SMED30023731
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Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ Neoblast 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
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., 2020SMED30023731 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30023731 aligns in the following genomic locations: Homology
BLAST of SMED30023731 vs. Planmine SMEST
Match: SMESG000017989.1 (SMESG000017989.1) HSP 1 Score: 95.1301 bits (235), Expect = 1.732e-23 Identity = 64/88 (72.73%), Postives = 65/88 (73.86%), Query Frame = -1
Query: 83 LLDCNNNNVERIIIEDTPTSINEDVYEVISIGKFNIYLFSKYKKKTNISNDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPTC 346
+ DCNNNNVERIIIEDT TSINEDVYEVISI DDDMIPATYPIIILDDIVDDAPTCIDGD IVDNAPTC
Sbjct: 798 VFDCNNNNVERIIIEDTLTSINEDVYEVISI--------------------DDDMIPATYPIIILDDIVDDAPTCIDGDAIVDNAPTC 865
BLAST of SMED30023731 vs. Planmine SMEST
Match: SMESG000046659.1 (SMESG000046659.1) HSP 1 Score: 88.5817 bits (218), Expect = 2.981e-21 Identity = 61/84 (72.62%), Postives = 62/84 (73.81%), Query Frame = -1
Query: 83 NNNNVERIIIEDTPTSINEDVYEVISIGKFNIYLFSKYKKKTNISNDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPTC 334
NNNNVERIIIEDTP SINEDVYEVISI DDD MIPATYPIIILDDIVDDAP CIDGDDIVD+APTC
Sbjct: 541 NNNNVERIIIEDTPNSINEDVYEVISI-------------------DDDYMIPATYPIIILDDIVDDAPNCIDGDDIVDDAPTC 605
BLAST of SMED30023731 vs. Planmine SMEST
Match: SMESG000046659.1 (SMESG000046659.1) HSP 1 Score: 88.1965 bits (217), Expect = 3.758e-21 Identity = 61/84 (72.62%), Postives = 62/84 (73.81%), Query Frame = -1
Query: 83 NNNNVERIIIEDTPTSINEDVYEVISIGKFNIYLFSKYKKKTNISNDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPTC 334
NNNNVERIIIEDTP SINEDVYEVISI DDD MIPATYPIIILDDIVDDAP CIDGDDIVD+APTC
Sbjct: 515 NNNNVERIIIEDTPNSINEDVYEVISI-------------------DDDYMIPATYPIIILDDIVDDAPNCIDGDDIVDDAPTC 579
BLAST of SMED30023731 vs. Planmine SMEST
Match: SMESG000058180.1 (SMESG000058180.1) HSP 1 Score: 84.3445 bits (207), Expect = 9.209e-20 Identity = 63/86 (73.26%), Postives = 65/86 (75.58%), Query Frame = -1
Query: 86 LDCNNNNVERIIIEDTPTSINEDVYEVISIGKFNIYLFSKYKKKTNISNDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT 343
+DC NNNVERII EDTPTSINE VYEVISI +DDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT
Sbjct: 460 MDCINNNVERIIFEDTPTSINEVVYEVISI------------------DDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT 527
BLAST of SMED30023731 vs. Planmine SMEST
Match: SMESG000058180.1 (SMESG000058180.1) HSP 1 Score: 84.3445 bits (207), Expect = 9.847e-20 Identity = 63/86 (73.26%), Postives = 65/86 (75.58%), Query Frame = -1
Query: 86 LDCNNNNVERIIIEDTPTSINEDVYEVISIGKFNIYLFSKYKKKTNISNDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT 343
+DC NNNVERII EDTPTSINE VYEVISI +DDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT
Sbjct: 451 MDCINNNVERIIFEDTPTSINEVVYEVISI------------------DDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT 518 The following BLAST results are available for this feature:
BLAST of SMED30023731 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30023731 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30023731 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30023731 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30023731 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30023731 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30023731 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30023731 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30023731 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30023731 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30023731 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30023731 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30023731 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30023731 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 >SMED30023731 ID=SMED30023731|Name=SMED30023731|organism=Schmidtea mediterranea sexual|type=transcript|length=403bpback to top protein sequence of SMED30023731-orf-1 >SMED30023731-orf-1 ID=SMED30023731-orf-1|Name=SMED30023731-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=119bp MEKVSKFVYDFINILLDCNNNNVERIIIEDTPTSINEDVYEVISIGKFNIback 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
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