SMED30023907
Overview
Neoblast Clusters
Zeng et. al., 2018
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 AppEmbryonic 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., 2020SMED30023907 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 8
Homology
BLAST of SMED30023907 vs. Planmine SMEST
Match: SMESG000042253.1 (SMESG000042253.1) HSP 1 Score: 138.272 bits (347), Expect = 8.797e-41 Identity = 65/67 (97.01%), Postives = 65/67 (97.01%), Query Frame = -1 Query: 108 VCPNYGVSHKLDDPVLSDIKAPINVMLQRHLIRAPTFERIELQHWDGEHPYSIRRPTGEAGIQRSGY 308 VCPNYGVSHKLDDPVLSDIKA INVMLQRHLIRAPTFERIELQHWDGEHPYSIRRPTGEA IQRSGY Sbjct: 18 VCPNYGVSHKLDDPVLSDIKASINVMLQRHLIRAPTFERIELQHWDGEHPYSIRRPTGEAVIQRSGY 84
BLAST of SMED30023907 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1) HSP 1 Score: 79.337 bits (194), Expect = 5.720e-16 Identity = 61/188 (32.45%), Postives = 89/188 (47.34%), Query Frame = -1 Query: 141 RDPRTMDGFWNDDSRVTVRFPTDATRRYEIQVI-------------S*QR*ESPDGQDENELPSVEIKRETGRNPAREARQHLGQAERSERQNQMENQHSTELTQLDKC*HRHRMHAQYRRVC-----------PNYGVSHKLDDPVLSDIKAPINVMLQRHLIRAPTFERIELQHWDGEHPYSIRRP 632 RDP G W+D+SRVT+ P+ + RY QV+ S R S +E ELPS+ IKRE G NPAREARQ A + + ++E ++ + R R+ R + P YGVS +LDDP L+ + AP +++ L+++ T H G+H Y+ R P Sbjct: 1640 RDPH---GSWSDNSRVTLEIPSASAARYR-QVLWDNGYLLSTYGDSSWPR-RSEYQAEEIELPSIAIKREPGHNPAREARQRAKYA--AMKMEELERKYHRKAVSA-----RQRLAQVNRDIASGSIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVQS-TLRNQLGSHQTGDHTYASRHP 1814
BLAST of SMED30023907 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1) HSP 1 Score: 77.411 bits (189), Expect = 2.837e-15 Identity = 63/195 (32.31%), Postives = 94/195 (48.21%), Query Frame = -1 Query: 141 PFLDGTRDPRTMDGFWNDDSRVTVRFPTDATRRYEIQVI-------------S*QR*ESPDGQDENELPSVEIKRETGRNPAREARQHLGQAER-SERQNQMENQHSTELTQLDKC*HRHRMHAQYRRVC-----------PNYGVSHKLDDPVLSDIKAPINVMLQRHLIRAPTFERIELQHWDGEHPYSIRRP 650 P D RDP G W+D+SRVT++ P+ + RY QV+ S R S +E ELPS+ IKRE G NPAREARQ +AE + + ++E ++ + R R+ R + P YGVS +LDDP L + AP +++ L+++ R+ + G+H Y+ R P Sbjct: 1124 PSNDNRRDPH---GNWSDNSRVTLQIPSASAARYR-QVLWDNGYLLSTYGDSSWPR-RSEYQAEEIELPSIAIKREPGHNPAREARQ---RAEYVAMKMEELERKYHRKAVLA-----RQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQ-TGDHTYASRHP 1304
BLAST of SMED30023907 vs. Planmine SMEST
Match: SMESG000004883.1 (SMESG000004883.1) HSP 1 Score: 72.0182 bits (175), Expect = 3.163e-14 Identity = 62/187 (33.16%), Postives = 87/187 (46.52%), Query Frame = -1 Query: 141 RDPRTMDGFWNDDSRVTVRFPTDATRRYEIQVI------------S*QR*ESPDGQDENELPSVEIKRETGRNPAREARQHLGQAERSERQNQMENQHSTELTQLDKC*HRHRMHAQYRRVC-----------PNYGVSHKLDDPVLSDIKAPINVMLQRHLIRAPTFERIELQHWDGEHPYSIRRP 632 RDP G W+D+SRVT++ P+ + RY QV+ S S +E ELPSV IKRE G NPAREARQ A + + + + Q L R R+ R + P YGVS +LDDP L+ + AP +++ L+R+ R+ G+H Y+ R P Sbjct: 83 RDPH---GSWSDNSRVTLQIPSASAARYR-QVLWDNGYLLSTYGDSSWPRRSEYQAEEVELPSVAIKREPGHNPAREARQRAEYAAMKKEELERKYQRKAVLA-------RQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVRSTLRNRLGSSQ-TGDHTYASRHP 257
BLAST of SMED30023907 vs. Planmine SMEST
Match: SMESG000014849.1 (SMESG000014849.1) HSP 1 Score: 73.1738 bits (178), Expect = 6.121e-14 Identity = 54/166 (32.53%), Postives = 81/166 (48.80%), Query Frame = -1 Query: 207 RDPRTMDGFWNDDSRVTVRFPTDATRRYEIQVI-------------S*QR*ESPDGQDENELPSVEIKRETGRNPAREARQHLGQAERSERQNQMENQHSTELTQLDKC*HRHRMHAQYRRVC-----------PNYGVSHKLDDPVLSDIKAPINVMLQRHLIRA 632 RDP G W+D+SRVT++ P+ + RY QV+ S R S +E ELPS+ IKRE G NPAREARQ A + + ++E ++ + R R+ R + P YGVS +LDDP L+ + AP +++ L+++ Sbjct: 877 RDPH---GNWSDNSRVTLQIPSASAARYR-QVLWDNGYLLSTYGDSSWPR-RSEYRAEEIELPSIAIKREPGHNPAREARQRAEYA--AMKMEELERKYHRKAVLA-----RQRLAQVNRDIASGVIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVQS 1030 The following BLAST results are available for this feature:
BLAST of SMED30023907 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30023907 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30023907 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30023907 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30023907 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30023907 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30023907 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30023907 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30023907 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30023907 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30023907 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30023907 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30023907 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30023907 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 >SMED30023907 ID=SMED30023907|Name=SMED30023907|organism=Schmidtea mediterranea sexual|type=transcript|length=998bpback 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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