SMED30026061
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., 2020SMED30026061 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 7Note: Hover over icons to view figure legend
Homology
BLAST of SMED30026061 vs. Planmine SMEST
Match: SMESG000039041.1 (SMESG000039041.1) HSP 1 Score: 219.55 bits (558), Expect = 2.164e-70 Identity = 109/136 (80.15%), Postives = 117/136 (86.03%), Query Frame = 3 Query: 366 FRLDDSWIDASRITVRFPAHASNRCRQAMLDTGFTVS*VKEARFGRQ*QLEEIELPCVAIKREPGRNPAGEIRGHAVFLLARLEEHQRQTNAQVESARRYLANVNDDIAAGRIPSTDGYAPPYNTSFNLDDSSLNT 773 F LDDSWID+SRITVRFPAHA+NRCRQA+ D GFTVS KE+RFG+Q EEI+LP VAIKREPGRN A EIRGHA FL+A LEEHQRQT+A VESARRYLANVNDDIA GRI STDGYAP YNTSFNLDD LNT Sbjct: 13 FGLDDSWIDSSRITVRFPAHAANRCRQALWDAGFTVSQAKESRFGQQRPSEEIKLPFVAIKREPGRNSAREIRGHAEFLIAPLEEHQRQTDAHVESARRYLANVNDDIAKGRILSTDGYAPSYNTSFNLDDRRLNT 148 HSP 2 Score: 67.3958 bits (163), Expect = 2.164e-70 Identity = 31/49 (63.27%), Postives = 40/49 (81.63%), Query Frame = 1 Query: 775 KSKALDVVVSRRILPRNMKAERERNYEYREHPYARTTPRRDDYKRHYGP 921 SK ++VVV RILPRNM+ E+E+ E+REHPYAR PRRD++KR+YGP Sbjct: 149 NSKTINVVVPWRILPRNMRTEKEQIDEHREHPYARINPRRDNHKRYYGP 197
BLAST of SMED30026061 vs. Planmine SMEST
Match: SMESG000042239.1 (SMESG000042239.1) HSP 1 Score: 205.297 bits (521), Expect = 6.943e-61 Identity = 101/136 (74.26%), Postives = 113/136 (83.09%), Query Frame = 3 Query: 369 RLDDSWIDASRITVRFPAHASNRCRQAMLDTGFTVS*VKEARFGRQ*QLEEIELPCVAIKREPGRNPAGEIRGHAVFLLARLEEHQRQTNAQVESARRYLANVNDDIAAGRIPSTDGYAPPYNTSFNLDDSSLNTK 776 R ++SWID SR+TVRFPAHA+NRC QAM D GFTVS V+E+R G Q+EE+EL VAIKREPGRNPA EIRG A FLLA LEEHQRQT+ QV+ ARRYLA+VN+DIAAGRI TD YAPPYNTSFNLDD LNTK Sbjct: 50 RANESWIDESRVTVRFPAHAANRCLQAMCDAGFTVSQVRESRSGTPQQMEEVELRFVAIKREPGRNPAREIRGQAEFLLASLEEHQRQTDIQVDRARRYLASVNEDIAAGRIACTDCYAPPYNTSFNLDDERLNTK 185
BLAST of SMED30026061 vs. Planmine SMEST
Match: SMESG000000026.1 (SMESG000000026.1) HSP 1 Score: 116.316 bits (290), Expect = 1.995e-58 Identity = 59/71 (83.10%), Postives = 61/71 (85.92%), Query Frame = 3 Query: 561 RNPAGEIRGHAVFLLARLEEHQRQTNAQVESARRYLANVNDDIAAGRIPSTDGYAPPYNTSFNLDDSSLNT 773 RNPA EIRGHA FLLARLEEHQ QT+AQ+ESARRYLANVNDDIA RI STDG AP YNTSFNLDD LNT Sbjct: 77 RNPAREIRGHAEFLLARLEEHQLQTDAQMESARRYLANVNDDIAKRRILSTDGNAPSYNTSFNLDDRRLNT 147 HSP 2 Score: 77.0258 bits (188), Expect = 1.995e-58 Identity = 43/73 (58.90%), Postives = 46/73 (63.01%), Query Frame = 2 Query: 356 LKLFSFRRFVDRCIPDHGTLPRTCVKSMSPGHVGYGIHRVLGQGGKVWKTIAIGGDRAPVCCHKTRTGTQPGR 574 L + S RF+DR I DHG LPRT KS+SPG VG GIHR QG KV T IGGDR PVC HKT P R Sbjct: 9 LSIQSKFRFMDRLILDHGALPRTRGKSVSPGPVGCGIHRTPSQGVKVRTTTTIGGDRTPVCRHKTGARRNPAR 81 HSP 3 Score: 74.3294 bits (181), Expect = 1.995e-58 Identity = 35/51 (68.63%), Postives = 41/51 (80.39%), Query Frame = 1 Query: 778 SKALDVVVSRRILPRNMKAERERNYEYREHPYARTTPRRDDYKRHYGPNCN 930 SKA++VVV RRILP NM E+E+ E+REHPYAR PRR+ YKRHYGP CN Sbjct: 149 SKAINVVVPRRILPPNMMTEKEQIDEHREHPYARINPRRESYKRHYGPYCN 199
BLAST of SMED30026061 vs. Planmine SMEST
Match: SMESG000057616.1 (SMESG000057616.1) HSP 1 Score: 162.54 bits (410), Expect = 3.353e-56 Identity = 82/103 (79.61%), Postives = 88/103 (85.44%), Query Frame = 3 Query: 465 FTVS*VKEARFGRQ*QLEEIELPCVAIKREPGRNPAGEIRGHAVFLLARLEEHQRQTNAQVESARRYLANVNDDIAAGRIPSTDGYAPPYNTSFNLDDSSLNT 773 FTVS VKE+R G+Q E+IELP VAIKRE GRNPA EIRGHA FLLA LEEHQRQT+AQVE+ARRYLANVN+DI GRI STDGYAPPYNTSFNLDD LNT Sbjct: 16 FTVSQVKESRSGQQRPYEKIELPFVAIKREQGRNPAREIRGHAEFLLAHLEEHQRQTDAQVENARRYLANVNNDIVTGRILSTDGYAPPYNTSFNLDDRRLNT 118 HSP 2 Score: 77.0258 bits (188), Expect = 3.353e-56 Identity = 36/49 (73.47%), Postives = 43/49 (87.76%), Query Frame = 1 Query: 778 SKALDVVVSRRILPRNMKAERERNYEYREHPYARTTPRRDDYKRHYGPN 924 SKA+DVVV RRIL R+M+A +ERN E+REHPYAR PRRD++KRHYGPN Sbjct: 120 SKAVDVVVPRRILSRDMRAGKERNDEHREHPYARMNPRRDNFKRHYGPN 168 HSP 3 Score: 51.6026 bits (122), Expect = 7.391e-7 Identity = 28/69 (40.58%), Postives = 42/69 (60.87%), Query Frame = 3 Query: 384 WIDASRITVRFPAHASNRCRQAMLDTGFTVS*VKEARFGRQ*--QLEEIELPCVAIKREPGRNPAGEIR 584 W D SR+T+R ++ + R RQ + D G+ ++ + R+ + +EIELP +AIKREP RN A E R Sbjct: 177 WSDDSRVTLRISSNTAARYRQVLWDQGYELATYGGPGWPRRPNDRGDEIELPSIAIKREPDRNSAREAR 245
BLAST of SMED30026061 vs. Planmine SMEST
Match: SMESG000011208.1 (SMESG000011208.1) HSP 1 Score: 201.06 bits (510), Expect = 2.042e-55 Identity = 99/133 (74.44%), Postives = 109/133 (81.95%), Query Frame = 3 Query: 378 DSWIDASRITVRFPAHASNRCRQAMLDTGFTVS*VKEARFGRQ*QLEEIELPCVAIKREPGRNPAGEIRGHAVFLLARLEEHQRQTNAQVESARRYLANVNDDIAAGRIPSTDGYAPPYNTSFNLDDSSLNTK 776 DSWID SRITVRFP HA+NRCRQAMLD GFTVS VKE+RFG Q +E+EL VAIKR+PG NPA IR A FLLARLEEHQRQT+ V+ ARRYL NVNDDIAAGRI STDGY+PPYNTSFNL D LN++ Sbjct: 68 DSWIDESRITVRFPPHAANRCRQAMLDAGFTVSQVKESRFGTLQQTKEVELLFVAIKRKPGHNPARGIRSQAEFLLARLEEHQRQTDIHVDQARRYLDNVNDDIAAGRIASTDGYSPPYNTSFNLHDERLNSR 200 The following BLAST results are available for this feature:
BLAST of SMED30026061 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30026061 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30026061 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30026061 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30026061 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30026061 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30026061 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30026061 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30026061 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30026061 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30026061 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30026061 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30026061 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30026061 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 >SMED30026061 ID=SMED30026061|Name=SMED30026061|organism=Schmidtea mediterranea sexual|type=transcript|length=2575bpback to top protein sequence of SMED30026061-orf-1 >SMED30026061-orf-1 ID=SMED30026061-orf-1|Name=SMED30026061-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=138bp MNILKLFSFRRFVDRCIPDHGTLPRTCVKSMSPGHVGYGIHRVLGQGGKVback to top Annotated Terms
The following terms have been associated with this transcript:
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