SMED30008507
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., 2020SMED30008507 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30008507 aligns in the following genomic locations:
Homology
BLAST of SMED30008507 vs. Planmine SMEST
Match: SMESG000008335.1 (SMESG000008335.1) HSP 1 Score: 378.637 bits (971), Expect = 5.433e-117 Identity = 181/186 (97.31%), Postives = 182/186 (97.85%), Query Frame = 2 Query: 2003 RSEIQWRDMERTTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQLERKYRYLANQKRRRLARINEDITNGHIPSSDDHLPSYRVAYDPRDPALLELDAPVHLVFPKLLLQPDIKDILEDRGTEEHVYSRRRLSRKETTNLAKN 2560 RSEIQWRDME TTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQLERKYRYLANQKRRRLARINEDITNGHIPSSD HLPSYRVA+DP DPALLELDAPVHLVFPKLLLQPDIKDILEDR TEEHVYSRRRLSRKETTNLAKN Sbjct: 88 RSEIQWRDMESTTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQLERKYRYLANQKRRRLARINEDITNGHIPSSDGHLPSYRVAHDPSDPALLELDAPVHLVFPKLLLQPDIKDILEDRVTEEHVYSRRRLSRKETTNLAKN 273 HSP 2 Score: 159.073 bits (401), Expect = 5.568e-40 Identity = 75/75 (100.00%), Postives = 75/75 (100.00%), Query Frame = 2 Query: 1160 MRSENINTNQKRPPISKNHMSCESPRHIKSVLGDITSIFIMNESMRHSAKSYATEEPKEDIMDKSRGFIMEDGGE 1384 MRSENINTNQKRPPISKNHMSCESPRHIKSVLGDITSIFIMNESMRHSAKSYATEEPKEDIMDKSRGFIMEDGGE Sbjct: 1 MRSENINTNQKRPPISKNHMSCESPRHIKSVLGDITSIFIMNESMRHSAKSYATEEPKEDIMDKSRGFIMEDGGE 75 HSP 3 Score: 90.1225 bits (222), Expect = 4.643e-18 Identity = 42/44 (95.45%), Postives = 43/44 (97.73%), Query Frame = 3 Query: 2781 AMNAIKWIGSEKKLRRENNGLHQQCIQLSRELQRIKATWVEPSQ 2912 +MNAIKWIGSEKKLRRENNGLHQQCIQLSRELQ IKATWVEPSQ Sbjct: 274 SMNAIKWIGSEKKLRRENNGLHQQCIQLSRELQWIKATWVEPSQ 317
BLAST of SMED30008507 vs. Planmine SMEST
Match: SMESG000054252.1 (SMESG000054252.1) HSP 1 Score: 240.35 bits (612), Expect = 1.507e-72 Identity = 116/177 (65.54%), Postives = 141/177 (79.66%), Query Frame = 2 Query: 2000 GRSEIQWRDMERTTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQLERKYRYLANQKRRRLARINEDITNGHIPSSDDHLPSYRVAYDPRDPALLELDAPVHLVFPKLLLQPDIKDILEDRGTEEHVYSRRRLS 2530 G W+D++ TTLTVP+ FAGRY QALW+ GYTIST+GTP+WP R++N + D ELPS++IKREPGRNP REIRQ+ EG L+R EQLE +YR+L +++ LARIN DI +G IPSSD HLP+Y +AYD RDPALLE DA VHLV PK LLQPDI+DILED+G E H YSRRRL+ Sbjct: 13 GTHSGNWKDVDLTTLTVPTLFAGRYTQALWNLGYTISTYGTPKWPYRKTNGPEGDFELPSILIKREPGRNPTREIRQKAEGELHRLEQLEWRYRFLVKRQKEHLARINRDIASGRIPSSDMHLPAYGIAYDHRDPALLEGDALVHLVVPKSLLQPDIRDILEDQGVEAHAYSRRRLT 189
BLAST of SMED30008507 vs. Planmine SMEST
Match: SMESG000054252.1 (SMESG000054252.1) HSP 1 Score: 242.276 bits (617), Expect = 2.457e-71 Identity = 116/177 (65.54%), Postives = 141/177 (79.66%), Query Frame = 2 Query: 2000 GRSEIQWRDMERTTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQLERKYRYLANQKRRRLARINEDITNGHIPSSDDHLPSYRVAYDPRDPALLELDAPVHLVFPKLLLQPDIKDILEDRGTEEHVYSRRRLS 2530 G W+D++ TTLTVP+ FAGRY QALW+ GYTIST+GTP+WP R++N + D ELPS++IKREPGRNP REIRQ+ EG L+R EQLE +YR+L +++ LARIN DI +G IPSSD HLP+Y +AYD RDPALLE DA VHLV PK LLQPDI+DILED+G E H YSRRRL+ Sbjct: 13 GTHSGNWKDVDLTTLTVPTLFAGRYTQALWNLGYTISTYGTPKWPYRKTNGPEGDFELPSILIKREPGRNPTREIRQKAEGELHRLEQLEWRYRFLVKRQKEHLARINRDIASGRIPSSDMHLPAYGIAYDHRDPALLEGDALVHLVVPKSLLQPDIRDILEDQGVEAHAYSRRRLT 189
BLAST of SMED30008507 vs. Planmine SMEST
Match: SMESG000047667.1 (SMESG000047667.1) HSP 1 Score: 261.151 bits (666), Expect = 6.745e-71 Identity = 126/180 (70.00%), Postives = 148/180 (82.22%), Query Frame = 2 Query: 2000 GRSEIQWRDMERTTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQLERKYRYLANQKRRRLARINEDITNGHIPSSDDHLPSYRVAYDPRDPALLELDAPVHLVFPKLLLQPDIKDILEDRGTEEHVYSRRRLSRKE 2539 G S + RD+ERTTLTVPS+FAGRYRQALWD+GY+IST+GTPEWPNR + DED +LPSLVIKREPGRNPAREIRQE+E LY+ EQLER+YR LANQ+ RRL +I DI++G IP SD +LP Y VAYDP++PALL LDAPV+LV PK LLQPDI+D L D+G EEH YS R L RK+ Sbjct: 1560 GSSSSKCRDVERTTLTVPSKFAGRYRQALWDRGYSISTYGTPEWPNRNPDRRDEDIKLPSLVIKREPGRNPAREIRQESEEALYKLEQLERRYRRLANQQGRRLVKITMDISSGRIPISDGYLPDYGVAYDPKNPALLALDAPVYLVVPKRLLQPDIRDALNDKGNEEHAYSCRHLMRKD 1739
BLAST of SMED30008507 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1) HSP 1 Score: 228.409 bits (581), Expect = 1.230e-66 Identity = 109/181 (60.22%), Postives = 138/181 (76.24%), Query Frame = 2 Query: 1994 ILGRSEIQWRDMERTTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQLERKYRYLANQKRRRLARINEDITNGHIPSSDDHLPSYRVAYDPRDPALLELDAPVHLVFPKLLLQPDIKDILEDRGTEEHVYSRRRLSRK 2536 ++G S QW+D ERTTL +PS+FAGRYRQALWD Y++ST+GT EWPNR DED ELPSL IKREPGRN AR+IR E E L +++ LERKYR+ A+ +R+RL RIN+DI +G I SSD +LP Y +A+DP DPALLEL APVH+ PK ++Q DI + L+DR +EEH YS+R L R+ Sbjct: 53 VIGNSGTQWKDDERTTLIIPSKFAGRYRQALWDGVYSLSTYGTSEWPNRSRIRHDEDVELPSLAIKREPGRNTARKIRHEAEVALQQFDHLERKYRWKASLQRKRLMRINKDIASGRISSSDGYLPDYNIAFDPEDPALLELSAPVHMALPKHIMQRDILEALDDRTSEEHAYSQRPLKRE 233 The following BLAST results are available for this feature:
BLAST of SMED30008507 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30008507 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30008507 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30008507 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30008507 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30008507 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30008507 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30008507 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30008507 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30008507 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30008507 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30008507 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30008507 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30008507 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 >SMED30008507 ID=SMED30008507|Name=SMED30008507|organism=Schmidtea mediterranea sexual|type=transcript|length=3448bpback to top protein sequence of SMED30008507-orf-1 >SMED30008507-orf-1 ID=SMED30008507-orf-1|Name=SMED30008507-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=193bp MILGRSEIQWRDMERTTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRback to top protein sequence of SMED30008507-orf-2 >SMED30008507-orf-2 ID=SMED30008507-orf-2|Name=SMED30008507-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp MRSENINTNQKRPPISKNHMSCESPRHIKSVLGDITSIFIMNESMRHSAKback 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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