SMED30019990
Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ 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 AppSub-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., 2020SMED30019990 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Alignments
SMED30019990 aligns in the following genomic locations:
Homology
BLAST of SMED30019990 vs. Ensembl Zebrafish
Match: adora4a (adenosine A4 receptor a [Source:ZFIN;Acc:ZDB-GENE-131127-239]) HSP 1 Score: 50.447 bits (119), Expect = 2.210e-6 Identity = 62/258 (24.03%), Postives = 114/258 (44.19%), Query Frame = 1 Query: 457 PLLCLSVGEVVYVLITTVTA--FAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNSIIITLFNGLYAIIMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGKMASSYICIFYFG----PPMALAGFSYILCFYKLGNPGSSTVIVTK--SQRRLVITLSTSFVVIFIQSCFYPL----SIILFEGKEHLCHLTRRHFTWLILHNSLVNPVAFLSMYAY-----KRKYFR 1179 P CL V V L+ A A++ DM+V + + C + ++ +Q + T + V R L +C P +Y+ + K S II + A ++G++P ++++ + + + ++++C + ++ SY+ F F PP+A+ Y FYK+ + T +Q+ + S V+ C+ PL SI+ + ++ + L NS VNPV +YAY KR+Y R Sbjct: 46 PTFCLIVSLSVADLLVGAVAVPLALIVDMHVKMS---FHACLFISCFLIVPLQASVLTLLAIAVDRCLRVCIPFRYKSTVTKKRSWIIAAVCWMLAFMLGFLPMFGWYNHDTLAQH--NSTSIDCEF-VAVISISYLVHFIFEGCFLPPLAVMTALYYYVFYKIRRQSRGALGETGPYTQKEQKLASSLVLVLALFAVCWLPLHIIQSIMFYNHSVYVPSIALYSGILLSHANSAVNPV----VYAYKVPKMKREYMR 293
BLAST of SMED30019990 vs. Ensembl Nematostella
Match: EDO45454 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RSP6]) HSP 1 Score: 54.299 bits (129), Expect = 4.014e-8 Identity = 65/274 (23.72%), Postives = 120/274 (43.80%), Query Frame = 1 Query: 400 NIFMIAISLKDANLKGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNSIIITLFNGLYAI-IMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGK--MASSYICIFYFGPPMALAGFSYILCFYKL--------GNPGSSTVIVTKSQRRLVITLSTSFVVIFIQSCFYPLSII----LFEGKEHLCHLTRRHFTWLILHNSLVNPVAF-LSMYAYKRKY 1173 N+F++A+++ D ++ +LC+ + T V+ V G + C+V G + L + T L+ V RY I +P KY++ + +++ L G++ I +G IP + D+E Y P C+ K + +I Y P+ L G+ Y F ++ NP S+ + Q IT + + V + C+ P SII F G+ +T+L + +SL+NPV + ++ A++++Y Sbjct: 62 NMFVVALAVSDTSMG-----VLCMP-----FTFGTLVSGGWVFGK----------SFCYVHGFTGMTLALASIYTMSLISVNRYFCIVKPAKYQELFKKRRTVLYIL--GVWTIAFIGSIPPFFL-DDE---GYGFQPGKAMCLYKFETNLTFTIFIECVYIACPILLIGYCYSSVFREVYRTNKVFAPNPQSTDQLRAHIQ-ETKITKTLAIVFLGFSLCWVPASIIDTLGSFSGEPPFERPVYLAYTYLAMISSLINPVIYGVTSRAFRQEY 308
BLAST of SMED30019990 vs. Planmine SMEST
Match: SMESG000079521.1 (SMESG000079521.1) HSP 1 Score: 617.461 bits (1591), Expect = 0.000e+0 Identity = 311/312 (99.68%), Postives = 311/312 (99.68%), Query Frame = 1 Query: 286 VQSSTLSTDSIYLDFPRCGDVGAEVAYXXXXXXXSISGNIFMIAISLKDANLKGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNSIIITLFNGLYAIIMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGKMASSYICIFYFGPPMALAGFSYILCFYKLGNPGSSTVIVTKSQRRLVITLSTSFVVIFIQSCFYPLSIILFEGKEHLCHLTRRHFTWLILHNSLVNPVAFLSMYAYKRKYFRSGVVSSTFNETRAT 1221 VQSSTLSTDSIYLDFPRCGDVGAEVAYLVLVLVLSISGNIFMIAISLKDANLKGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNSIIITLFNGLYAIIMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGKMASSYICIFYFGPPM LAGFSYILCFYKLGNPGSSTVIVTKSQRRLVITLSTSFVVIFIQSCFYPLSIILFEGKEHLCHLTRRHFTWLILHNSLVNPVAFLSMYAYKRKYFRSGVVSSTFNETRAT Sbjct: 7 VQSSTLSTDSIYLDFPRCGDVGAEVAYLVLVLVLSISGNIFMIAISLKDANLKGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNSIIITLFNGLYAIIMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGKMASSYICIFYFGPPMVLAGFSYILCFYKLGNPGSSTVIVTKSQRRLVITLSTSFVVIFIQSCFYPLSIILFEGKEHLCHLTRRHFTWLILHNSLVNPVAFLSMYAYKRKYFRSGVVSSTFNETRAT 318
BLAST of SMED30019990 vs. Planmine SMEST
Match: SMESG000002315.1 (SMESG000002315.1) HSP 1 Score: 108.612 bits (270), Expect = 2.846e-26 Identity = 78/286 (27.27%), Postives = 146/286 (51.05%), Query Frame = 1 Query: 337 CGDVGAEVAYXXXXXXXSISGNIFMIAISLKDANL-KGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNS----IIITLFNGLYAIIMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGKMASSYICIFYFGPPMALAGFSYILCFYKL---GNPGSSTVIVTKSQRRLVITLSTSFVVIFIQSCFYPLSIILFEGKEHLCHLTRRHFTWLILHNSLVNPVAFLSMYAYKRK 1170 CG + YL +V ++++ GN ++ ++ ++ KGGMLP+ L++ ++++ + +T +L ++ VY L+ C + + + + + H +L V R++AIC P +Y+ + K + + LF + I+ +PS N F+ Y +PS L C+ YI + +GPP +A F YI C Y L G S+ V K Q RL + ++V++ I C YP +I + +C+L +R ++ IL+NS+V+P+ ++S+ R+ Sbjct: 11 CGAQTITLIYLSIVYIVALGGNTIILTVAWFNSEFRKGGMLPMFTLAICDMIFAHMAILTF--ILNMISEVYLKYTLHNCSLNSMIGSAVSAYVVYHHAILAVTRFIAICHPTRYKTILTTKTTGLFIFFVILFVTIITILTYLLPSPW---NSFMHPY-YNPSMLCCIYGSNWGIVLYIVLVVYGPPFHIATFCYIRCLYILKIKGKSSSTNSAVDKKQTRLAYIMLINYVIVNINCCLYPAAIYIETDDPMVCNLWKRFLSYCILNNSVVSPIVYISLNKKIRQ 290 The following BLAST results are available for this feature:
BLAST of SMED30019990 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30019990 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30019990 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30019990 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 1
BLAST of SMED30019990 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30019990 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30019990 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30019990 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30019990 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30019990 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30019990 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30019990 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 1
BLAST of SMED30019990 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30019990 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 2
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30019990 ID=SMED30019990|Name=SMED30019990|organism=Schmidtea mediterranea sexual|type=transcript|length=1307bpback to top protein sequence of SMED30019990-orf-1 >SMED30019990-orf-1 ID=SMED30019990-orf-1|Name=SMED30019990-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=272bp MIAISLKDANLKGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIRback 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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