SMED30020818
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., 2020SMED30020818 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Homology
BLAST of SMED30020818 vs. Planmine SMEST
Match: SMESG000017552.1 (SMESG000017552.1) HSP 1 Score: 351.288 bits (900), Expect = 1.229e-109 Identity = 173/185 (93.51%), Postives = 177/185 (95.68%), Query Frame = 3 Query: 198 MKKFYTLTFNSTGQKAGSDKLFNIKPQLSYFLENTNVNHFTNIRTDAPARHLPGSIDDYGNKIFENSLSELRLLTIENNADPYLIELYYMIYVFLNGSMEIPIDDAVRFWNKIKITDILGFYPSEQIDQLLTKPFELEGLQSKILYALNIFRNLIAEVVTFDILLNYKYLHFFCNKLYFNITKNF 752 MKKF TLT +STGQKAGSDKLFNIKPQLSYFLENTNVNHF NIRTDAP R LPGSIDDYGNKIFEN LSELRLLTIENNADPYLIELYY IYVFLNGSMEIPIDDAVRFWNKIKITDILG YPSEQIDQLLTKPFELEGLQSKILYALNIFR+LIA+VVTFDILLNYKYL+FFCNKLYFNITKNF Sbjct: 1 MKKFNTLTLDSTGQKAGSDKLFNIKPQLSYFLENTNVNHFMNIRTDAPVRPLPGSIDDYGNKIFENRLSELRLLTIENNADPYLIELYYKIYVFLNGSMEIPIDDAVRFWNKIKITDILGSYPSEQIDQLLTKPFELEGLQSKILYALNIFRDLIADVVTFDILLNYKYLNFFCNKLYFNITKNF 185
BLAST of SMED30020818 vs. Planmine SMEST
Match: SMESG000012629.1 (SMESG000012629.1) HSP 1 Score: 312.383 bits (799), Expect = 1.781e-99 Identity = 158/185 (85.41%), Postives = 167/185 (90.27%), Query Frame = 3 Query: 198 MKKFYTLTFNSTGQKAGSDKLFNIKPQLSYFLENTNVNHFTNIRTDAPARHLPGSIDDYGNKIFENSLSELRLLTIENNADPYLIELYYMIYVFLNGSMEIPIDDAVRFWNKIKITDILGFYPSEQIDQLLTKPFELEGLQSKILYALNIFRNLIAEVVTFDILLNYKYLHFFCNKLYFNITKNF 752 MKKF NST QKAGSDKLFN K QLSY LENTNVN+F NIRTDAP LPGSID+YGNKIFENSLSELRL+TIENNADPYLIEL Y IYVFLNGSMEIPIDDAV+FWNKIK+TDILG Y S+QIDQLLTKP ELEGLQSKILYALNIFR+LIA+VVTFDILLNYKYL+FFCNKLYFNITKNF Sbjct: 1 MKKFDN--SNSTEQKAGSDKLFNTKSQLSYILENTNVNNFMNIRTDAPVGPLPGSIDNYGNKIFENSLSELRLITIENNADPYLIELCYKIYVFLNGSMEIPIDDAVKFWNKIKLTDILGSYASQQIDQLLTKPLELEGLQSKILYALNIFRDLIADVVTFDILLNYKYLNFFCNKLYFNITKNF 183
BLAST of SMED30020818 vs. Planmine SMEST
Match: SMESG000017552.1 (SMESG000017552.1) HSP 1 Score: 278.1 bits (710), Expect = 5.903e-83 Identity = 136/144 (94.44%), Postives = 139/144 (96.53%), Query Frame = 3 Query: 321 NIRTDAPARHLPGSIDDYGNKIFENSLSELRLLTIENNADPYLIELYYMIYVFLNGSMEIPIDDAVRFWNKIKITDILGFYPSEQIDQLLTKPFELEGLQSKILYALNIFRNLIAEVVTFDILLNYKYLHFFCNKLYFNITKNF 752 NIRTDAP R LPGSIDDYGNKIFEN LSELRLLTIENNADPYLIELYY IYVFLNGSMEIPIDDAVRFWNKIKITDILG YPSEQIDQLLTKPFELEGLQSKILYALNIFR+LIA+VVTFDILLNYKYL+FFCNKLYFNITKNF Sbjct: 2 NIRTDAPVRPLPGSIDDYGNKIFENRLSELRLLTIENNADPYLIELYYKIYVFLNGSMEIPIDDAVRFWNKIKITDILGSYPSEQIDQLLTKPFELEGLQSKILYALNIFRDLIADVVTFDILLNYKYLNFFCNKLYFNITKNF 145
BLAST of SMED30020818 vs. Planmine SMEST
Match: SMESG000003342.1 (SMESG000003342.1) HSP 1 Score: 170.629 bits (431), Expect = 4.477e-44 Identity = 126/256 (49.22%), Postives = 159/256 (62.11%), Query Frame = 3 Query: 1524 KAVDTLDLCKLTTSYKQTPFIELSKSSITYTSYTPCTKSISLHPTPSKHQSPAPNIKLTKSCTTFTTCSNYTPYNNENLLDNSISNNPITPTTTCDLNINYTTTSNTAQQINNNILTKSITTTQTYNMGRFYQNFLMHFNEYDNTYDTYEHNDYTPFYHSLVE----IFQSPIYNNKDTIIPTDDFYIHFITTTRPTSDINLTKSNMTFITCNDKTTVNYNLPKTFNLEHKFNYLEIYYLNNDTYDHETSSCFQPL 2279 +A++TLD K T+S T I+LSKSS T+T+Y PC K P +KLTKS TTFTTCS Y NENL +NSISNNPIT +TCD N TT++ N ILT TTQ YNMGR+YQN ++ +E DNTY+T++H D+ P L + IFQSPIY + D ++IH +TT RPTS I LTKSN T TCNDKTT N+N PKT+NL +KF++ + Y+ D YD+E SCF P Sbjct: 228 EAIETLDFFKHTSS--PTSCIKLSKSSTTFTNYIPCNK--------------LPTLKLTKSNTTFTTCS---IYKNENLFENSISNNPITSPSTCDTN---YTTTSNTTPETNKILTMPPMTTQMYNMGRYYQNLTIYLDENDNTYETFDHYDFKPLCRPLGDPSDDIFQSPIYIQNGNMNQNDGYFIHSLTTKRPTSAIILTKSNTTTTTCNDKTTTNHNQPKTYNLAYKFSFTDTLYVGEDEYDYEIESCFLPF 461 HSP 2 Score: 117.472 bits (293), Expect = 9.064e-27 Identity = 75/179 (41.90%), Postives = 101/179 (56.42%), Query Frame = 3 Query: 138 NRYHYFTLFSSEPN*SHGKSMKKFY-TLTFNSTGQKAGSDKLFNIKPQLSYFLENTNVNHFTNIRTDAPARHLPGSIDDYGNKIFENSLSELRLLTIENNADPYLIELYYMIYVFLNGSMEIPIDDAVRFWNKIKITDILGFYPSEQIDQLLTKPFELEGLQSKILYALNIFRNLIAEV 671 NR +L +P H SMKKF TLTF+STG K+GSDK K ++ L N +N A ++ D IF+ SL ELR L EN+ DP+LIEL+Y ++VFLNG+ EI I DA R+WN+I T ++ + LLTKPF + QS+I YAL F++ I +V Sbjct: 60 NRREDISLAEKKP---HKTSMKKFINTLTFDSTGPKSGSDKFSIFKQPFTFTLANAKMN-----TCPAETQNTLSPTD----TIFQTSLFELRQLAEENDHDPHLIELHYRMFVFLNGTTEITITDATRYWNEISTTCTFDANITQTMQLLLTKPFNYDDSQSRINYALKTFQDAITDV 226
BLAST of SMED30020818 vs. Planmine SMEST
Match: SMESG000014823.1 (SMESG000014823.1) HSP 1 Score: 138.272 bits (347), Expect = 6.229e-37 Identity = 73/135 (54.07%), Postives = 95/135 (70.37%), Query Frame = 3 Query: 1887 TTQTYNMGRFYQNFLMHFNEYDNTYDTYEHNDYTPFYHSLVE----IFQSPIYNNKDTIIPTDDFYIHFITTTRPTSDINLTKSNMTFITCNDKTTVNYNLPKTFNLEHKFNYLEIYYLNNDTYDHETSSCFQPL 2279 TTQTYN+GR+YQN ++ +EYDNTY+TY+H D+ P L + IFQSPIY D I D ++IH +TT RPTSDINLTKSN+T TCNDKTT N+N PKT+NL +KF++ + YL + YD+E S + P Sbjct: 5 TTQTYNLGRYYQNLTIYLDEYDNTYETYDHYDFKPLCRPLGDPSDDIFQSPIYIQNDHINQNDGYFIHSLTTKRPTSDINLTKSNITITTCNDKTTTNHNEPKTYNLAYKFSFTDTIYLCQNKYDYEIESRYLPF 139 The following BLAST results are available for this feature:
BLAST of SMED30020818 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30020818 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30020818 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30020818 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30020818 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30020818 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30020818 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30020818 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30020818 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30020818 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30020818 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30020818 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30020818 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30020818 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 >SMED30020818 ID=SMED30020818|Name=SMED30020818|organism=Schmidtea mediterranea sexual|type=transcript|length=3226bpback to top protein sequence of SMED30020818-orf-1 >SMED30020818-orf-1 ID=SMED30020818-orf-1|Name=SMED30020818-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=251bp MGRFYQNFLMHFNEYDNTYDTYEHNDYTPFYHSLVEIFQSPIYNNKDTIIback to top protein sequence of SMED30020818-orf-2 >SMED30020818-orf-2 ID=SMED30020818-orf-2|Name=SMED30020818-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=308bp MKKFYTLTFNSTGQKAGSDKLFNIKPQLSYFLENTNVNHFTNIRTDAPARback to top |