SMED30000214
Overview
Neoblast Clusters
Zeng et. al., 2018
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 AppEmbryonic 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., 2020SMED30000214 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 10
Alignments
SMED30000214 aligns in the following genomic locations:
Homology
BLAST of SMED30000214 vs. TrEMBL
Match: Q868D5 (Uncharacterized protein Dryg OS=Dugesia ryukyuensis OX=79738 GN=Dryg PE=2 SV=1) HSP 1 Score: 140.584 bits (353), Expect = 6.117e-32 Identity = 119/450 (26.44%), Postives = 191/450 (42.44%), Query Frame = 1 Query: 175 LQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKSFQNFKAKSFPTFQECSTCNAFIELLIWNNHTETALSNLMKYTQETYCNLVKASKKQKCTIMINSKKSYILKFLRKMMTKELFCKIFLNCTNPSDQTLRNHFYDFLLNSKDVYPTEFFEFFYQKHNYPWNFSEYSMFNSLSSRQKKSSHIYEFFQGFIKNLKPNRNNSLISYWDYKYFFEESNNINEIYSWKFFEHFFISHGK-----------DEGXXXXXXXXXXIKNRFGKLSCQLCEIIGPFLLNNWFDKLTVSQQQILINPKTCKDFSNIKECYKTIEIIINYWKGIRNK--DSVSIDFTCWSLLKCK---KRNNLMTPFNNKMTTETVQ----CTVCKRFSEIISETSNEKNFIKDASDAFRLIFCPSIF-KTQKECSDFLSKDFKNLLQTLSSRIQQYYLCRIACPNKMT 1461 +Q D YY+ +C N T P K FC Y K+ + FPT EC TC ++ + WN+H+E A+ NL+ YT + +C VK S K +C +N K + +FL K+M FC++ L C D +F ++ + D Y FFE+F+ + NY +F Y FN Q Y + Q F + P+ N + + ++YF++ N + +FF +F ++ D F Y + + C CE I W + + C + N E + EII + I ++ + +S+ C+ + +C + N M F T Q C VCK FS++ S + F + D F ++C +F K + C FL + N+L L I + YLC C K++ Sbjct: 16 IQGHDYHN-YYEHYCDGNYYTSPTKFYFCHYLKTTTESETVPFPTISECKTCKELLKRITWNSHSEKAVENLLDYTTKHFCENVKRSTKVECQSKLNEYKPKMKEFLVKIMKNGKFCEVLLKCAEKKDVLFTTYFTEYTTDWTDFYSMPFFEYFFNRENYSEDFYPYHFFNYFYHYQDNEHPTY-YHQYFYET--PHTENHMFPHEYFQYFYK--NKTTNYFPHQFFHEYFFNNQYTSPTFNHNNFYDYFFTDEYHGFFERDQKPSEKFCNRCENIPESKFLKWAKSVDIKMLTDAGYKVMCSEL-NTTESERCREIISHIGTVILHELENVLSVKNVCYKIYRCPMNLETTNEMHSFYYDTFDFTRQTSKRCEVCKAFSDVFSSGIDRDLFEEMVVDQFEKVYCNKLFPKKEHMCKKFLKNELPNILNKLRVSIHRDYLCNSTCNGKLS 458
BLAST of SMED30000214 vs. Planmine SMEST
Match: SMESG000000723.1 (SMESG000000723.1) HSP 1 Score: 884.789 bits (2285), Expect = 0.000e+0 Identity = 446/447 (99.78%), Postives = 447/447 (100.00%), Query Frame = 1 Query: 127 MSTIGCLLIFLSSIVALQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKSFQNFKAKSFPTFQECSTCNAFIELLIWNNHTETALSNLMKYTQETYCNLVKASKKQKCTIMINSKKSYILKFLRKMMTKELFCKIFLNCTNPSDQTLRNHFYDFLLNSKDVYPTEFFEFFYQKHNYPWNFSEYSMFNSLSSRQKKSSHIYEFFQGFIKNLKPNRNNSLISYWDYKYFFEESNNINEIYSWKFFEHFFISHGKDEGXXXXXXXXXXIKNRFGKLSCQLCEIIGPFLLNNWFDKLTVSQQQILINPKTCKDFSNIKECYKTIEIIINYWKGIRNKDSVSIDFTCWSLLKCKKRNNLMTPFNNKMTTETVQCTVCKRFSEIISETSNEKNFIKDASDAFRLIFCPSIFKTQKECSDFLSKDFKNLLQTLSSRIQQYYLCRIACPNKMTSI 1467 MSTIGCLLIFLSSIVALQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKSFQNFKAKSFPTFQECSTCNAFIELLIWNNHTETALSNLMKYTQETYCNLVKASKKQKCTIMINSKKSYILKFLRKMMTKELFCKIFLNCTNPSDQTLRNHFYDFLLNSKDVYPTEFFEFFYQKHNYPWNFSEYSMFNSLSSRQ+KSSHIYEFFQGFIKNLKPNRNNSLISYWDYKYFFEESNNINEIYSWKFFEHFFISHGKDEGFNFYYFFNNYIKNRFGKLSCQLCEIIGPFLLNNWFDKLTVSQQQILINPKTCKDFSNIKECYKTIEIIINYWKGIRNKDSVSIDFTCWSLLKCKKRNNLMTPFNNKMTTETVQCTVCKRFSEIISETSNEKNFIKDASDAFRLIFCPSIFKTQKECSDFLSKDFKNLLQTLSSRIQQYYLCRIACPNKMTSI Sbjct: 1 MSTIGCLLIFLSSIVALQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKSFQNFKAKSFPTFQECSTCNAFIELLIWNNHTETALSNLMKYTQETYCNLVKASKKQKCTIMINSKKSYILKFLRKMMTKELFCKIFLNCTNPSDQTLRNHFYDFLLNSKDVYPTEFFEFFYQKHNYPWNFSEYSMFNSLSSRQEKSSHIYEFFQGFIKNLKPNRNNSLISYWDYKYFFEESNNINEIYSWKFFEHFFISHGKDEGFNFYYFFNNYIKNRFGKLSCQLCEIIGPFLLNNWFDKLTVSQQQILINPKTCKDFSNIKECYKTIEIIINYWKGIRNKDSVSIDFTCWSLLKCKKRNNLMTPFNNKMTTETVQCTVCKRFSEIISETSNEKNFIKDASDAFRLIFCPSIFKTQKECSDFLSKDFKNLLQTLSSRIQQYYLCRIACPNKMTSI 447
BLAST of SMED30000214 vs. Planmine SMEST
Match: SMESG000000719.1 (SMESG000000719.1) HSP 1 Score: 155.992 bits (393), Expect = 6.771e-41 Identity = 125/487 (25.67%), Postives = 217/487 (44.56%), Query Frame = 1 Query: 142 CLLIFLSSIVALQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKSFQNFKAKSFPTFQECSTCNAFIELLIWNNHTETALSNLMKYTQETYCNLVKASKKQKCTIMINSKKSYILKFLRKMMTKELFCKIFLNCTNPSDQTLRNHFYDFLLNSKDVYPTEFFEFFYQKHNYPWNFSEYSMFNSLSSRQKKSSHIYEFFQGFIKNLKPNRNNSLISYWDYKYFF-------------------EESNNINEIYSWKFFEHFFIS-----HGKDEGXXXXXXXXXXIKNRFGKLSCQLCEIIGPFLLNNWFDKLTVSQQQILINPKTCKDFSNIK--ECYKTIEIIINYWKGIRNK--DSVSIDFTCWSLLKCKKRNNLMTPFNNKMTTE-------------TVQCTVCKRFSEIISETSNEKNFIKDASDAFRLIFCPSIF-KTQKECSDFLSKDFKNLLQTLSSRIQQYYLCRIAC---PNKMTSI 1467 C L+ LS+I ++D +Y +C + T P K FC+Y K + + FPT EC+ C F++ + WN+H+E A+ NL+KYT +C VK + +C +N + I +FL KMM FC++ L C+ ++F + + D Y FFE+F+ +Y +F Y FN + Q+ Y + + F +N P ++++ Y ++YFF + S+ ++ Y + FF+ FF + KD+ ++F C+ CE I W + + + ++L + SN+K E K E+I++ + I +K +S+ C + +C P N +M TE T QC VC + + S ++ F K + F++ +C +F K + EC FL + N+L + + + YLC + C PN + S+ Sbjct: 6 CSLLLLSAIQIQGSYD----FYSHYCSGSYYTDPSKVYFCQYVKGPSDMEKVPFPTGGECTACKEFLKRITWNSHSEEAVDNLLKYTTNHFCEDVKRTTSSECKTKLNEYRPKIKEFLVKMMKDSSFCEVLLKCSEKKGVLFMSYFSQYKPDWMDFYSMPFFEYFFNLKSYSHDFYPYHFFNYFYNYQETGFPSYTYLEHFYEN--PKNDSTMHPYRFFEYFFSNDSSKSTFFPFKFFEYFFKNSHYESDFYPYTFFQEFFSDEYYNYYSKDQKPT----------DKF----CKRCENIPAERFLKWANSIDI---KMLTDAGYIAMCSNMKSTEKEKCREMILHVGRVILHKLESVLSVKSICHQIYRC--------PMNIEMKTEDFTFYEKPHPKKPTKQCEVCSLITNVYSNAMDKDIFEKYVVEIFQMKYCNKLFPKKENECKKFLKNELPNILNKIRVSLHKNYLCNLTCNANPNSLWSM 461 The following BLAST results are available for this feature:
BLAST of SMED30000214 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30000214 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30000214 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30000214 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30000214 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30000214 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30000214 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30000214 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of SMED30000214 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30000214 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30000214 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30000214 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30000214 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30000214 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 >SMED30000214 ID=SMED30000214|Name=SMED30000214|organism=Schmidtea mediterranea sexual|type=transcript|length=1487bpback to top protein sequence of SMED30000214-orf-1 >SMED30000214-orf-1 ID=SMED30000214-orf-1|Name=SMED30000214-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=453bp MSTIGCLLIFLSSIVALQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKSback 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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