SMED30029711
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., 2020SMED30029711 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 22
Alignments
SMED30029711 aligns in the following genomic locations:
Homology
BLAST of SMED30029711 vs. Ensembl Human
Match: DYDC1 (DPY30 domain containing 1 [Source:HGNC Symbol;Acc:HGNC:23460]) HSP 1 Score: 47.3654 bits (111), Expect = 1.362e-6 Identity = 22/42 (52.38%), Postives = 28/42 (66.67%), Query Frame = -1 Query: 64 EAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVEN 189 E+ +L H+G L GLA + RP DPIEYLA ++YKY EN Sbjct: 2 ESIYLQKHLGACLTQGLAEVARVRPVDPIEYLALWIYKYKEN 43
BLAST of SMED30029711 vs. Ensembl Human
Match: DYDC1 (DPY30 domain containing 1 [Source:HGNC Symbol;Acc:HGNC:23460]) HSP 1 Score: 47.3654 bits (111), Expect = 6.854e-6 Identity = 22/42 (52.38%), Postives = 28/42 (66.67%), Query Frame = -1 Query: 64 EAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVEN 189 E+ +L H+G L GLA + RP DPIEYLA ++YKY EN Sbjct: 2 ESIYLQKHLGACLTQGLAEVARVRPVDPIEYLALWIYKYKEN 43
BLAST of SMED30029711 vs. TrEMBL
Match: A7RSS0 (Predicted protein (Fragment) OS=Nematostella vectensis OX=45351 GN=v1g92230 PE=4 SV=1) HSP 1 Score: 55.8398 bits (133), Expect = 1.844e-6 Identity = 27/45 (60.00%), Postives = 32/45 (71.11%), Query Frame = -1 Query: 55 EAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENY 189 ++E+L HVG AL LGLA I RP DPIEYLA +L KYVEN + Sbjct: 2 DSEYLKKHVGEALSLGLAEIVNKRPVDPIEYLAFWLRKYVENTEF 46
BLAST of SMED30029711 vs. TrEMBL
Match: V4A1N7 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_229340 PE=4 SV=1) HSP 1 Score: 55.8398 bits (133), Expect = 3.702e-6 Identity = 22/46 (47.83%), Postives = 34/46 (73.91%), Query Frame = -1 Query: 43 FLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQV 180 FL HVG +L + LA + RPKDPIEY+ ++L+ +++N+ +QKQV Sbjct: 5 FLRKHVGESLVICLAEVAEKRPKDPIEYIGQWLHNHIKNQQHQKQV 50
BLAST of SMED30029711 vs. TrEMBL
Match: A0A2B4RW87 (DPY30 domain-containing protein 1 OS=Stylophora pistillata OX=50429 GN=Dydc1 PE=4 SV=1) HSP 1 Score: 58.9214 bits (141), Expect = 4.811e-6 Identity = 28/47 (59.57%), Postives = 33/47 (70.21%), Query Frame = -1 Query: 46 AEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQ 186 +E+L HVG AL GLA I RP DPIEYLA +L KYVENE + K+ Sbjct: 3 SEYLKKHVGKALASGLAEIAEKRPVDPIEYLAHWLRKYVENEEFAKK 49
BLAST of SMED30029711 vs. TrEMBL
Match: A0A3M6TVQ4 (Uncharacterized protein OS=Pocillopora damicornis OX=46731 GN=pdam_00024773 PE=4 SV=1) HSP 1 Score: 58.9214 bits (141), Expect = 5.395e-6 Identity = 28/49 (57.14%), Postives = 34/49 (69.39%), Query Frame = -1 Query: 40 AEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQVM 186 +E+L HVG AL GLA I RP DPIEYLA +L KYVENE + K+ + Sbjct: 3 SEYLKKHVGKALASGLAEIAEKRPVDPIEYLAHWLRKYVENEEFAKKEL 51
BLAST of SMED30029711 vs. Ensembl Nematostella
Match: EDO45464 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RSS0]) HSP 1 Score: 55.8398 bits (133), Expect = 2.549e-10 Identity = 27/45 (60.00%), Postives = 32/45 (71.11%), Query Frame = -1 Query: 55 EAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENY 189 ++E+L HVG AL LGLA I RP DPIEYLA +L KYVEN + Sbjct: 2 DSEYLKKHVGEALSLGLAEIVNKRPVDPIEYLAFWLRKYVENTEF 46
BLAST of SMED30029711 vs. Planmine SMEST
Match: SMESG000039804.1 (SMESG000039804.1) HSP 1 Score: 251.136 bits (640), Expect = 1.424e-83 Identity = 120/121 (99.17%), Postives = 121/121 (100.00%), Query Frame = 3 Query: 723 MELSRSKEVKFNEEIIELPASPRFNLSTSHREFISNDNQNSCDNNKLYQTGCVGRTPQEMAGIMVNYPGITEHKRRYKWPHGDIEFESIINPGYEGLFERIKIKNPEPVEQISEYNRRFVW 1085 MELSRSKEVKFNEEIIELPASPRFNLSTSHREFISND+QNSCDNNKLYQTGCVGRTPQEMAGIMVNYPGITEHKRRYKWPHGDIEFESIINPGYEGLFERIKIKNPEPVEQISEYNRRFVW Sbjct: 1 MELSRSKEVKFNEEIIELPASPRFNLSTSHREFISNDSQNSCDNNKLYQTGCVGRTPQEMAGIMVNYPGITEHKRRYKWPHGDIEFESIINPGYEGLFERIKIKNPEPVEQISEYNRRFVW 121
BLAST of SMED30029711 vs. Planmine SMEST
Match: SMESG000039803.1 (SMESG000039803.1) HSP 1 Score: 143.665 bits (361), Expect = 1.292e-40 Identity = 68/80 (85.00%), Postives = 73/80 (91.25%), Query Frame = -1 Query: 4 MSIGSRSATSYSQQTANKEAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQVMLSVIHVNS*ILV 243 MSIGSRSATSYSQQTANKEAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQ+ + ++ IL+ Sbjct: 1 MSIGSRSATSYSQQTANKEAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQMEMDEYNLQQEILL 80 The following BLAST results are available for this feature:
BLAST of SMED30029711 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 2
BLAST of SMED30029711 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30029711 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30029711 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30029711 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30029711 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30029711 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30029711 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 4
BLAST of SMED30029711 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30029711 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30029711 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30029711 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 1
BLAST of SMED30029711 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30029711 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 2
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30029711 ID=SMED30029711|Name=SMED30029711|organism=Schmidtea mediterranea sexual|type=transcript|length=1185bpback to top protein sequence of SMED30029711-orf-1 >SMED30029711-orf-1 ID=SMED30029711-orf-1|Name=SMED30029711-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp MELSRSKEVKFNEEIIELPASPRFNLSTSHREFISNDNQNSCDNNKLYQTback to top Annotated Terms
The following terms have been associated with this transcript:
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