SMED30024165
Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ 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 AppSub-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., 2020SMED30024165 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 10
Alignments
SMED30024165 aligns in the following genomic locations:
Homology
BLAST of SMED30024165 vs. Planmine SMEST
Match: SMESG000029095.1 (SMESG000029095.1) HSP 1 Score: 117.472 bits (293), Expect = 1.008e-34 Identity = 55/99 (55.56%), Postives = 68/99 (68.69%), Query Frame = 2 Query: 59 MNTFSLVALFIVINYCQSSKTPERCSTKLAPAAKSCDLKYADLSDFCKDGYATINKVCKGVDTLNCAVKYKSFDVECSERKDIFWRLCGPIYKTYQALC 355 M+ SL A+ ++ YC S E+C +L PAAK CD KYA+ +FC GYA INKVCKGVDT+ CA+KYK F C ER+D FW+ CGP+YK YQ LC Sbjct: 1 MSRISLFAIVYLVAYCHCS---EQCDRELVPAAKDCDRKYAETDNFCNGGYAKINKVCKGVDTIECALKYKKFGEACRERQDYFWKNCGPVYKIYQTLC 96
BLAST of SMED30024165 vs. Planmine SMEST
Match: SMESG000020501.1 (SMESG000020501.1) HSP 1 Score: 111.694 bits (278), Expect = 2.500e-32 Identity = 54/100 (54.00%), Postives = 66/100 (66.00%), Query Frame = 2 Query: 59 MNTFSLVALFIVINYCQSSKTPERCSTKLAPAAKSCDLKYADLSDFCKDGYATINKVCKGVDTLNCAVKYKSFDVECSERKDIFWRLCGPIYKTYQALCG 358 M+ S+ AL VI YC S RC +LAPAAK CD KYA+ FC GYA INKVCKGVDT+ C ++YK F V+C ER++ FW C +YKTYQ +C Sbjct: 1 MSKLSIFALLFVIAYCHCSP---RCDLELAPAAKRCDKKYAETDAFCNGGYAAINKVCKGVDTIECGLEYKRFAVKCKERQNNFWNDCDQVYKTYQTVCA 97
BLAST of SMED30024165 vs. Planmine SMEST
Match: SMESG000028420.1 (SMESG000028420.1) HSP 1 Score: 98.2117 bits (243), Expect = 5.442e-27 Identity = 46/103 (44.66%), Postives = 64/103 (62.14%), Query Frame = 2 Query: 59 MNTFSLVALFIVINYCQSSK---TPERCSTKLAPAAKSCDLKYADLSDFCKDGYATINKVCKGVDTLNCAVKYKSFDVECSERKDIFWRLCGPIYKTYQALCG 358 MN S+ ALF V+ S+K +PE+C L PAAK CD +Y + FC GY I+K CKG D++ C V+Y +C+E++D FW++CGP+YKTY C Sbjct: 1 MNKISVYALFAVVVIVNSTKWVPSPEKCLKILTPAAKGCDSRYTETDLFCSVGYKHIDKSCKGHDSVECGVQYAKHKDDCTEKQDYFWKVCGPVYKTYSDECA 103
BLAST of SMED30024165 vs. Planmine SMEST
Match: SMESG000061767.1 (SMESG000061767.1) HSP 1 Score: 87.4261 bits (215), Expect = 1.380e-22 Identity = 41/105 (39.05%), Postives = 58/105 (55.24%), Query Frame = 2 Query: 59 MNTFSLVALFIVINYCQSSK---TPERCSTKLAPAAKSCDLKYADLSDFCKDGYATINKVCKGVDTLNCAVKYKSFDVECSERKDIFWRLCGPIYKTYQALCGIP 364 M S+ F+ + S+K RCS L PAA+ CD KY + +FC GY INK CKG +T++C ++ D +C E++DIFW LC +Y Y+ C P Sbjct: 1 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASP 105
BLAST of SMED30024165 vs. Planmine SMEST
Match: SMESG000022139.1 (SMESG000022139.1) HSP 1 Score: 84.7297 bits (208), Expect = 9.368e-22 Identity = 41/106 (38.68%), Postives = 57/106 (53.77%), Query Frame = 2 Query: 59 MNTFSLVA--LFIVINYCQSSKTPE-RCSTKLAPAAKSCDLKYADLSDFCKDGYATINKVCKGVDTLNCAVKYKSFDVECSERKDIFWRLCGPIYKTYQALCGIPS 367 M FS++A +F+ + P RC L PA+K CD Y + +FC G+A +NKVC G DT+ C YK+F C E++D FW C P+Y Y+ C P Sbjct: 1 MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTTLCKEKQDNFWDECDPVYTAYRKECATPE 106 The following BLAST results are available for this feature:
BLAST of SMED30024165 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30024165 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30024165 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30024165 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30024165 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30024165 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30024165 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30024165 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30024165 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30024165 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30024165 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30024165 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30024165 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30024165 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 >SMED30024165 ID=SMED30024165|Name=SMED30024165|organism=Schmidtea mediterranea sexual|type=transcript|length=467bpback to top protein sequence of SMED30024165-orf-1 >SMED30024165-orf-1 ID=SMED30024165-orf-1|Name=SMED30024165-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp FIIKKTIYFYFNYKPHFEKMNTFSLVALFIVINYCQSSKTPERCSTKLAPback to top Annotated Terms
The following terms have been associated with this transcript:
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