SMED30026854
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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., 2020SMED30026854 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 6Note: Hover over icons to view figure legend
Alignments
SMED30026854 aligns in the following genomic locations: Homology
BLAST of SMED30026854 vs. Planmine SMEST
Match: SMESG000029285.1 (SMESG000029285.1) HSP 1 Score: 217.238 bits (552), Expect = 7.024e-68 Identity = 147/189 (77.78%), Postives = 159/189 (84.13%), Query Frame = 2
Query: 32 TRIIER*INCLLLQNAIEDKDIKREIKMRNISNVXXXXXXXXXXXXXXXXXXXXXXAAMKPFKRSYANVVQNQSQYLDXXXXXXXXXXXXXXXXXXXXXENTLTRREPFRNNNRFLDQRSLPSRPSVLPTQNRSDFSNSYERSNRRYE*LRSN**WGCKEV*LIRVQCPNIKCSHCKKASHLKFQCFDL 598
TRIIE+ + LLQ+AIEDKD+KREIKMRNI NVKEI+EIITKIEEINKEMKN+DIAAMKPFKR+Y+NVVQNQ+QYL + RQ QQHQRFRENTL +REPFRNNNRFLDQRSLPSRPS LPTQNRSDFSNSYERSNRRYE WGCKEV IR QCPNIKCSHCKKA HLKFQCF+L
Sbjct: 305 TRIIEKKLTAFLLQDAIEDKDVKREIKMRNIFNVKEIEEIITKIEEINKEMKNKDIAAMKPFKRTYSNVVQNQNQYL-----VQQYRQSQPTQQHQRFRENTLPQREPFRNNNRFLDQRSLPSRPSGLPTQNRSDFSNSYERSNRRYEQC-----WGCKEVGQIRAQCPNIKCSHCKKAGHLKFQCFNL 483
BLAST of SMED30026854 vs. Planmine SMEST
Match: SMESG000029285.1 (SMESG000029285.1) HSP 1 Score: 217.238 bits (552), Expect = 1.076e-67 Identity = 147/189 (77.78%), Postives = 159/189 (84.13%), Query Frame = 2
Query: 32 TRIIER*INCLLLQNAIEDKDIKREIKMRNISNVXXXXXXXXXXXXXXXXXXXXXXAAMKPFKRSYANVVQNQSQYLDXXXXXXXXXXXXXXXXXXXXXENTLTRREPFRNNNRFLDQRSLPSRPSVLPTQNRSDFSNSYERSNRRYE*LRSN**WGCKEV*LIRVQCPNIKCSHCKKASHLKFQCFDL 598
TRIIE+ + LLQ+AIEDKD+KREIKMRNI NVKEI+EIITKIEEINKEMKN+DIAAMKPFKR+Y+NVVQNQ+QYL + RQ QQHQRFRENTL +REPFRNNNRFLDQRSLPSRPS LPTQNRSDFSNSYERSNRRYE WGCKEV IR QCPNIKCSHCKKA HLKFQCF+L
Sbjct: 310 TRIIEKKLTAFLLQDAIEDKDVKREIKMRNIFNVKEIEEIITKIEEINKEMKNKDIAAMKPFKRTYSNVVQNQNQYL-----VQQYRQSQPTQQHQRFRENTLPQREPFRNNNRFLDQRSLPSRPSGLPTQNRSDFSNSYERSNRRYEQC-----WGCKEVGQIRAQCPNIKCSHCKKAGHLKFQCFNL 488
BLAST of SMED30026854 vs. Planmine SMEST
Match: SMESG000064279.1 (SMESG000064279.1) HSP 1 Score: 179.874 bits (455), Expect = 8.819e-57 Identity = 121/173 (69.94%), Postives = 130/173 (75.14%), Query Frame = 2
Query: 113 MRNISNVXXXXXXXXXXXXXXXXXXXXXXAAMKPFKRSYANVVQNQSQYLDXXXXXXXXXXXXXXXXXXXXXENTLTRREPFRNNNRFLDQRSLPSRPSVLPTQNRSDFSNSYERSNRRYE*LRSN**WGCKEV*LIRVQCPNIKCSHCKKASHLKFQCFDLRGTQSYRYQQN 631
MRNISNVKEIKEIITKIEEINKE KNEDIAAMKPFKRSYANV + ++ + Q + + RREP RNNNRFLDQ+SLPSRPSVLP QNRSDFSNSYE+SNRRYE LRS WGCKEV IR Q PNIK SHCKK+ H KFQCFD RGTQSYRYQQN
Sbjct: 1 MRNISNVKEIKEIITKIEEINKERKNEDIAAMKPFKRSYANVKKLSKIKINIYLNNIDNQNQDNNIKDFE----KILRREPIRNNNRFLDQKSLPSRPSVLPIQNRSDFSNSYEQSNRRYELLRSKQRWGCKEVGHIRAQYPNIKSSHCKKSGHFKFQCFDRRGTQSYRYQQN 169
BLAST of SMED30026854 vs. Planmine SMEST
Match: SMESG000009301.1 (SMESG000009301.1) HSP 1 Score: 164.081 bits (414), Expect = 1.635e-53 Identity = 79/105 (75.24%), Postives = 84/105 (80.00%), Query Frame = 2
Query: 329 ENTLTRREPFRNNNRFLDQRSLPSRPSVLPTQNRSDFSNSYERSNRRYE*LRSN**WGCKEV*LIRVQCPNIKCSHCKKASHLKFQCFDLRGTQSYRYQQNWQQL 643
+NTL RREPFRNNNR L +R LPSR S+LP QNRSD SNSYERSN+RYE LRS WGCKEV IR Q PNIKCS CKKA H KFQCFDLRGTQSYRYQQN +
Sbjct: 546 KNTLPRREPFRNNNRLLSERILPSRSSLLPIQNRSDISNSYERSNKRYEQLRSKQCWGCKEVEHIRAQYPNIKCSQCKKAGHFKFQCFDLRGTQSYRYQQNMAAI 650 HSP 2 Score: 64.3142 bits (155), Expect = 1.635e-53 Identity = 29/35 (82.86%), Postives = 31/35 (88.57%), Query Frame = 1
Query: 631 LAAITDQGDDENMMSDSEYLNGNAPTHEEVIGTID 735
+AAI DQGDDENMMSDSEY NGNAPT EEVIG I+
Sbjct: 647 MAAIIDQGDDENMMSDSEYPNGNAPTEEEVIGAIN 681
BLAST of SMED30026854 vs. Planmine SMEST
Match: SMESG000037636.1 (SMESG000037636.1) HSP 1 Score: 145.976 bits (367), Expect = 9.991e-44 Identity = 72/93 (77.42%), Postives = 78/93 (83.87%), Query Frame = 2
Query: 365 NNRFLDQRSLPSRPSVLPTQNRSDFSNSYERSNRRYE*LRSN**WGCKEV*LIRVQCPNIKCSHCKKASHLKFQCFDLRGTQSYRYQQNWQQL 643
NN+FLDQ+SLPSRPSVLPTQNRS+FSNSYERSNRRYE LRS W KEV IR Q PNIKCS+CKKA HLKF CFDLRGT+SYRYQQN +
Sbjct: 1127 NNQFLDQKSLPSRPSVLPTQNRSNFSNSYERSNRRYEQLRSKQCWRYKEVGHIRAQYPNIKCSYCKKAGHLKFHCFDLRGTESYRYQQNMAAI 1219 HSP 2 Score: 49.2914 bits (116), Expect = 9.991e-44 Identity = 21/32 (65.62%), Postives = 26/32 (81.25%), Query Frame = 1
Query: 631 LAAITDQGDDENMMSDSEYLNGNAPTHEEVIG 726
+AAI QGDD+ MMSDS+Y N NAPT EE++G
Sbjct: 1216 MAAIAYQGDDKKMMSDSKYQNANAPTQEELLG 1247 The following BLAST results are available for this feature:
BLAST of SMED30026854 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30026854 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30026854 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30026854 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30026854 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30026854 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30026854 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30026854 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30026854 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30026854 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30026854 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30026854 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30026854 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30026854 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 >SMED30026854 ID=SMED30026854|Name=SMED30026854|organism=Schmidtea mediterranea sexual|type=transcript|length=745bpback to top protein sequence of SMED30026854-orf-1 >SMED30026854-orf-1 ID=SMED30026854-orf-1|Name=SMED30026854-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=122bp MRNISNVKEIKEIITKIEEINKEMKNEDIAAMKPFKRSYANVVQNQSQYLback to top Annotated Terms
The following terms have been associated with this transcript:
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