SMED30001640
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., 2020SMED30001640 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 10
Alignments
SMED30001640 aligns in the following genomic locations:
Homology
BLAST of SMED30001640 vs. TrEMBL
Match: A0A2H1CCY5 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_004900 PE=4 SV=1) HSP 1 Score: 54.6842 bits (130), Expect = 3.251e-6 Identity = 41/116 (35.34%), Postives = 54/116 (46.55%), Query Frame = 2 Query: 203 LLFFVIAITDLQLGHAQLINCYVCIGCPNPF--VISGAMTSPNCSSCMT------TTALTVISKTCITGTCVTISGIAGTSN-----TCCSTNLCNTGSEFKVPIAVVIGLPVLAS 511 LL+F I D Q I CY C+ CP PF + +G +C C T T ALT +TC+T T I+ + GT+ CC N CN GS K P V+ + VL + Sbjct: 19 LLYFCALIVDAQ------ITCYECMNCPRPFSTIGTGVSLKKDCKYCRTEDMYNKTGALTSSKRTCVTNTDSCINSLNGTNEGVTEIGCCRWNACNMGSRMK-PTMVIASVLVLGA 127
BLAST of SMED30001640 vs. Planmine SMEST
Match: SMESG000031270.1 (SMESG000031270.1) HSP 1 Score: 154.836 bits (390), Expect = 6.205e-49 Identity = 83/114 (72.81%), Postives = 93/114 (81.58%), Query Frame = 2 Query: 188 MISKLLLFFVIAITDLQLGHAQLINCYVCIGCPNPFVISGAMTS-PNCSSCMTTTALTVISKTCITGTCVTISGIAGTSNTCCSTNLCNTGSEFKVPIAVVIGLPVLASLLRAY 526 MISKLLLFFVIAITDLQLGH QLINCY C+GC NPFVIS A+T+ S TT+AL +++KTC + TC TI+ G +N CCSTNLCNTGSEFKVPIAVVIGLPVLASL RAY Sbjct: 1 MISKLLLFFVIAITDLQLGHTQLINCYACVGCSNPFVISSALTATNCSSCTTTTSALNIVTKTCASITCNTITSYIGATNICCSTNLCNTGSEFKVPIAVVIGLPVLASLFRAY 114
BLAST of SMED30001640 vs. Planmine SMEST
Match: SMESG000007247.1 (SMESG000007247.1) HSP 1 Score: 127.872 bits (320), Expect = 6.582e-39 Identity = 64/67 (95.52%), Postives = 65/67 (97.01%), Query Frame = 2 Query: 188 MISKLLLFFVIAITDLQLGHAQLINCYVCIGCPNPFVISGAMTSPNCSSCMTTTALTVISKTCITGT 388 MISKLLLFFVIAITDLQLGHAQLINCYVC GCPNPF+ISGAMTS NCSSCMTTTALTVISKTCITGT Sbjct: 1 MISKLLLFFVIAITDLQLGHAQLINCYVCAGCPNPFIISGAMTSTNCSSCMTTTALTVISKTCITGT 67
BLAST of SMED30001640 vs. Planmine SMEST
Match: SMESG000031234.1 (SMESG000031234.1) HSP 1 Score: 129.028 bits (323), Expect = 7.299e-39 Identity = 74/101 (73.27%), Postives = 85/101 (84.16%), Query Frame = 2 Query: 227 TDLQLGHAQLINCYVCIGCPNPFVISGAMTSPNCSSCMTTT-ALTVISKTCITGTCVTISGIAGTSNTCCSTNLCNTGSEFKVPIAVVIGLPVLASLLRAY 526 +DLQLGH+QLINCY C+GC NPFVIS A+T+ NCSSC TTT AL +++KTC + TC TI+ G +N CCSTNLCNTGSEFKVPIAVVIGLPVLASL RAY Sbjct: 12 SDLQLGHSQLINCYACVGCSNPFVISSALTATNCSSCTTTTSALNIVTKTCASITCNTITSFIGPTNICCSTNLCNTGSEFKVPIAVVIGLPVLASLFRAY 112
BLAST of SMED30001640 vs. Planmine SMEST
Match: SMESG000007344.1 (SMESG000007344.1) HSP 1 Score: 88.1965 bits (217), Expect = 8.714e-23 Identity = 46/107 (42.99%), Postives = 59/107 (55.14%), Query Frame = 2 Query: 188 MISKLLLFFVIAITDLQLGHAQLINCYVCIGCPNPFVISGAMTSPNCSSCMTTTALTVISKTCITGTCVTISGIAGTSNTCCSTNLCNTGSEFKVPIAVVIGLPVLA 508 M K L AI Q AQ I+CY C GCP PFV +G T NC+SC+ T L +++K+C G C I G S +CC+TNLCN G F V A ++ +LA Sbjct: 1 MAFKFLFLLAFAIAHFQQNSAQTISCYTCFGCPVPFVTAGITTFSNCTSCLKMTTLNIVTKSCNPGACGANIDITGVSTSCCNTNLCNVGQRFTVQRAGIVIAMMLA 107
BLAST of SMED30001640 vs. Planmine SMEST
Match: SMESG000028039.1 (SMESG000028039.1) HSP 1 Score: 75.8702 bits (185), Expect = 3.999e-18 Identity = 40/109 (36.70%), Postives = 60/109 (55.05%), Query Frame = 2 Query: 188 MISKLLLFFVIAITDLQLGHAQLINCYVCIGCPNPFVISGAMTSPNCSSCMTTTALTVISKTCITGTCVTISGIAGTSNTCCSTNLCNTGSEFKVPIAVVIGLPVLASL 514 M K + IA+ + + Q INCY C+GCPNPFV S A+ NC+SC TTT ++I+KT + + + + G S CC+TNLCN G I + ++ ++ Sbjct: 1 MTIKFIFLLTIALASIHQNYGQTINCYTCVGCPNPFVASSAIVITNCTSCYTTTLYSIITKT-CSLASCSSASVLGASVACCNTNLCNKGHWLTASTGGFISVALMVTM 108 The following BLAST results are available for this feature:
BLAST of SMED30001640 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30001640 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30001640 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30001640 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30001640 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30001640 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30001640 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30001640 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of SMED30001640 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30001640 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30001640 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30001640 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30001640 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30001640 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 >SMED30001640 ID=SMED30001640|Name=SMED30001640|organism=Schmidtea mediterranea sexual|type=transcript|length=544bpback to top protein sequence of SMED30001640-orf-1 >SMED30001640-orf-1 ID=SMED30001640-orf-1|Name=SMED30001640-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp MISKLLLFFVIAITDLQLGHAQLINCYVCIGCPNPFVISGAMTSPNCSSCback 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
|