SMED30026794
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., 2020SMED30026794 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 7
Alignments
SMED30026794 aligns in the following genomic locations:
Homology
BLAST of SMED30026794 vs. TrEMBL
Match: A0A1S6KMK3 (Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1) HSP 1 Score: 473.011 bits (1216), Expect = 2.734e-168 Identity = 229/230 (99.57%), Postives = 229/230 (99.57%), Query Frame = -2 Query: 11 MKSQNQLGKVRVSQIALKDEIVHKSMRTLINQSGTRPKVYPFIHNKVLIPGDYRNLIEQFQIPTKMHSTIGIQEELPTHIFCHQLGSNLCWRCSRKMVNRKLKEQIETDLTNSEPEMFLRLICIENVLKDMNLPLFSNSETAPWKSGLSNSETFSDGPLFFPNSQKTAQIELENVSNEISNLASNIKEKKKFTNKEINYRMINSNKTIQDSKREKKSMKYVEPPVFESFY 700 MKSQNQLGKVRVSQIALKDEIVHKSMRTLINQSGTRPKVYPFIHNKVLIPGDYRNLIEQFQIPTKMHSTIGIQEELPTHIFCHQLGSNLCWRCSRKMVNRKLKEQIETDLTNSEPEMFLRLICIENVLKDMNLPLFSNSETAPWKSGLSNSETFSDGPLFFPNSQKTAQIELENVSNEISNLASNIKEKKKFTNKE NYRMINSNKTIQDSKREKKSMKYVEPPVFESFY Sbjct: 1 MKSQNQLGKVRVSQIALKDEIVHKSMRTLINQSGTRPKVYPFIHNKVLIPGDYRNLIEQFQIPTKMHSTIGIQEELPTHIFCHQLGSNLCWRCSRKMVNRKLKEQIETDLTNSEPEMFLRLICIENVLKDMNLPLFSNSETAPWKSGLSNSETFSDGPLFFPNSQKTAQIELENVSNEISNLASNIKEKKKFTNKEFNYRMINSNKTIQDSKREKKSMKYVEPPVFESFY 230
BLAST of SMED30026794 vs. Planmine SMEST
Match: SMESG000039479.1 (SMESG000039479.1) HSP 1 Score: 468.003 bits (1203), Expect = 7.296e-170 Identity = 227/230 (98.70%), Postives = 228/230 (99.13%), Query Frame = -2 Query: 11 MKSQNQLGKVRVSQIALKDEIVHKSMRTLINQSGTRPKVYPFIHNKVLIPGDYRNLIEQFQIPTKMHSTIGIQEELPTHIFCHQLGSNLCWRCSRKMVNRKLKEQIETDLTNSEPEMFLRLICIENVLKDMNLPLFSNSETAPWKSGLSNSETFSDGPLFFPNSQKTAQIELENVSNEISNLASNIKEKKKFTNKEINYRMINSNKTIQDSKREKKSMKYVEPPVFESFY 700 MKSQNQLGKV+VSQIALKDEIVHKSMRTLINQSGTRPKVYPFIHNKVL PGDYRNLIEQFQIPTKMHSTIGIQEELPTHIFCHQLGSNLCWRCSRKMVNRKLKEQIETDLTNSEPEMFLRLICIENVLKDMNLPLFSNSETAPWKSGLSNSETFSDGPLFFPNSQKTAQIELENVSNEISNLASNIKEKKKFTNKEINYRMINSNKTIQDSKRE KSMKYVEPPVFESFY Sbjct: 1 MKSQNQLGKVKVSQIALKDEIVHKSMRTLINQSGTRPKVYPFIHNKVLNPGDYRNLIEQFQIPTKMHSTIGIQEELPTHIFCHQLGSNLCWRCSRKMVNRKLKEQIETDLTNSEPEMFLRLICIENVLKDMNLPLFSNSETAPWKSGLSNSETFSDGPLFFPNSQKTAQIELENVSNEISNLASNIKEKKKFTNKEINYRMINSNKTIQDSKRENKSMKYVEPPVFESFY 230
BLAST of SMED30026794 vs. Planmine SMEST
Match: SMESG000039476.1 (SMESG000039476.1) HSP 1 Score: 152.525 bits (384), Expect = 1.319e-45 Identity = 88/229 (38.43%), Postives = 129/229 (56.33%), Query Frame = -2 Query: 26 QNQLGKVRVSQIALKDEIVHKSMRTLINQSGTRPKVYPFIHNKVLIPGDYRNLIEQFQIPTKMHSTIGIQEELPTHIFCHQLGSNLCWRCSRKMVNRKLKEQIETDLTNSEPEMFLRLICIENVLKDMNLPLFSNSETAPWKSGLSNSET--FSDGPLFFPNSQKTAQIELENVSNEISNLASNIKEKKKFTNKEINYRMINSNKTIQDSKREK-----KSMKYVEPPV 691 Q QLGKV + DE VH +R L+N + +H KVLIPGD+++LI Q++I +M S +I+C+QLGSNLCWRCSRK+V+ +LK +I L N +P++ RLIC+ENVLK+MNLPLFS+SE W + +S S+ PLFFP SN + ++ E KK+ + R + N + + + EK +S++++ PPV Sbjct: 7 QKQLGKVNLDYNISNDESVHSGLRQLLNTTNHLSNKSQIVHTKVLIPGDFQSLISQYRISDRMLSNADSSMIDDLNIYCNQLGSNLCWRCSRKIVDNRLKSEIHKALPNPDPDILPRLICVENVLKNMNLPLFSSSEVDDWNNCKLDSGVNKISNEPLFFP-----------YFSNPGDSFSAESSEMKKYETNGM--RHVTFNTSFMEEEHEKHPTHRRSIQFISPPV 222 The following BLAST results are available for this feature:
BLAST of SMED30026794 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30026794 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30026794 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30026794 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30026794 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30026794 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30026794 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30026794 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of SMED30026794 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30026794 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30026794 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30026794 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30026794 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30026794 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 >SMED30026794 ID=SMED30026794|Name=SMED30026794|organism=Schmidtea mediterranea sexual|type=transcript|length=740bpback to top protein sequence of SMED30026794-orf-1 >SMED30026794-orf-1 ID=SMED30026794-orf-1|Name=SMED30026794-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=231bp MKSQNQLGKVRVSQIALKDEIVHKSMRTLINQSGTRPKVYPFIHNKVLIPback 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
|