SMED30035813
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., 2020SMED30035813 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 8
Alignments
SMED30035813 aligns in the following genomic locations:
Homology
BLAST of SMED30035813 vs. TrEMBL
Match: A0A4S2LB75 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_008429 PE=4 SV=1) HSP 1 Score: 115.931 bits (289), Expect = 2.271e-28 Identity = 61/139 (43.88%), Postives = 83/139 (59.71%), Query Frame = 3 Query: 132 TEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVWDPLLQGLD--RNALKTKAPEFEFRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMVACPTLSGLPIV 542 +Y +G Q+ T +H+RG VSHQW+GP +Y+ P +RY +E + Q L RN + E PH+ P++ WP RP F+S HNKWLNEH+ T IPRDARLFYNEEDW+K+K+MV L + + Sbjct: 11 VRRYTSGVQNQHTFHEHHHNRGAVSHQWRGPAYYIPGPQARYLHLEEFKNTQEQELVLYRNNHWCRYNPPEAVKPHNRDPLHLVWPRRPVFYSAHHNKWLNEHADTLIPRDARLFYNEEDWIKYKHMVETAKLPAISLT 149
BLAST of SMED30035813 vs. TrEMBL
Match: A0A267FB16 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig001692g1 PE=4 SV=1) HSP 1 Score: 92.0485 bits (227), Expect = 3.209e-19 Identity = 55/137 (40.15%), Postives = 74/137 (54.01%), Query Frame = 3 Query: 126 EATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVW-DPLLQGLDRNALKTKAPEFE--------FRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMV 509 +A KY++GPQ+ ++ SRG VSHQW+GPGFY R+T P +V DP+ QGLD+ A + P H+ P ++W RP F S H NEH + DARLFYNE+DW K+K M+ Sbjct: 10 QARLKYLSGPQNLVIPCAVRPSRGAVSHQWRGPGFYQ-SETHRFTDPPQVTRDPVGQGLDKTAAVSGWPSAASSTTGVGCHAAEHAPAPYAERWHGRPVFFSAEHQTLSNEHPAGPVAPDARLFYNEDDWEKYKYML 145
BLAST of SMED30035813 vs. TrEMBL
Match: A0A267GR19 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig001692g2 PE=4 SV=1) HSP 1 Score: 92.4337 bits (228), Expect = 4.529e-19 Identity = 55/137 (40.15%), Postives = 74/137 (54.01%), Query Frame = 3 Query: 126 EATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVW-DPLLQGLDRNALKTKAPEFE--------FRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMV 509 +A KY++GPQ+ ++ SRG VSHQW+GPGFY R+T P +V DP+ QGLD+ A + P H+ P ++W RP F S H NEH + DARLFYNE+DW K+K M+ Sbjct: 36 QARLKYLSGPQNLVIPCAIRPSRGAVSHQWRGPGFYQ-SETHRFTDPPQVTRDPVGQGLDKTAAVSGWPSAASSTTGVGCHAAEHAPAPYAERWRGRPVFFSAEHQTLSNEHPAGPVAPDARLFYNEDDWEKYKYML 171
BLAST of SMED30035813 vs. TrEMBL
Match: A0A267GAX5 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig001692g3 PE=4 SV=1) HSP 1 Score: 92.0485 bits (227), Expect = 8.065e-19 Identity = 55/137 (40.15%), Postives = 74/137 (54.01%), Query Frame = 3 Query: 126 EATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVW-DPLLQGLDRNALKTKAPEFEFRYP--------HSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMV 509 +A KY++GPQ+ ++ SRG VSHQW+GPGFY R+T P +V DP+ QGLD+ A + P H+ P ++W RP F S H NEH + DARLFYNE+DW K+K M+ Sbjct: 44 QARLKYLSGPQNLVIPCAVRPSRGAVSHQWRGPGFYQ-SETHRFTDPPQVTRDPVGQGLDKTAAVSGWPSAASSTTGVGCHAAEHAPAPYAERWRGRPVFFSAEHQTLSNEHPAGPVAPDARLFYNEDDWEKYKYML 179
BLAST of SMED30035813 vs. TrEMBL
Match: A0A504YLX6 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_03096 PE=4 SV=1) HSP 1 Score: 77.0258 bits (188), Expect = 1.864e-14 Identity = 38/88 (43.18%), Postives = 49/88 (55.68%), Query Frame = 3 Query: 372 QKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMVACPTLSGLPIVPQSRPVIKPTGKRRIKCP------QDHDFYF 617 ++WP P F+S HNKWL+EH+ T IPRDARLFYNEEDW+KFK+M L I + ++ C +D FYF Sbjct: 9 KEWPKHPIFYSAHHNKWLSEHADTLIPRDARLFYNEEDWIKFKHMANTAKQPNLSISDVREINCRAFSDAKLVCKKGKKPYEDMKFYF 96
BLAST of SMED30035813 vs. Planmine SMEST
Match: SMESG000004300.1 (SMESG000004300.1) HSP 1 Score: 364.385 bits (934), Expect = 7.130e-130 Identity = 172/173 (99.42%), Postives = 172/173 (99.42%), Query Frame = 3 Query: 99 MESDYQCRNEATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVWDPLLQGLDRNALKTKAPEFEFRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMVACPTLSGLPIVPQSRPVIKPTGKRRIKCPQDHDFYF 617 MESDYQCRNEATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVWDPLLQGLDRNALKTKAPEFEFRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMVACPTL GLPIVPQSRPVIKPTGKRRIKCPQDHDFYF Sbjct: 1 MESDYQCRNEATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVWDPLLQGLDRNALKTKAPEFEFRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMVACPTLPGLPIVPQSRPVIKPTGKRRIKCPQDHDFYF 173 The following BLAST results are available for this feature:
BLAST of SMED30035813 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30035813 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30035813 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30035813 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30035813 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30035813 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30035813 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30035813 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 5
BLAST of SMED30035813 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30035813 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30035813 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30035813 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30035813 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30035813 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 1
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30035813 ID=SMED30035813|Name=SMED30035813|organism=Schmidtea mediterranea sexual|type=transcript|length=740bpback to top protein sequence of SMED30035813-orf-1 >SMED30035813-orf-1 ID=SMED30035813-orf-1|Name=SMED30035813-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=174bp MESDYQCRNEATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLback to top Annotated Terms
The following terms have been associated with this transcript:
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