SMED30000479
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., 2020SMED30000479 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Homology
BLAST of SMED30000479 vs. TrEMBL
Match: A0A2H1VDJ2 (SFRICE_007015 OS=Spodoptera frugiperda OX=7108 GN=SFRICE_007015 PE=4 SV=1) HSP 1 Score: 62.003 bits (149), Expect = 1.099e-6 Identity = 40/118 (33.90%), Postives = 63/118 (53.39%), Query Frame = 3 Query: 207 VSRLEQNMNFIQHEHCQMLEGLQKQIDKLREENHDLQFQLVMRSDRNKDLDNKTLSKPKDSN-QNNPKLLTDQLHHLKQELD---GEKRKNKELLEQLEILKNKSEEIPKDIQYVETL 548 V+ LE ++ F+Q +H QML GL +I+ LRE N DLQFQL+ NK+ K + P + N +NN L ++ L+QE E + + QL++L + + P I + T+ Sbjct: 39 VAHLEHSVRFLQEQHRQMLSGLHAEIEALRERNRDLQFQLIF----NKESSPKASTPPAEENTENNEAKLKREVTRLEQEASTARSEAKAAEARALQLQLLVDAQTDYPLTIMKLRTV 152
BLAST of SMED30000479 vs. TrEMBL
Match: A0A4S2LV80 (CCDC92 domain-containing protein OS=Opisthorchis felineus OX=147828 GN=CRM22_004613 PE=4 SV=1) HSP 1 Score: 60.4622 bits (145), Expect = 3.508e-6 Identity = 38/111 (34.23%), Postives = 64/111 (57.66%), Query Frame = 3 Query: 168 EGENKEVIYLKKTVSRLEQNMNFIQHEHCQMLEGLQKQIDKLREENHDLQFQLVMRSDRNKDLDNKTLSKPKDSNQNNPKLLTDQLHHLKQELDGEKRKNKELLEQLEILK 500 EGENK V+ LE+++ ++ +H +L GL ++I+ LR N DLQF+LVM K +K ++P ++ L ++ + L+Q+L+ E+ NK L+ QLE L+ Sbjct: 36 EGENK--------VAVLEESIEYLCKQHAFVLNGLYEEIENLRRANKDLQFRLVMCCCVTKGGKHKGKAEPTTCSRTAEDLASEVI-ELRQQLEKERFMNKTLVHQLETLQ 137
BLAST of SMED30000479 vs. TrEMBL
Match: A0A4E0R410 (CCDC92 domain-containing protein OS=Fasciola hepatica OX=6192 GN=D915_007508 PE=4 SV=1) HSP 1 Score: 60.077 bits (144), Expect = 4.417e-6 Identity = 38/106 (35.85%), Postives = 62/106 (58.49%), Query Frame = 3 Query: 183 EVIYLKKTVSRLEQNMNFIQHEHCQMLEGLQKQIDKLREENHDLQFQLVMRSDRNKDLDNKTLSKPKDSNQNNPKLLTDQLHHLKQELDGEKRKNKELLEQLEILK 500 E + + +S LE+N+NF++ +H ML+ L ++I+ LR+ N LQF+LVM S + K P S +N L ++ LK+ LD EK +N+ LL Q+E ++ Sbjct: 41 EFVSGESKISTLEKNINFLRAQHEVMLKSLHEEIENLRKSNKALQFRLVMCSC-SASCHMKIDETPSGSLTSN---LESEVQTLKKLLDEEKHRNQSLLAQMEAMQ 142
BLAST of SMED30000479 vs. TrEMBL
Match: A0A2H1C599 (CCDC92 domain-containing protein OS=Fasciola hepatica OX=6192 GN=D915_11181 PE=4 SV=1) HSP 1 Score: 56.225 bits (134), Expect = 7.794e-6 Identity = 37/98 (37.76%), Postives = 59/98 (60.20%), Query Frame = 3 Query: 207 VSRLEQNMNFIQHEHCQMLEGLQKQIDKLREENHDLQFQLVMRSDRNKDLDNKTLSKPKDSNQNNPKLLTDQLHHLKQELDGEKRKNKELLEQLEILK 500 +S LE+N+NF++ +H ML+ L ++I+ LR+ N LQF+LVM S + K P S +N L ++ LK+ LD EK +N+ LL Q+E ++ Sbjct: 49 ISTLEKNINFLRAQHEVMLKSLHEEIENLRKSNKALQFRLVMCSC-SASCHMKIDETPSGSLTSN---LESEVQTLKKLLDEEKHRNQSLLAQMEAMQ 142
BLAST of SMED30000479 vs. Ensembl Cavefish
Match: ccdc92 (coiled-coil domain containing 92 [Source:NCBI gene;Acc:103025601]) HSP 1 Score: 48.521 bits (114), Expect = 8.162e-6 Identity = 29/103 (28.16%), Postives = 54/103 (52.43%), Query Frame = 3 Query: 183 EVIYLKKTVSRLEQNMNFIQHEHCQMLEGLQKQIDKLREENHDLQFQLVMRSDRNKDLDNKTLSKPKDSNQNNPKLLTDQLHHLKQELDGEKRKNKELLEQLE 491 E + L+ + ++N+ F+Q +H L+GL +I +L++ DL ++L +RS S P DS + + L + L+ +L ++++N ELL LE Sbjct: 4 ENVTLENQLHSAQKNLLFLQQDHATTLKGLHAEIRRLQQHCTDLTYELTVRS-----------SDPNDSGEARCRELQQRCEELEAQLKAKEQENAELLRDLE 95
BLAST of SMED30000479 vs. Planmine SMEST
Match: SMESG000029735.1 (SMESG000029735.1) HSP 1 Score: 748.043 bits (1930), Expect = 0.000e+0 Identity = 368/369 (99.73%), Postives = 368/369 (99.73%), Query Frame = 3 Query: 54 MSEVGFSSISAPGLSRDLVNKPFKNSYSFISENAYVKPEGENKEVIYLKKTVSRLEQNMNFIQHEHCQMLEGLQKQIDKLREENHDLQFQLVMRSDRNKDLDNKTLSKPKDSNQNNPKLLTDQLHHLKQELDGEKRKNKELLEQLEILKNKSEEIPKDIQYVETLEPVAFTDNNVFISPDIRISLNPLAVSTFHHDSGSFIMKTPLTVQDCEMVIQTLLQKIDCTPNMRENSVSSRSLSGNQRLKLIPGIKKPLQPIKPMSRGSSNIKLASLTGSQTVKTIGLPSTQKLIPILSHKNETIKLEHESQGFNGSRKSDRDHKILDNLPISAEVKTGSSLPALPKPNDFNQAEKHRRLHMLQKKRLDQYNNR 1160 MSEVGFSSISAPGLSRDLVNKPFKNSYSFISENAYVKPEGENKEVIYLKKTVSRLEQNMNFIQHEHCQMLEGLQKQIDKLREENHDLQFQLVMRSDRNKDLDNKTLSKPKDSNQNNPKLLTDQLHHLKQELDGEKRKNKELLEQLEILKNKSEEIPKDIQYVETLEP AFTDNNVFISPDIRISLNPLAVSTFHHDSGSFIMKTPLTVQDCEMVIQTLLQKIDCTPNMRENSVSSRSLSGNQRLKLIPGIKKPLQPIKPMSRGSSNIKLASLTGSQTVKTIGLPSTQKLIPILSHKNETIKLEHESQGFNGSRKSDRDHKILDNLPISAEVKTGSSLPALPKPNDFNQAEKHRRLHMLQKKRLDQYNNR Sbjct: 1 MSEVGFSSISAPGLSRDLVNKPFKNSYSFISENAYVKPEGENKEVIYLKKTVSRLEQNMNFIQHEHCQMLEGLQKQIDKLREENHDLQFQLVMRSDRNKDLDNKTLSKPKDSNQNNPKLLTDQLHHLKQELDGEKRKNKELLEQLEILKNKSEEIPKDIQYVETLEPAAFTDNNVFISPDIRISLNPLAVSTFHHDSGSFIMKTPLTVQDCEMVIQTLLQKIDCTPNMRENSVSSRSLSGNQRLKLIPGIKKPLQPIKPMSRGSSNIKLASLTGSQTVKTIGLPSTQKLIPILSHKNETIKLEHESQGFNGSRKSDRDHKILDNLPISAEVKTGSSLPALPKPNDFNQAEKHRRLHMLQKKRLDQYNNR 369
BLAST of SMED30000479 vs. Planmine SMEST
Match: SMESG000029735.1 (SMESG000029735.1) HSP 1 Score: 742.265 bits (1915), Expect = 0.000e+0 Identity = 367/370 (99.19%), Postives = 368/370 (99.46%), Query Frame = 3 Query: 54 MSEVGFSSISAPGLSRDLVNKPFKNSYSFISENAYVKPEGENKEVIYLKKTVSRLEQNMNFIQHEHCQMLEGLQKQIDKLREENHDLQFQLVMRSDRNKDLDNKTLSKPKDSNQNNPKLLTDQLHHLKQELDGEKRKNKELLEQLEILKNKSEEIPKDIQYVETLEPVAFTDNNVFISPDIRISLNPLAVSTFHHDSGSFIMKTPLTVQDCEMVIQTLLQKIDCTPNMRENSVSSRSLSGNQRLKLIPGIKKPLQPIKPMSRGSSNIKLASLTGSQTVKTIGLPSTQKLIPILSHKNETIKLE-HESQGFNGSRKSDRDHKILDNLPISAEVKTGSSLPALPKPNDFNQAEKHRRLHMLQKKRLDQYNNR 1160 MSEVGFSSISAPGLSRDLVNKPFKNSYSFISENAYVKPEGENKEVIYLKKTVSRLEQNMNFIQHEHCQMLEGLQKQIDKLREENHDLQFQLVMRSDRNKDLDNKTLSKPKDSNQNNPKLLTDQLHHLKQELDGEKRKNKELLEQLEILKNKSEEIPKDIQYVETLEP AFTDNNVFISPDIRISLNPLAVSTFHHDSGSFIMKTPLTVQDCEMVIQTLLQKIDCTPNMRENSVSSRSLSGNQRLKLIPGIKKPLQPIKPMSRGSSNIKLASLTGSQTVKTIGLPSTQKLIPILSHKNETIKL+ HESQGFNGSRKSDRDHKILDNLPISAEVKTGSSLPALPKPNDFNQAEKHRRLHMLQKKRLDQYNNR Sbjct: 1 MSEVGFSSISAPGLSRDLVNKPFKNSYSFISENAYVKPEGENKEVIYLKKTVSRLEQNMNFIQHEHCQMLEGLQKQIDKLREENHDLQFQLVMRSDRNKDLDNKTLSKPKDSNQNNPKLLTDQLHHLKQELDGEKRKNKELLEQLEILKNKSEEIPKDIQYVETLEPAAFTDNNVFISPDIRISLNPLAVSTFHHDSGSFIMKTPLTVQDCEMVIQTLLQKIDCTPNMRENSVSSRSLSGNQRLKLIPGIKKPLQPIKPMSRGSSNIKLASLTGSQTVKTIGLPSTQKLIPILSHKNETIKLDRHESQGFNGSRKSDRDHKILDNLPISAEVKTGSSLPALPKPNDFNQAEKHRRLHMLQKKRLDQYNNR 370 The following BLAST results are available for this feature:
BLAST of SMED30000479 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30000479 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30000479 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30000479 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30000479 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30000479 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30000479 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30000479 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 4
BLAST of SMED30000479 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 1
BLAST of SMED30000479 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30000479 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30000479 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30000479 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30000479 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 2
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30000479 ID=SMED30000479|Name=SMED30000479|organism=Schmidtea mediterranea sexual|type=transcript|length=1282bpback to top protein sequence of SMED30000479-orf-1 >SMED30000479-orf-1 ID=SMED30000479-orf-1|Name=SMED30000479-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=370bp MSEVGFSSISAPGLSRDLVNKPFKNSYSFISENAYVKPEGENKEVIYLKKback 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
|