SMED30009089
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., 2020SMED30009089 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30009089 aligns in the following genomic locations:
Homology
BLAST of SMED30009089 vs. Planmine SMEST
Match: SMESG000008022.1 (SMESG000008022.1) HSP 1 Score: 456.447 bits (1173), Expect = 3.095e-162 Identity = 240/242 (99.17%), Postives = 242/242 (100.00%), Query Frame = 3 Query: 294 MFSVPVRQRLLKSVFELQNESEKLMQTLRDADVIKNDDMKSPSPLDEXXXXXXXXXXXXXXXQNELRQGSDLKADVEIFETICRRRAVESIPENQRKFYNEVIQFASEEFIECYLVPFSDFNLTLPDFSAPNLRVAGRYHCLICSLKKRSTFAFKFRQDLKIQFTKIKKHLMEHFTVNPDASDIRKQSRNIKRKECRKRKIDNDCVILGQVPAKKFVQENKQKTAALLNEIMNGDIIEISSV 1019 MFSVPVRQRLLKSVFELQNESEKLMQTLRDADV+KNDDMKSPSPLDESDNVDDASDVVSVKSQNELRQGSDLKADVEIFETICRRRAVESIPENQRKFYNEVIQFASEEFIECYLVPFSDFNLTLPDFSAPNLRVAGRYHCLICSLKKRSTFAFKFRQDLKIQFTKIKKHLMEHFTVNPDASDIRKQSRNIKRKECRKRKIDNDCVILGQVPAKKFVQENKQKTAALLNEIMNGDIIEISS+ Sbjct: 1 MFSVPVRQRLLKSVFELQNESEKLMQTLRDADVLKNDDMKSPSPLDESDNVDDASDVVSVKSQNELRQGSDLKADVEIFETICRRRAVESIPENQRKFYNEVIQFASEEFIECYLVPFSDFNLTLPDFSAPNLRVAGRYHCLICSLKKRSTFAFKFRQDLKIQFTKIKKHLMEHFTVNPDASDIRKQSRNIKRKECRKRKIDNDCVILGQVPAKKFVQENKQKTAALLNEIMNGDIIEISSL 242
BLAST of SMED30009089 vs. Planmine SMEST
Match: SMESG000047524.1 (SMESG000047524.1) HSP 1 Score: 93.9745 bits (232), Expect = 2.601e-21 Identity = 64/240 (26.67%), Postives = 126/240 (52.50%), Query Frame = 3 Query: 120 MISCLRLSGFNSFIDYTIFNETTVLWIEKYVGIRCSLLPPEERLTFIDGEFINSPETYMFSVPVRQRLLKSVFELQNESEKLMQTLRDADVIKNDDMKSPSPLDEXXXXXXXXXXXXXXXQNELRQG----SDLKADVEIFET-ICRRRAVESIPENQRKFYNEVIQFASEEFIECYLVPFSDFNLTLPDFSAPNLRVAGRYHCLICSLKKRSTFAFKFR--QDLKIQFTKIKKHLMEHF 818 ++SCL ++ D+ F+ T V +E Y+ R S++ +R+ ++ GEFI+ PE +MF+ +R RLLK+ + + + ++++M S + + ++ ++ +N L + S L + + E + R R ++ N K+YN++++ A++ FIEC L+P DF+L++P+ + +L G YHC +C+ +K++ KFR + + +T I HL H+ Sbjct: 30 VLSCLEIAELLEPDDFINFSHTNVDILENYIRCRTSVMEINDRIPYLSGEFIHFPEKFMFTPGMRNRLLKAAKLISKDVYAAVFESNQTSDCESNEMSCDSNNNSTTPMNKLQPQNNISIENSLIENQFLLSPLNSSIIKQELDMNRSRHLQ----NMEKYYNDIVKNAAKNFIECSLIPDVDFHLSIPENDSTDL--IGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHY 263
BLAST of SMED30009089 vs. Planmine SMEST
Match: SMESG000047524.1 (SMESG000047524.1) HSP 1 Score: 93.5893 bits (231), Expect = 2.782e-21 Identity = 64/240 (26.67%), Postives = 126/240 (52.50%), Query Frame = 3 Query: 120 MISCLRLSGFNSFIDYTIFNETTVLWIEKYVGIRCSLLPPEERLTFIDGEFINSPETYMFSVPVRQRLLKSVFELQNESEKLMQTLRDADVIKNDDMKSPSPLDEXXXXXXXXXXXXXXXQNELRQG----SDLKADVEIFET-ICRRRAVESIPENQRKFYNEVIQFASEEFIECYLVPFSDFNLTLPDFSAPNLRVAGRYHCLICSLKKRSTFAFKFR--QDLKIQFTKIKKHLMEHF 818 ++SCL ++ D+ F+ T V +E Y+ R S++ +R+ ++ GEFI+ PE +MF+ +R RLLK+ + + + ++++M S + + ++ ++ +N L + S L + + E + R R ++ N K+YN++++ A++ FIEC L+P DF+L++P+ + +L G YHC +C+ +K++ KFR + + +T I HL H+ Sbjct: 18 VLSCLEIAELLEPDDFINFSHTNVDILENYIRCRTSVMEINDRIPYLSGEFIHFPEKFMFTPGMRNRLLKAAKLISKDVYAAVFESNQTSDCESNEMSCDSNNNSTTPMNKLQPQNNISIENSLIENQFLLSPLNSSIIKQELDMNRSRHLQ----NMEKYYNDIVKNAAKNFIECSLIPDVDFHLSIPENDSTDL--IGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHY 251
BLAST of SMED30009089 vs. Planmine SMEST
Match: SMESG000072339.1 (SMESG000072339.1) HSP 1 Score: 68.5514 bits (166), Expect = 1.286e-12 Identity = 73/284 (25.70%), Postives = 129/284 (45.42%), Query Frame = 3 Query: 69 IDIEDVENHILTNTNQKMISCLRLSGFNSFIDYTIFNETTVLWIEKYVGIRCSLLPPEERLTFIDGEFINSPETYMFSVPVRQRLLKSVFELQNE----SEKLMQTLRDADVIKND------DMKSPSPLD---------EXXXXXXXXXXXXXXXQNELRQGSDL----------KADVEIFETICR-----RRAVESIPENQRKFYNEVIQFASEEFIECYLVPFSDFNLTLPDFSAPNLRVAGRYHCLICSLKKRSTFAFKFRQDLKIQFTKIKKHLMEHF 818 I+I D N++ ++ K + +L FN+ D FN+T++ +E+Y+ ++CSL+ ER ++DG+ I +P+ +M S +R R+ K+V + N S L Q L + + I +K+ PL +S N + S+N L S L K+ ++ I R ++ +E + EN FY+ + F C+L+P DF++ + + + N + + Y+ +C+L F +DLK T IK H HF Sbjct: 3 INIFDALNYLTGSS--KTSARFKLCDFNTITDLLSFNDTSIDKMEEYIQLQCSLMDLAERSIYLDGDDIQNPKCFMISPGLRNRICKAVSTIVNSMNGASLSLSQKLLNHNFIDYGFKDNIVSVKNIKPLSITDNMFMNQKSFNSTNIQTKALATSKNNLANISKLYTPINSKKIVKSSNKLDNPIARGKKVDQKLIELVTEN---FYHTIANDQPLNFDNCHLIPKKDFDIKI-NLNYKNFQNSKFYY--VCNLCNGKLVKFNLNKDLKPIQTGIKSHNRTHF 278
BLAST of SMED30009089 vs. Planmine SMEST
Match: SMESG000072330.1 (SMESG000072330.1) HSP 1 Score: 60.8474 bits (146), Expect = 3.072e-10 Identity = 76/261 (29.12%), Postives = 114/261 (43.68%), Query Frame = 3 Query: 117 KMISCLRLSGFNSFIDYTIFNETTVLWIEKYVGIRCSLLPPEERLTFIDGEFINSPETYMFSVPVRQRLLKSV------FE---LQNESEK-------LMQTLRDADVIKNDD---MKSPSPLDEXXXXXXXXXXXXXXXQNELRQGSDLKADVEIFET----IC-----RRRAVESIPENQRKFYNEVIQFASEEFIECYLVPFSDFNLTLPDFSAPNLRVAGRYHCLICSLKKRSTFAFKFRQDLKIQFTKIKKHLMEH 815 K+ + L L F D+ FN TV IEKY+ I+CSL+P R +++ + SP ++ S +R RLLK+V FE L N K L Q L + D N + M S + LD S+N S +S N Q ++ +E+ IC + V N +++ + ++ E ++ LVP +F+L S G Y C C+ KK FKF LK+ + IK HL +H Sbjct: 17 KVANWLELCKFELMDDFLNFNNNTVDKIEKYIQIQCSLMPINVRQLYLNESDLLSPTKFLISPGLRNRLLKAVDILVSYFEINSLNNSIHKSFCMENMLYQKLSETDSGNNTNNNLMFSANILDISENDSRISAPKHYESTNS-SQTLGYESTLEVINNNDSEICLANQSKDLQVGEFKINIDQYFEDFVEVLKRE-LDFNLVPKENFDLEFHFNSDSISNSYGNYICYYCNKKK---LKFKFTAMLKVVYGNIKSHLKKH 272 The following BLAST results are available for this feature:
BLAST of SMED30009089 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30009089 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30009089 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30009089 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30009089 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30009089 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30009089 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30009089 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30009089 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30009089 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30009089 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30009089 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30009089 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30009089 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 >SMED30009089 ID=SMED30009089|Name=SMED30009089|organism=Schmidtea mediterranea sexual|type=transcript|length=1252bpback to top protein sequence of SMED30009089-orf-1 >SMED30009089-orf-1 ID=SMED30009089-orf-1|Name=SMED30009089-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=393bp MIDIEDVENHILTNTNQKMISCLRLSGFNSFIDYTIFNETTVLWIEKYVGback to top Annotated Terms
The following terms have been associated with this transcript:
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