SMED30005997
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., 2020SMED30005997 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 9
Alignments
SMED30005997 aligns in the following genomic locations:
Homology
BLAST of SMED30005997 vs. Ensembl Sea Lamprey
Match: rbm4.2 (RNA binding motif protein 4.2 [Source:ZFIN;Acc:ZDB-GENE-030131-3019]) HSP 1 Score: 46.595 bits (109), Expect = 1.059e-6 Identity = 21/67 (31.34%), Postives = 34/67 (50.75%), Query Frame = 1 Query: 82 NLIVQGIPPSTTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKILNTMRNLYMSGRRIFVEL 282 + V + P T+ +L F+ FGPV + +++D +VHM DD + + GRRI V+L Sbjct: 79 KMYVGNVTPDCTNVELRAKFEEFGPVAECDIVKDYAFVHMEREDDARAAIRALDGSEFKGRRILVQL 145
BLAST of SMED30005997 vs. Ensembl Sea Lamprey
Match: syncripl (synaptotagmin binding, cytoplasmic RNA interacting protein, like [Source:ZFIN;Acc:ZDB-GENE-030131-3104]) HSP 1 Score: 45.4394 bits (106), Expect = 5.303e-6 Identity = 21/70 (30.00%), Postives = 37/70 (52.86%), Query Frame = 1 Query: 73 QVMNLIVQGIPPSTTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKILNTMRNLYMSGRRIFVEL 282 +V L V+ + + T L D F VFG +E+ ++D +VH +RDD +K ++ M + G + + L Sbjct: 344 KVKVLFVRNLASAVTEEILQDTFSVFGKLERVKKLKDYAFVHFEDRDDAVKAMDEMNGKPLEGEPLVIVL 413
BLAST of SMED30005997 vs. Planmine SMEST
Match: SMESG000050405.1 (SMESG000050405.1) HSP 1 Score: 365.925 bits (938), Expect = 1.673e-130 Identity = 178/179 (99.44%), Postives = 178/179 (99.44%), Query Frame = 1 Query: 79 MNLIVQGIPPSTTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKILNTMRNLYMSGRRIFVELDSGMGMNREREQMPYHEPMPNPYSGWTEIPRDVGHSYDYGMPQERFSKTDVDPWKQVIPEQNLNGSRSDERLITESYVYVDPHGYSRDPTMRPAPEYYYRIKLLDSKSKHP 615 MNLIVQGIPP TTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKILNTMRNLYMSGRRIFVELDSGMGMNREREQMPYHEPMPNPYSGWTEIPRDVGHSYDYGMPQERFSKTDVDPWKQVIPEQNLNGSRSDERLITESYVYVDPHGYSRDPTMRPAPEYYYRIKLLDSKSKHP Sbjct: 1 MNLIVQGIPPLTTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKILNTMRNLYMSGRRIFVELDSGMGMNREREQMPYHEPMPNPYSGWTEIPRDVGHSYDYGMPQERFSKTDVDPWKQVIPEQNLNGSRSDERLITESYVYVDPHGYSRDPTMRPAPEYYYRIKLLDSKSKHP 179 The following BLAST results are available for this feature:
BLAST of SMED30005997 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30005997 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30005997 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30005997 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30005997 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30005997 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30005997 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30005997 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30005997 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30005997 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 2
BLAST of SMED30005997 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30005997 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30005997 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30005997 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 1
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30005997 ID=SMED30005997|Name=SMED30005997|organism=Schmidtea mediterranea sexual|type=transcript|length=705bpback to top protein sequence of SMED30005997-orf-1 >SMED30005997-orf-1 ID=SMED30005997-orf-1|Name=SMED30005997-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=180bp MNLIVQGIPPSTTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKIback 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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