SMED30026900
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., 2020SMED30026900 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Homology
BLAST of SMED30026900 vs. Planmine SMEST
Match: SMESG000032267.1 (SMESG000032267.1) HSP 1 Score: 553.903 bits (1426), Expect = 0.000e+0 Identity = 271/271 (100.00%), Postives = 271/271 (100.00%), Query Frame = 2 Query: 2 NYIILLLCLFNVISINTIKLAEAKQRLSNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDTLPLNKGKPVQLTTKKRSYMIKEMKAAQWNNIIRSTKKMLEPVKEYNIFAFEPAGVVYI 814 NYIILLLCLFNVISINTIKLAEAKQRLSNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDTLPLNKGKPVQLTTKKRSYMIKEMKAAQWNNIIRSTKKMLEPVKEYNIFAFEPAGVVYI Sbjct: 5 NYIILLLCLFNVISINTIKLAEAKQRLSNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDTLPLNKGKPVQLTTKKRSYMIKEMKAAQWNNIIRSTKKMLEPVKEYNIFAFEPAGVVYI 275
BLAST of SMED30026900 vs. Planmine SMEST
Match: SMESG000032278.1 (SMESG000032278.1) HSP 1 Score: 151.754 bits (382), Expect = 3.186e-44 Identity = 77/186 (41.40%), Postives = 119/186 (63.98%), Query Frame = 2 Query: 83 SNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDT 640 SN C R+ ++C+L + S C+ W ++++ KI +I E TT+C K + Y+C + D + +++ C Q CD Y+LC+ G+K+ET KSIK N+ + +DT+II +KSK +C+ISA C +CES K I+ +FS CK+L+ N + FDNL+P ++FY+LP+KN L GSVF V +T Sbjct: 32 SNLECARDLRFCNLAIMSPTSNCIPW-KLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNT 216
BLAST of SMED30026900 vs. Planmine SMEST
Match: SMESG000032278.1 (SMESG000032278.1) HSP 1 Score: 151.754 bits (382), Expect = 3.784e-44 Identity = 77/186 (41.40%), Postives = 119/186 (63.98%), Query Frame = 2 Query: 83 SNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDT 640 SN C R+ ++C+L + S C+ W ++++ KI +I E TT+C K + Y+C + D + +++ C Q CD Y+LC+ G+K+ET KSIK N+ + +DT+II +KSK +C+ISA C +CES K I+ +FS CK+L+ N + FDNL+P ++FY+LP+KN L GSVF V +T Sbjct: 36 SNLECARDLRFCNLAIMSPTSNCIPW-KLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNT 220
BLAST of SMED30026900 vs. Planmine SMEST
Match: SMESG000032278.1 (SMESG000032278.1) HSP 1 Score: 151.754 bits (382), Expect = 5.351e-44 Identity = 77/186 (41.40%), Postives = 119/186 (63.98%), Query Frame = 2 Query: 83 SNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDT 640 SN C R+ ++C+L + S C+ W ++++ KI +I E TT+C K + Y+C + D + +++ C Q CD Y+LC+ G+K+ET KSIK N+ + +DT+II +KSK +C+ISA C +CES K I+ +FS CK+L+ N + FDNL+P ++FY+LP+KN L GSVF V +T Sbjct: 47 SNLECARDLRFCNLAIMSPTSNCIPW-KLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNT 231
BLAST of SMED30026900 vs. Planmine SMEST
Match: SMESG000032456.1 (SMESG000032456.1) HSP 1 Score: 149.058 bits (375), Expect = 1.683e-40 Identity = 80/202 (39.60%), Postives = 122/202 (60.40%), Query Frame = 2 Query: 86 NNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICD-PYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDTLPLNKGKPVQLTTKKR 688 ++ CV ++ YC G ++ S C+ W++ + +K I KTT+C K + Y C T +W+YC+ C+ Y+LC DGI WETF+KS+KL IP KFDT+ IL+KS+ +C ISAQC+ C S ++ I N F+ C++LE++ D + ISF NL +Y FY+LP++ L+G VF++ L T P + + KR Sbjct: 10 DSECVHDKAYCINGESSWKSPCIPWAQSTK-YKSVNIFLKTTLCKKENNDYWCATS--------VSWNYCQPSRCELSYNLCEDGISWETFEKSVKLKIPNKFDTVTILQKSESECAISAQCRMCRSVEQMIGNLFNGCQLLEVSRDHTRSISFPNLLHSTKYHFYILPIQEGRLMGFVFKLYLLTKISKPCLPYSIKSVKR 202 The following BLAST results are available for this feature:
BLAST of SMED30026900 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30026900 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30026900 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30026900 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30026900 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30026900 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30026900 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30026900 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30026900 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30026900 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30026900 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30026900 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30026900 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30026900 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 >SMED30026900 ID=SMED30026900|Name=SMED30026900|organism=Schmidtea mediterranea sexual|type=transcript|length=930bpback to top protein sequence of SMED30026900-orf-1 >SMED30026900-orf-1 ID=SMED30026900-orf-1|Name=SMED30026900-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=272bp NYIILLLCLFNVISINTIKLAEAKQRLSNNNCVRNRKYCHLGFTTLHSLCback 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
|