SMED30027562
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., 2020SMED30027562 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 10
Alignments
SMED30027562 aligns in the following genomic locations:
Homology
BLAST of SMED30027562 vs. TrEMBL
Match: A0A5J4NWQ9 (HMG box domain-containing protein OS=Paragonimus westermani OX=34504 GN=DEA37_0013666 PE=4 SV=1) HSP 1 Score: 62.3882 bits (150), Expect = 7.640e-8 Identity = 29/88 (32.95%), Postives = 48/88 (54.55%), Query Frame = 1 Query: 316 IKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTN 579 +++A +HG+P+K S LNVY++E + + K+ KL+ V ++K+L+ SE Y K KA YE ++ W D+ F N Sbjct: 137 VQYAHKHGMPRKPPISGLNVYIREKLCDLKGQSITKVATKLRDAVQNWKSLSPSEQATYGLKAQQLKAAYEKELEAWASEHDLRFTRN 224
BLAST of SMED30027562 vs. TrEMBL
Match: A0A4E0RQF0 (HMG box domain-containing protein OS=Fasciola hepatica OX=6192 GN=D915_001227 PE=4 SV=1) HSP 1 Score: 58.151 bits (139), Expect = 1.567e-6 Identity = 28/96 (29.17%), Postives = 54/96 (56.25%), Query Frame = 1 Query: 292 AETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTN 579 A +++ + + +A HG+P+K S LNVY+QE ++ + K+ +L+ V D+ L++ E ++Y+ K + KA+YE ++ W + F N Sbjct: 94 AWSEKQKSLMYAHRHGMPRKPPASGLNVYIQEKLSDLKGMSLNKVTLRLRDAVKDWNALSEDERKIYSAKATELKAEYEKELQSWATEHKLRFTKN 189
BLAST of SMED30027562 vs. TrEMBL
Match: A0A504YQ35 (HMG box domain-containing protein OS=Fasciola gigantica OX=46835 GN=FGIG_03396 PE=4 SV=1) HSP 1 Score: 58.151 bits (139), Expect = 2.476e-6 Identity = 28/96 (29.17%), Postives = 54/96 (56.25%), Query Frame = 1 Query: 292 AETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTN 579 A +++ + + +A HG+P+K S LNVY+QE ++ + K+ +L+ V D+ L++ E ++Y+ K + KA+YE ++ W + F N Sbjct: 122 AWSEKRKSLMYAHRHGMPRKPPASGLNVYIQEKLSDLKGMSLNKVTLRLRDAVKDWNALSEDERKIYSAKATELKAEYEKELQSWATEHKLRFTKN 217
BLAST of SMED30027562 vs. Planmine SMEST
Match: SMESG000022880.1 (SMESG000022880.1) HSP 1 Score: 360.533 bits (924), Expect = 6.450e-128 Identity = 189/191 (98.95%), Postives = 190/191 (99.48%), Query Frame = 1 Query: 22 MQRKIINTILRGVSKIAFEKPPNSIYFLYFRENYLKLKSETEFNNLPFDKKTLMNVVRDQFKSLSGXXXXXXXXXXRIVNEDYIKMKNMEAETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTNRRKVA 594 MQRKIINTILRGVSKIAFEKPPNSIYFLYFRENYLKLKSETEFNNLPFDKKTLMNVVRDQFKSLSGEEKKELEEKLRIVNEDYIKMKNMEAETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSE+QVYNDKFSAFK DYETLMKEWTKAKDVPFLTNRRKVA Sbjct: 1 MQRKIINTILRGVSKIAFEKPPNSIYFLYFRENYLKLKSETEFNNLPFDKKTLMNVVRDQFKSLSGEEKKELEEKLRIVNEDYIKMKNMEAETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSELQVYNDKFSAFKTDYETLMKEWTKAKDVPFLTNRRKVA 191
BLAST of SMED30027562 vs. Planmine SMEST
Match: SMESG000022878.1 (SMESG000022878.1) HSP 1 Score: 93.2041 bits (230), Expect = 3.990e-23 Identity = 54/184 (29.35%), Postives = 106/184 (57.61%), Query Frame = 1 Query: 43 TILRGVSKIAFEKPPNSIYFLYFRENYLKLKSETEFNNLPFDKKTLMNVVRDQFKSLSGXXXXXXXXXXRIVNEDYIKMKNMEAETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTNRRKVA 594 + +R +SKI +KPP S++ ++ R N K +S + ++++++ +++K LS E + L+ L+I N +Y+++ + + K +II FAE++G+PK+ S LN++++E P + + + +V D+KNL +E+ YN++F K ++ MKEW +PF NR+++A Sbjct: 7 SFIRKISKIKLDKPPASVFGMFLRLNNSKHQSGNNNKSDITNRRSML----EKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIVRYNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLA 186
BLAST of SMED30027562 vs. Planmine SMEST
Match: SMESG000022878.1 (SMESG000022878.1) HSP 1 Score: 76.6406 bits (187), Expect = 4.259e-17 Identity = 42/133 (31.58%), Postives = 78/133 (58.65%), Query Frame = 1 Query: 196 DQFKSLSGXXXXXXXXXXRIVNEDYIKMKNMEAETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTNRRKVA 594 +++K LS E + L+ L+I N +Y+++ + + K +II FAE++G+PK+ S LN++++E P + + + +V D+KNL +E+ YN++F K ++ MKEW +PF NR+++A Sbjct: 28 EKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIVRYNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLA 160 The following BLAST results are available for this feature:
BLAST of SMED30027562 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30027562 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30027562 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30027562 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30027562 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30027562 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30027562 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30027562 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 3
BLAST of SMED30027562 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30027562 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30027562 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30027562 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30027562 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30027562 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 3
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30027562 ID=SMED30027562|Name=SMED30027562|organism=Schmidtea mediterranea sexual|type=transcript|length=715bpback to top protein sequence of SMED30027562-orf-1 >SMED30027562-orf-1 ID=SMED30027562-orf-1|Name=SMED30027562-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=203bp MQRKIINTILRGVSKIAFEKPPNSIYFLYFRENYLKLKSETEFNNLPFDKback 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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