SMED30030201
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., 2020SMED30030201 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Alignments
SMED30030201 aligns in the following genomic locations:
Homology
BLAST of SMED30030201 vs. Planmine SMEST
Match: SMESG000030881.1 (SMESG000030881.1) HSP 1 Score: 370.163 bits (949), Expect = 1.914e-145 Identity = 196/211 (92.89%), Postives = 201/211 (95.26%), Query Frame = 1 Query: 1054 MQIQNNYKYPRNLNVSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRXXXXXXXXXXXXXXAVTVSATSKDLCQSNCGRIRWKKRIGVSDDVDLDSESICGDYKYPVLNDSAKITFSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNSYEF 1686 MQIQNNYKYPRNLNVSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRPTPPIGRKKPIPIKAVTVSATSKDLCQSNCG IR KKRIG SDDVDLDSESICGDYKYPVLNDSAKI+FSNIPM+KKSVSTN DDTYLVN D+ELSDL+F RPPQTI D+DYLHNLQ EVNSYEF Sbjct: 1 MQIQNNYKYPRNLNVSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRPTPPIGRKKPIPIKAVTVSATSKDLCQSNCGPIRSKKRIGFSDDVDLDSESICGDYKYPVLNDSAKISFSNIPMLKKSVSTNT-DDTYLVNNDEELSDLEFSFRPPQTINDDDYLHNLQKEVNSYEF 210 HSP 2 Score: 121.709 bits (304), Expect = 1.914e-145 Identity = 67/91 (73.63%), Postives = 75/91 (82.42%), Query Frame = 2 Query: 1820 NCENMSNRNAVVLISDNAIPTGFGKSNLLKTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDKKLPNYSTIESAIMNNDQKVK 2092 NCEN+SNRN VVLIS+NAIPT F KSNLL+T LENETT AEITLSNESRNI TAGF L QTPA+L ++D KL N++ I IMNNDQKVK Sbjct: 256 NCENISNRN-VVLISENAIPTSFDKSNLLRTLLENETTSAEITLSNESRNIVSTAGFDLTQTPASLTNTDLKLSNFN-ISPTIMNNDQKVK 344 HSP 3 Score: 67.0106 bits (162), Expect = 1.914e-145 Identity = 31/43 (72.09%), Postives = 36/43 (83.72%), Query Frame = 3 Query: 1692 EMSETEMNNYHQK*FASKNVNPKLSWKCSTCSSGNSNHSLECQ 1820 ++SE EMNNYHQK F SKN+N K+SWKCSTCSS NS SLEC+ Sbjct: 213 KISENEMNNYHQKLFGSKNINSKVSWKCSTCSSENSYDSLECK 255
BLAST of SMED30030201 vs. Planmine SMEST
Match: SMESG000003624.1 (SMESG000003624.1) HSP 1 Score: 261.922 bits (668), Expect = 3.551e-77 Identity = 149/183 (81.42%), Postives = 155/183 (84.70%), Query Frame = 1 Query: 1129 MAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRXXXXXXXXXXXXXXAVTVSATSKDLCQSNCGRIRWKKRIGVSDDVDLDSESICGDYKYPVLNDSAKITFSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS 1677 M IR++K +SSP K ILEKLDK TT ITEADKLA+ + SNPYSRP PPIGRKKPIPIKAVTVSATSKDLCQSNCGRIRWKKRIGVSDDVDLDSESI G+YKYPVLNDSAKITFSNIPMVKKSVSTN DTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS Sbjct: 1 MPIRYTKVVVSSPGKNILEKLDKFTTAITEADKLAASFL-------------TSNPYSRPPPPIGRKKPIPIKAVTVSATSKDLCQSNCGRIRWKKRIGVSDDVDLDSESIFGNYKYPVLNDSAKITFSNIPMVKKSVSTNTAGDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS 170 HSP 2 Score: 161.77 bits (408), Expect = 1.972e-41 Identity = 80/91 (87.91%), Postives = 83/91 (91.21%), Query Frame = 2 Query: 1814 MPNCENMSNRNAVVLISDNAIPTGFGKSNLLKTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDKKLPNYSTIESAIMNNDQK 2086 + N + N NAVVLISDNAIPTGFGKSNLL+TPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSD KLPNYSTIESAIMNND K Sbjct: 161 LHNLQGEVNSNAVVLISDNAIPTGFGKSNLLRTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDIKLPNYSTIESAIMNNDHK 251
BLAST of SMED30030201 vs. Planmine SMEST
Match: SMESG000002138.1 (SMESG000002138.1) HSP 1 Score: 199.904 bits (507), Expect = 1.113e-59 Identity = 101/113 (89.38%), Postives = 104/113 (92.04%), Query Frame = 2 Query: 1814 MPNCENMSNRNAVVLISDNAIPTGFGKSNLLKTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDKKLPNYSTIESAIMNNDQKVKIPNSQIFSTIQISSLVWSFG 2152 + N + N NAVVL SDNAIPTGFGKSNLL+TPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSD KLPNYSTIESAIMNNDQKVKIPNSQIFSTIQISSLVWS G Sbjct: 80 LHNLQGEVNSNAVVLKSDNAIPTGFGKSNLLRTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDIKLPNYSTIESAIMNNDQKVKIPNSQIFSTIQISSLVWSSG 192 HSP 2 Score: 157.918 bits (398), Expect = 2.726e-44 Identity = 74/75 (98.67%), Postives = 74/75 (98.67%), Query Frame = 1 Query: 1453 ESICGDYKYPVLNDSAKITFSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS 1677 ESICGDYKYPVLNDSAKI FSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS Sbjct: 15 ESICGDYKYPVLNDSAKINFSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS 89
BLAST of SMED30030201 vs. Planmine SMEST
Match: SMESG000004159.1 (SMESG000004159.1) HSP 1 Score: 167.162 bits (422), Expect = 7.551e-49 Identity = 83/91 (91.21%), Postives = 85/91 (93.41%), Query Frame = 2 Query: 1814 MPNCENMSNRNAVVLISDNAIPTGFGKSNLLKTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDKKLPNYSTIESAIMNNDQK 2086 MPNCENMSNRNAVVLI DNAIPTG GKSNLL+TPLENETTCAEI LSNESRNIAFTAGF LAQTPA+L DSD KLPNYSTIESAIMNNDQK Sbjct: 1 MPNCENMSNRNAVVLIFDNAIPTGLGKSNLLRTPLENETTCAEIALSNESRNIAFTAGFDLAQTPASLTDSDIKLPNYSTIESAIMNNDQK 91 The following BLAST results are available for this feature:
BLAST of SMED30030201 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30030201 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30030201 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30030201 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30030201 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30030201 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30030201 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30030201 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30030201 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30030201 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30030201 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30030201 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30030201 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30030201 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 4
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30030201 ID=SMED30030201|Name=SMED30030201|organism=Schmidtea mediterranea sexual|type=transcript|length=2177bpback to top protein sequence of SMED30030201-orf-1 >SMED30030201-orf-1 ID=SMED30030201-orf-1|Name=SMED30030201-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=215bp MQIQNNYKYPRNLNVSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLTback to top protein sequence of SMED30030201-orf-2 >SMED30030201-orf-2 ID=SMED30030201-orf-2|Name=SMED30030201-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=115bp MPNCENMSNRNAVVLISDNAIPTGFGKSNLLKTPLENETTCAEITLSNESback to top Annotated Terms
The following terms have been associated with this transcript:
|