SMED30015493
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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., 2020SMED30015493 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Homology
BLAST of SMED30015493 vs. Planmine SMEST
Match: SMESG000026733.1 (SMESG000026733.1) HSP 1 Score: 100.908 bits (250), Expect = 1.375e-26 Identity = 58/121 (47.93%), Postives = 80/121 (66.12%), Query Frame = 3
Query: 261 MDGLWVDYDSRITVKFPPRPAVLCRQALWHTSYTVSSVGEPSSPINPRSRDEEVELPSVSIKRE-----AR---QRAEYTLPELEELSRRTRWEIIMA*RHLNWINADIAS*HIPSTNRYA 599
M +W D D R+T+K P A RQ+LW SY+++++G+ S PI +SRD E+EL S++IKRE AR QRAE++L LEEL R+ +W++ M RHL INA IA+ IPST+ YA
Sbjct: 1 MSLIWCDED-RVTIKVTPDMAAQYRQSLWDVSYSLATLGDNSWPIRDKSRDNEIELLSLAIKREPDRNLAREPCQRAEFSLYRLEELVRKFQWKVRMTQRHLKQINATIATGEIPSTDGYA 120
BLAST of SMED30015493 vs. Planmine SMEST
Match: SMESG000014849.1 (SMESG000014849.1) HSP 1 Score: 92.4337 bits (228), Expect = 4.911e-22 Identity = 51/124 (41.13%), Postives = 72/124 (58.06%), Query Frame = 3
Query: 249 DTRTMDGLWVDYDSRITVKFPPRPAVLCRQALWHTSYTVSSVGEPSSPINPRSRDEEVELPSVSIK--------REARQRAEYTLPELEELSRRTRWEIIMA*RHLNWINADIAS*HIPSTNRY 596
+ R G W D +SR+T++ P A RQ LW Y +S+ G+ S P R EE+ELPS++IK REARQRAEY ++EEL R+ + ++A + L +N DIAS IPST+ +
Sbjct: 875 NRRDPHGNWSD-NSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYRAEEIELPSIAIKREPGHNPAREARQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGVIPSTDGF 997 HSP 2 Score: 30.0314 bits (66), Expect = 4.911e-22 Identity = 12/26 (46.15%), Postives = 16/26 (61.54%), Query Frame = 1
Query: 598 PSTEISFKLDDPELMDMDALINVVVP 675
P +SF+LDDP L M A +V+P
Sbjct: 999 PEYGVSFELDDPRLTQMTAPTKMVIP 1024
BLAST of SMED30015493 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1) HSP 1 Score: 87.8113 bits (216), Expect = 4.417e-21 Identity = 51/127 (40.16%), Postives = 73/127 (57.48%), Query Frame = 3
Query: 240 STGDTRTMDGLWVDYDSRITVKFPPRPAVLCRQALWHTSYTVSSVGEPSSPINPRSRDEEVELPSVSIK--------REARQRAEYTLPELEELSRRTRWEIIMA*RHLNWINADIAS*HIPSTNRY 596
S + R G W D +SR+T++ P A RQ LW Y +S+ G+ S P + EE+ELPS++IK REARQRAEY ++EEL R+ + ++A + L +N DIAS IPST+ +
Sbjct: 1125 SNDNRRDPHGNWSD-NSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAEYVAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGF 1250 HSP 2 Score: 31.5722 bits (70), Expect = 4.417e-21 Identity = 13/26 (50.00%), Postives = 17/26 (65.38%), Query Frame = 1
Query: 598 PSTEISFKLDDPELMDMDALINVVVP 675
P +SF+LDDP LM M A +V+P
Sbjct: 1252 PEYGVSFELDDPRLMQMTAPTKMVIP 1277
BLAST of SMED30015493 vs. Planmine SMEST
Match: SMESG000032540.1 (SMESG000032540.1) HSP 1 Score: 87.0409 bits (214), Expect = 4.660e-21 Identity = 54/121 (44.63%), Postives = 74/121 (61.16%), Query Frame = 3
Query: 261 MDGLWVDYDSRITVKFPPRPAVLCRQALWHTSYTVSSVGEPSSPINPRSRDEEVELPSVSIKRE--------ARQRAEYTLPELEELSRRTRWEIIMA*RHLNWINADIAS*HIPSTNRYA 599
++ W+ Y SR+T++FP AV CRQA+W +++S V E S + RS ++V+LP V+IKRE R +AEY L LEE R+T E+ A RHL IN DIA+ IPST+ YA
Sbjct: 5 LENSWI-YASRVTLRFPAHSAVRCRQAMWDAGFSISPVRE--SRMGSRSNTDDVDLPFVAIKREPGRNPAREIRGQAEYLLARLEEHKRQTDHEVDKARRHLEEINWDIAAGIIPSTDGYA 122
BLAST of SMED30015493 vs. Planmine SMEST
Match: SMESG000023390.1 (SMESG000023390.1) HSP 1 Score: 88.9669 bits (219), Expect = 5.512e-21 Identity = 54/120 (45.00%), Postives = 71/120 (59.17%), Query Frame = 3
Query: 264 DGLWVDYDSRITVKFPPRPAVLCRQALWHTSYTVSSVGEPSSPINPRSRDEEVELPSVSIKRE--------ARQRAEYTLPELEELSRRTRWEIIMA*RHLNWINADIAS*HIPSTNRYA 599
D W+D SR+TV+FP R CRQ LW ++VS V E + R DE+V+LP V+IKRE R +AE+ L LEE R+T+ ++ A RHL IN IA+ IPST+RYA
Sbjct: 359 DHSWIDA-SRVTVRFPARSVARCRQVLWDAGFSVSPVRESRTAT--RRDDEKVDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTKRQVNRARRHLAEINKAIATGDIPSTDRYA 475 HSP 2 Score: 30.0314 bits (66), Expect = 5.512e-21 Identity = 14/28 (50.00%), Postives = 16/28 (57.14%), Query Frame = 1
Query: 595 TPSTEISFKLDDPELMDMDALINVVVPR 678
P +SF LDDP L +NVVVPR
Sbjct: 475 APPYNVSFNLDDPNLAGEAEAMNVVVPR 502 The following BLAST results are available for this feature:
BLAST of SMED30015493 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30015493 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30015493 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30015493 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30015493 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30015493 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30015493 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30015493 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30015493 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30015493 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30015493 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30015493 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30015493 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30015493 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 >SMED30015493 ID=SMED30015493|Name=SMED30015493|organism=Schmidtea mediterranea sexual|type=transcript|length=680bpback to top protein sequence of SMED30015493-orf-1 >SMED30015493-orf-1 ID=SMED30015493-orf-1|Name=SMED30015493-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=141bp MSNKEAKVKKSLMTPLTDQSREKSIYTGNNRRMKHAAEVRCPKSTGDTRTback to top Annotated Terms
The following terms have been associated with this transcript:
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