SMED30011612
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., 2020SMED30011612 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30011612 aligns in the following genomic locations:
Homology
BLAST of SMED30011612 vs. Planmine SMEST
Match: SMESG000014679.1 (SMESG000014679.1) HSP 1 Score: 249.21 bits (635), Expect = 2.247e-81 Identity = 134/142 (94.37%), Postives = 136/142 (95.77%), Query Frame = 2 Query: 2 LISVLETVEVRLKAIHRDDELKRGYLLQRCLKKLSSTLLLNWKEMARLNESMGCLAKFREWLKIKMELLRSTKEMLFGIDENWNNDYKQTEWKDRRSKEKEMNNQVKPKRSFYAEKVVKQLQSSGKSASNKVECIKCEGEHY 427 LISVLETVEV LKAIHRD+ELKRGYLLQRCLKKLSSTLLLNWKEMARLNESM CLAKFREWLKIKMELLRSTKEMLF IDENWNNDYKQTEWKDRRSK KEM+NQVK KRSFYAEKVVKQLQSS KSASNKVECIKCEGEHY Sbjct: 387 LISVLETVEVHLKAIHRDNELKRGYLLQRCLKKLSSTLLLNWKEMARLNESMSCLAKFREWLKIKMELLRSTKEMLFSIDENWNNDYKQTEWKDRRSKGKEMDNQVKSKRSFYAEKVVKQLQSSVKSASNKVECIKCEGEHY 528
BLAST of SMED30011612 vs. Planmine SMEST
Match: SMESG000034883.1 (SMESG000034883.1) HSP 1 Score: 173.326 bits (438), Expect = 4.867e-52 Identity = 92/131 (70.23%), Postives = 108/131 (82.44%), Query Frame = 2 Query: 2 LISVLETVEVRLKAIHRDDELKRGYLLQRCLKKLSSTLLLNWKEMARLNESMGCLAKFREWLKIKMELLRSTKEMLFGIDENWNNDYKQTEWKDRRSKEKEMNNQVKPKRSFYAEKVVKQLQSSGKSASNK 394 LI VLETVEVRLK+I+RDDELK GY LQRCLKKLSS+LL+N KEMARLNESMGCLAKFREWL+IK+E LRSTKEMLFG+D W K+ EWK++RSK KEM++QVKPKRSF + K+LQS+ N+ Sbjct: 143 LIRVLETVEVRLKSINRDDELKSGYFLQRCLKKLSSSLLVNRKEMARLNESMGCLAKFREWLQIKVEFLRSTKEMLFGMDGKWKK-VKRPEWKNQRSKWKEMDDQVKPKRSF----MRKKLQSNYSQVENQ 268
BLAST of SMED30011612 vs. Planmine SMEST
Match: SMESG000074922.1 (SMESG000074922.1) HSP 1 Score: 91.6633 bits (226), Expect = 8.818e-23 Identity = 47/63 (74.60%), Postives = 52/63 (82.54%), Query Frame = 2 Query: 2 LISVLETVEVRLKAIHRDDELKRGYLLQRCLKKLSSTLLLNWKEMARLNESMGCLAKFREWLK 190 LISVLETVE+RL I R+DELK GYLLQRCLKK S+ LLLN K+MARLNE M AKFREWL+ Sbjct: 260 LISVLETVEMRLLVIIREDELKSGYLLQRCLKKSSNPLLLNLKDMARLNEPMSFFAKFREWLQ 322
BLAST of SMED30011612 vs. Planmine SMEST
Match: SMESG000000863.1 (SMESG000000863.1) HSP 1 Score: 78.1814 bits (191), Expect = 1.649e-17 Identity = 38/62 (61.29%), Postives = 46/62 (74.19%), Query Frame = 2 Query: 242 ENWNNDYKQTEWKDRRSKEKEMNNQVKPKRSFYAEKVVKQLQSSGKSASNKVECIKCEGEHY 427 E+ DYK EW D+RSK K+M++QVK KRSF+AE V K Q+S KSASN +CIKCE EHY Sbjct: 176 ESGKKDYKPPEWMDQRSKWKQMDDQVKTKRSFFAENVAKPFQASRKSASNNWQCIKCEREHY 237
BLAST of SMED30011612 vs. Planmine SMEST
Match: SMESG000067372.1 (SMESG000067372.1) HSP 1 Score: 74.3294 bits (181), Expect = 1.508e-16 Identity = 38/68 (55.88%), Postives = 49/68 (72.06%), Query Frame = 2 Query: 224 MLFGIDENWNNDYKQTEWKDRRSKEKEMNNQVKPKRSFYAEKVVKQLQSSGKSASNKVECIKCEGEHY 427 MLFG+DE DYK+ E +RSK KEM+++VKPKRSFYA+KV K LQ+S K+ SNK +CI E + Sbjct: 1 MLFGMDEELKKDYKRPEMNGQRSKWKEMDDKVKPKRSFYADKVDKPLQASRKAVSNKWKCINSNSERH 68 The following BLAST results are available for this feature:
BLAST of SMED30011612 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30011612 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30011612 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30011612 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30011612 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30011612 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30011612 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30011612 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30011612 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30011612 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30011612 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30011612 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30011612 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30011612 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 >SMED30011612 ID=SMED30011612|Name=SMED30011612|organism=Schmidtea mediterranea sexual|type=transcript|length=441bpback to top protein sequence of SMED30011612-orf-1 >SMED30011612-orf-1 ID=SMED30011612-orf-1|Name=SMED30011612-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp LISVLETVEVRLKAIHRDDELKRGYLLQRCLKKLSSTLLLNWKEMARLNEback 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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