SMED30005958
Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ 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 AppSub-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., 2020SMED30005958 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30005958 aligns in the following genomic locations:
Homology
BLAST of SMED30005958 vs. Planmine SMEST
Match: SMESG000007060.1 (SMESG000007060.1) HSP 1 Score: 463.381 bits (1191), Expect = 4.742e-167 Identity = 255/255 (100.00%), Postives = 255/255 (100.00%), Query Frame = 1 Query: 28 MGFWFRVLVFVLSSTLNHGDLIYQNKEFQNEYFSTGGYSARFCAKNAKTKDLLLINPPDKNSRFTCYNTVEKCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSKYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDINCLKISVTKRAINCILDLTKLHSNDIIEVNITVKYGKRICNKPQFVGNIFIXXXXXXXXXXXXEWXXXXXXXXXXXXSHLIPFYMRRNNIISKSRIYFENIYETEN 792 MGFWFRVLVFVLSSTLNHGDLIYQNKEFQNEYFSTGGYSARFCAKNAKTKDLLLINPPDKNSRFTCYNTVEKCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSKYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDINCLKISVTKRAINCILDLTKLHSNDIIEVNITVKYGKRICNKPQFVGNIFIYKLKYSKSSVKYEWIIIILLTLAFALSHLIPFYMRRNNIISKSRIYFENIYETEN Sbjct: 1 MGFWFRVLVFVLSSTLNHGDLIYQNKEFQNEYFSTGGYSARFCAKNAKTKDLLLINPPDKNSRFTCYNTVEKCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSKYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDINCLKISVTKRAINCILDLTKLHSNDIIEVNITVKYGKRICNKPQFVGNIFIYKLKYSKSSVKYEWIIIILLTLAFALSHLIPFYMRRNNIISKSRIYFENIYETEN 255
BLAST of SMED30005958 vs. Planmine SMEST
Match: SMESG000033282.1 (SMESG000033282.1) HSP 1 Score: 66.2402 bits (160), Expect = 6.204e-12 Identity = 55/174 (31.61%), Postives = 85/174 (48.85%), Query Frame = 1 Query: 118 EYFSTGGYSARFCAKNAKTKDLLLINPPDKNS-RFTCYNTVEKCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSKYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDIN--CLKISVTKRAINCILDL-TKLHSNDIIEVNITVKYGKRICNKPQFVGNIFI 627 EYF+ GGY + FC KT D ++++ + + +C C+ GN + C LPCNF + N + +L +P F+++ L Y L IG S+ S+ +E N SD+N C +I T +I C+L L I+ V+I + YG CN+ Q +G I I Sbjct: 26 EYFNRGGYISLFCIN--KTDDNIILHKQNSYAVNISCNKMKIVCKSGNFYKCNLPCNFNLTALENNKKIFRLQRFEAPIFAISELEYYQNRSNLTIG-VSNKVSISSIRLENYHFNFSDVNVLCRQIWNTDSSIICLLHLKMTCVYYKILNVSILISYGNSSCNERQNLGFILI 196
BLAST of SMED30005958 vs. Planmine SMEST
Match: SMESG000033282.1 (SMESG000033282.1) HSP 1 Score: 66.2402 bits (160), Expect = 6.250e-12 Identity = 55/174 (31.61%), Postives = 85/174 (48.85%), Query Frame = 1 Query: 118 EYFSTGGYSARFCAKNAKTKDLLLINPPDKNS-RFTCYNTVEKCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSKYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDIN--CLKISVTKRAINCILDL-TKLHSNDIIEVNITVKYGKRICNKPQFVGNIFI 627 EYF+ GGY + FC KT D ++++ + + +C C+ GN + C LPCNF + N + +L +P F+++ L Y L IG S+ S+ +E N SD+N C +I T +I C+L L I+ V+I + YG CN+ Q +G I I Sbjct: 26 EYFNRGGYISLFCIN--KTDDNIILHKQNSYAVNISCNKMKIVCKSGNFYKCNLPCNFNLTALENNKKIFRLQRFEAPIFAISELEYYQNRSNLTIGVSNKV-SISSIRLENYHFNFSDVNVLCRQIWNTDSSIICLLHLKMTCVYYKILNVSILISYGNSSCNERQNLGFILI 196
BLAST of SMED30005958 vs. Planmine SMEST
Match: SMESG000033322.1 (SMESG000033322.1) HSP 1 Score: 61.6178 bits (148), Expect = 2.145e-10 Identity = 45/167 (26.95%), Postives = 81/167 (48.50%), Query Frame = 1 Query: 133 GGYSARFCAKNAKTKDLLLINPPDKNSRFTCYNTVE---KCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLS-KYGENDILKIGSSSDTFSLFDWDVEIKFNNNSDINCLKISVTKRAINCILDLTKLHSNDIIEVNITVKYGKRICNKPQFVGNI 621 GGY+AR C + + + + F+C + E +C+ ++++C +PCNF + + KL + PKF L + KY N L I S + L + I F+ N ++C + + +I C LD ++ + ++++I + YG+ ICN F+G I Sbjct: 31 GGYTARICLNHHPEN--VSVKTTMGDYVFSCRKSNETGTECKNKSVYSCPIPCNFSESAVKIGMKVYKLSHLSKPKFELAEKNLKYNSNGNLTIKSDASLPLLAADQINIDFSAN--VSCSRKYIQNYSIICRLDAQRIPIDQALDISINISYGE-ICNSKHFLGKI 192
BLAST of SMED30005958 vs. Planmine SMEST
Match: SMESG000033300.1 (SMESG000033300.1) HSP 1 Score: 59.6918 bits (143), Expect = 6.270e-10 Identity = 48/167 (28.74%), Postives = 81/167 (48.50%), Query Frame = 1 Query: 139 YSARFCAKNAKTKDLLLINPPDKNSRFTCYNTVE---KCQKGNIFNCFLPCNFRRFSFIKNSYLGKLVSIGSPKFSLNPLSK-YGENDILKIGSSSDTFSLFDWDVEIKFNNNSDINCLKISVTKRAINCILDLTKLHSNDIIEVNITVKYGKRICNKPQFVGNIFI 627 Y+AR C N +++ + P + F+C T E +C+ ++++C +PCN + + + KL PKF L K Y N L I S + L + I F+ N +CL+ + +I C LD ++ + ++++I + YG+ ICN QF NI I Sbjct: 33 YTARICL-NHHPENVSVNKTPMGDYVFSCRKTNETGTECKNKSVYSCPIPCNLSLQTVKIGTKIYKLSYSPKPKFELAEKDKKYNSNGDLTIKSDASLPLLAADQINIDFSAN--FSCLRKYIQNYSIICRLDAQRIPIDQALDISINISYGE-ICNSKQFTINITI 195 The following BLAST results are available for this feature:
BLAST of SMED30005958 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30005958 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30005958 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30005958 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30005958 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30005958 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30005958 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30005958 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30005958 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30005958 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30005958 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30005958 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30005958 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30005958 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 >SMED30005958 ID=SMED30005958|Name=SMED30005958|organism=Schmidtea mediterranea sexual|type=transcript|length=845bpback to top protein sequence of SMED30005958-orf-1 >SMED30005958-orf-1 ID=SMED30005958-orf-1|Name=SMED30005958-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=267bp RDYFSFLLFMGFWFRVLVFVLSSTLNHGDLIYQNKEFQNEYFSTGGYSARback to top InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
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