q +TQIRSLE AL SQE NA TYP++F VQ AYR+ Sbjct: 46 KTTYQRLTAAQRGWTEEKQLAQNQKTQIRSLEVALSASQESNAGTYPLVFAPVQIAYRD 104 HSP 2 Score: 45.0542 bits (105), Expect = 1.089e-18 Identity = 22/42 (52.38%), Postives = 31/42 (73.81%), Query Frame = 2 Query: 1013 METICSISQELTKLCQTNTELHSQLLQMSKRCQAIKST*IEP 1138 ME++ ++S++L K + NTELHSQL QMS+ Q I+ST EP Sbjct: 1 MESLRTLSRKLVKSRKENTELHSQLFQMSREIQKIRSTSGEP 42
BLAST of SMED30015077 vs. Planmine SMEST
Match: SMESG000049741.1 (SMESG000049741.1) HSP 1 Score: 68.9366 bits (167), Expect = 4.448e-17 Identity = 35/70 (50.00%), Postives = 42/70 (60.00%), Query Frame = 1 Query: 1138 KNIYQKLNET*RWFCEERQLVQALRTQIRSLETALLLSQEDNAVTYPVIFTQVQFAYREREEASQATKTS 1347 K +Y KL + + EERQLV +L+TQIR LE AL SQE AVTYP++F Q AYRE A T Sbjct: 65 KPLYLKLAAAQKGWAEERQLVTSLKTQIRGLEVALSASQEGAAVTYPLVFAPAQLAYRESNPTPSAMPTP 134 HSP 2 Score: 38.1206 bits (87), Expect = 4.448e-17 Identity = 18/48 (37.50%), Postives = 27/48 (56.25%), Query Frame = 2 Query: 995 IRIFSGMETICSISQELTKLCQTNTELHSQLLQMSKRCQAIKST*IEP 1138 IR M+ I + ELT+ Q N +LH QLL + + Q +K+T + P Sbjct: 14 IRTILDMDPIKLLQNELTRTQQANNDLHDQLLHLVREMQQLKATWVNP 61
BLAST of SMED30015077 vs. Planmine SMEST
Match: SMESG000031748.1 (SMESG000031748.1) HSP 1 Score: 70.8626 bits (172), Expect = 1.078e-16 Identity = 37/74 (50.00%), Postives = 49/74 (66.22%), Query Frame = 1 Query: 1135 TKNIYQKLNET*RWFCEERQLVQALRTQIRSLETALLLSQEDNAVTYPVIFTQVQFAYREREEASQA-TKTSRH 1353 K +YQ+L + + ERQLVQ LRTQI+ LETAL +SQE AVTYP++F Q AYR+ + S + K +RH Sbjct: 1301 VKVVYQRLEAAQKGWAGERQLVQNLRTQIKGLETALSVSQEGAAVTYPLVFAPAQLAYRDTLDPSTSKDKPNRH 1374 HSP 2 Score: 35.039 bits (79), Expect = 1.078e-16 Identity = 16/38 (42.11%), Postives = 25/38 (65.79%), Query Frame = 2 Query: 1028 SISQELTKLCQTNTELHSQLLQMSKRCQAIKST*IEPR 1141 ++ +EL K TN +LH QLLQ+++ IK T +EP+ Sbjct: 1262 ALQRELDKAHATNRDLHHQLLQLTREIPQIKGTWMEPK 1299 The following BLAST results are available for this feature:
BLAST of SMED30015077 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30015077 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30015077 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30015077 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30015077 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30015077 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30015077 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30015077 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30015077 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30015077 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30015077 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30015077 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30015077 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30015077 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 >SMED30015077 ID=SMED30015077|Name=SMED30015077|organism=Schmidtea mediterranea sexual|type=transcript|length=1416bpback to top protein sequence of SMED30015077-orf-1 >SMED30015077-orf-1 ID=SMED30015077-orf-1|Name=SMED30015077-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=193bp MANVKESNISNEISDEPVVREFRKSSSVGRRLALASLDVPSRVMHKVSNEback to top Annotated Terms
The following terms have been associated with this transcript:
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