GCR098
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., 2020SMED30007555 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 15
Homology
BLAST of GCR098 vs. TrEMBL
Match: A0A193KUB5 (GCR098 OS=Schmidtea mediterranea OX=79327 GN=gcr098 PE=2 SV=1) HSP 1 Score: 288.115 bits (736), Expect = 2.986e-92 Identity = 157/340 (46.18%), Postives = 239/340 (70.29%), Query Frame = 3 Query: 12 MNYSLNYTKTYSVNSPEENT---VIHLFSVYSIIVLFLIGSVTDSICLWRLKRLKCFANVKFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYGIYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVISVKLCYSYQRKSGLFSHYGSSQNVELNIVGKPSVANMILTIAPVSHKHQXXXXXXXXXXXXXXXXXXXPKNLLKLLKIVSNTNHFESIFYEIVPFLLHLLKFSVKSIIVQIFISLM 1022 M +LN T ++ EE ++ +F+++++I+LF GSV +S LWRL+ L+ NV+ A+ +L+ L +DLSNLIVSG +WL+N L V LSD+S KN+LCKSFNM TH C FLNQW +S +++ERC+F+++ K+NK+ FS+LR++IGLFLGFCLSFALFCNY+S+YG+ L++N Y+C V M+IY V YLE++LEF++PQ +T++SIV +++ LC++ + K GLF S + V L+ KPS+++ +L + +S K+QI+ I++ Y++ IIDI LDFPK+L ++ V+N+ FES +E + LHL KF K + V ++IS+M Sbjct: 1 MRLALNSTLKDNLLIKEELRQMYIMAMFNIFALIILFAFGSVANSFALWRLRNLEAVKNVRCGALFILRTMLFVDLSNLIVSGLFYWLINSLGVFNYLSDQSIFKNILCKSFNMLTHFCFFLNQWTVSIMALERCVFVISRKLNKSLFSMLRLRIGLFLGFCLSFALFCNYLSMYGLRLEENNTYSCDVLAEIMAIYLNLVPYLEMILEFLIPQTVTILSIVTMAILLCHTQRLKLGLFVRGQSDEEVGLDRTTKPSISHFVLLPSRLSEKNQIFLIHVCYILSIIDIGLDFPKSLTRMYFTVTNSIFFESFIFENILIALHLFKFCCKGVGVHVYISIM 340
BLAST of GCR098 vs. Planmine SMEST
Match: SMESG000016695.1 (SMESG000016695.1) HSP 1 Score: 620.542 bits (1599), Expect = 0.000e+0 Identity = 337/337 (100.00%), Postives = 337/337 (100.00%), Query Frame = 3 Query: 12 MNYSLNYTKTYSVNSPEENTVIHLFSVYSIIVLFLIGSVTDSICLWRLKRLKCFANVKFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYGIYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVISVKLCYSYQRKSGLFSHYGSSQNVELNIVGKPSVANMILTIAPVSHKHQXXXXXXXXXXXXXXXXXXXPKNLLKLLKIVSNTNHFESIFYEIVPFLLHLLKFSVKSIIVQIFISLM 1022 MNYSLNYTKTYSVNSPEENTVIHLFSVYSIIVLFLIGSVTDSICLWRLKRLKCFANVKFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYGIYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVISVKLCYSYQRKSGLFSHYGSSQNVELNIVGKPSVANMILTIAPVSHKHQIYFIYISYLICIIDICLDFPKNLLKLLKIVSNTNHFESIFYEIVPFLLHLLKFSVKSIIVQIFISLM Sbjct: 1 MNYSLNYTKTYSVNSPEENTVIHLFSVYSIIVLFLIGSVTDSICLWRLKRLKCFANVKFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYGIYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVISVKLCYSYQRKSGLFSHYGSSQNVELNIVGKPSVANMILTIAPVSHKHQIYFIYISYLICIIDICLDFPKNLLKLLKIVSNTNHFESIFYEIVPFLLHLLKFSVKSIIVQIFISLM 337
BLAST of GCR098 vs. Planmine SMEST
Match: SMESG000016694.1 (SMESG000016694.1) HSP 1 Score: 287.73 bits (735), Expect = 7.208e-96 Identity = 151/317 (47.63%), Postives = 230/317 (72.56%), Query Frame = 3 Query: 72 VIHLFSVYSIIVLFLIGSVTDSICLWRLKRLKCFANVKFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYGIYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVISVKLCYSYQRKSGLFSHYGSSQNVELNIVGKPSVANMILTIAPVSHKHQXXXXXXXXXXXXXXXXXXXPKNLLKLLKIVSNTNHFESIFYEIVPFLLHLLKFSVKSIIVQIFISLM 1022 ++ +F+++++I+LF GSV +S LWRL+ L+ NV+ A+ +L+ L +DLSNLIVSG +WL+N L V LSD+S KN+LCKSFNM TH C FLNQW +S +++ERC+F+++ K+NK+ FS+LR++IGLFLGFCLSFALFCNY+S+YG+ L++N Y+C V M+IY V YLE++LEF++PQ +T++SIV +++ LC++ + K GLF S + V L+ KPS+++ +L + +S K+QI+ I++ Y++ IIDI LDFPK+L ++ V+N+ FES +E + LHL KF K + V ++IS+M Sbjct: 3 IMAMFNIFALIILFAFGSVANSFALWRLRNLEAVKNVRCGALFILRTMLFVDLSNLIVSGLFYWLINSLGVFNYLSDQSIFKNILCKSFNMLTHFCFFLNQWTVSIMALERCVFVISRKLNKSLFSMLRLRIGLFLGFCLSFALFCNYLSMYGLRLEENNTYSCDVLAEIMAIYLNLVPYLEMILEFLIPQTVTILSIVTMAILLCHTQRLKLGLFVRGQSDEEVGLDRTTKPSISHFVLLPSRLSEKNQIFLIHVCYILSIIDIGLDFPKSLTRMYFTVTNSIFFESFIFENILIALHLFKFCCKGVGVHVYISIM 319
BLAST of GCR098 vs. Planmine SMEST
Match: SMESG000051040.1 (SMESG000051040.1) HSP 1 Score: 88.9669 bits (219), Expect = 9.558e-20 Identity = 50/165 (30.30%), Postives = 90/165 (54.55%), Query Frame = 3 Query: 183 KFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYG-IYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVI 674 K + +L+ I+++ NL SGFL WL N V + N++CK +N H + + +W+ +S++R ++ ++ + ++ YF++ R+KIG+ + F + + NY+ I+G I D +G C V F IYY + LEI E LP+ ITL ++++ Sbjct: 54 KIGGLFVLECVSIVEILNLFNSGFLNWLFNYTEVMLKIQSSKFGINLICKLYNFLPHTGLLIGEWLGVWLSVDRLLYTISKRKSRQYFTVFRLKIGMIMFFAVLLSALFNYLWIFGWILPDPSGHRQCYVLPEFFYIYYNFINKLEIFFEIFLPESITLTLLIIV 218 The following BLAST results are available for this feature:
BLAST of GCR098 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of GCR098 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of GCR098 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of GCR098 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of GCR098 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of GCR098 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of GCR098 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of GCR098 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of GCR098 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of GCR098 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of GCR098 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of GCR098 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of GCR098 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of GCR098 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 3
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30007555 ID=SMED30007555|Name=GCR098|organism=Schmidtea mediterranea sexual|type=transcript|length=1023bpback to top protein sequence of SMED30007555-orf-1 >SMED30007555-orf-1 ID=SMED30007555-orf-1|Name=SMED30007555-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=340bp QQQMNYSLNYTKTYSVNSPEENTVIHLFSVYSIIVLFLIGSVTDSICLWRback 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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