SMED30007370
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., 2020SMED30007370 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Alignments
SMED30007370 aligns in the following genomic locations:
Homology
BLAST of SMED30007370 vs. TrEMBL
Match: A0A4U5P0B1 (PH domain-containing protein OS=Steinernema carpocapsae OX=34508 GN=L596_013490 PE=4 SV=1) HSP 1 Score: 73.559 bits (179), Expect = 9.538e-12 Identity = 38/127 (29.92%), Postives = 69/127 (54.33%), Query Frame = 3 Query: 111 IRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRIRLNKVFKYIAVGKIC-NMVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTETSLD 488 +R G+L Y + FF S W C+++LY D T E+Y + + + LN++ YI VG + N++ RP+LP++V ID ++G + + +F FS ++++ W + I + + E S+D Sbjct: 6 VRTGWLLFYKKHFFR--SKWTRCFAVLYNDSTLEWYEKENSKNPIDSVSLNELVPYICVGYLSNNIIEIRPNLPANVSIDNLVGIKANAHPAQTHVHWFLFSCKQELDDWFKDITKTIEESVEGSVD 130
BLAST of SMED30007370 vs. TrEMBL
Match: A0A1I7YR72 (PH domain-containing protein OS=Steinernema glaseri OX=37863 PE=4 SV=1) HSP 1 Score: 72.4034 bits (176), Expect = 2.550e-11 Identity = 39/138 (28.26%), Postives = 70/138 (50.72%), Query Frame = 3 Query: 111 IRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRIRLNKVFKYIAVGKICNMVPS-RPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTETSLDSKLVRENMVNG 521 +R G+L Y + FF S WK C+++LY D T E++ H + + L ++ YI VG + N + RP LP D+ I ++G ++ + + +F F E++ W + I + + E ++D E++V G Sbjct: 6 VRTGWLLFYRKRFFS--SKWKKCFAVLYGDSTLEWFAKENSKHPIDSVSLRELVPYICVGPLSNNICEIRPKLPEDMSIHQLVGIKANTHESQAHVHWFLFDSPEEVDQWFKDITRTIEESVEGTVDKN---EDLVYG 138
BLAST of SMED30007370 vs. TrEMBL
Match: V4AF60 (PH domain-containing protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_233270 PE=4 SV=1) HSP 1 Score: 73.1738 bits (178), Expect = 1.012e-10 Identity = 41/117 (35.04%), Postives = 61/117 (52.14%), Query Frame = 3 Query: 111 IRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRIRLNKVFKYIAVGKICNMVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVL 461 I+ GYL Y++ FF S WK Y +LY D T +Y + ++L V K++AVG VP+RPDLP I +I FP K +++ + +DQ ++ WM+ I S L Sbjct: 18 IKTGYLKRYNKGFFS--SGWKQEYLVLYQDSTLAWYEDQGSYEPKGGVKLKNVCKFLAVGAYSQNVPNRPDLPPGGRITNLIAFPLKPDKK-AQVIWILCADQNELNSWMKDITSTL 131
BLAST of SMED30007370 vs. TrEMBL
Match: A0A4U5P0B5 (PH domain-containing protein OS=Steinernema carpocapsae OX=34508 GN=L596_013492 PE=4 SV=1) HSP 1 Score: 72.7886 bits (177), Expect = 1.396e-10 Identity = 41/131 (31.30%), Postives = 60/131 (45.80%), Query Frame = 3 Query: 90 LSSE*MIIRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRIRLNKVFKYIAVGKICNMVP-SRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTET 479 + E IR GYL Y FF WK CY++L+ D TF +Y DS + + L V YI VG +C+ +P RP++P D + ++G + +F F D+ W + I LP E Sbjct: 1 MEGERRKIRDGYLQRYKSGFFS--KKWKDCYAVLWSDSTFSWYDEKGDSSPVDSVFLKDVIPYICVGLLCDKMPVKRPEVPEDSTVHHLVGIGM--DPKAETVHWFMFGSDSDLEAWFKDITRTLPKPAEQ 127
BLAST of SMED30007370 vs. TrEMBL
Match: R7UAM5 (PH domain-containing protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_191509 PE=4 SV=1) HSP 1 Score: 70.8626 bits (172), Expect = 8.975e-10 Identity = 38/118 (32.20%), Postives = 58/118 (49.15%), Query Frame = 3 Query: 111 IRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRIRLNKVFKYIAVGKICNMVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLP 464 +R GYL Y + + WK Y ++Y D + ++ D L V Y+ VG C +P P+LP++ ID MI FP K S++ +F D+ ++ WM +I SVLP Sbjct: 8 VRSGYLQKYSKGM--LGEKWKRVYVVIYKDSSIFWFKKKDDPASKGNASLKNVCNYLTVGANCRAIPYSPELPANARIDFMIAFPQEPVKK-SKVHFFLCDDEAELNDWMTSISSVLP 122
BLAST of SMED30007370 vs. Planmine SMEST
Match: SMESG000045571.1 (SMESG000045571.1) HSP 1 Score: 286.574 bits (732), Expect = 1.924e-97 Identity = 171/171 (100.00%), Postives = 171/171 (100.00%), Query Frame = 3 Query: 303 MVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTETSLDSKLVRENMVNGDNKVETGTVNRHDPGYGKXXXXXXXXXXXXXXGYDPAIXXXXXXXXXXXXXVAMTMPMWAMSSAWCPPTIIHTGSPMLIDGTNTITVGNDITMPMGGD 815 MVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTETSLDSKLVRENMVNGDNKVETGTVNRHDPGYGKNTNYYYHNNPNYHYGYDPAIGAAAGLGLGMGLGVAMTMPMWAMSSAWCPPTIIHTGSPMLIDGTNTITVGNDITMPMGGD Sbjct: 1 MVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTETSLDSKLVRENMVNGDNKVETGTVNRHDPGYGKNTNYYYHNNPNYHYGYDPAIGAAAGLGLGMGLGVAMTMPMWAMSSAWCPPTIIHTGSPMLIDGTNTITVGNDITMPMGGD 171 The following BLAST results are available for this feature:
BLAST of SMED30007370 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30007370 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30007370 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30007370 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30007370 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30007370 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30007370 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30007370 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 5
BLAST of SMED30007370 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30007370 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30007370 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30007370 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30007370 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30007370 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 1
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30007370 ID=SMED30007370|Name=SMED30007370|organism=Schmidtea mediterranea sexual|type=transcript|length=966bpback to top protein sequence of SMED30007370-orf-1 >SMED30007370-orf-1 ID=SMED30007370-orf-1|Name=SMED30007370-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=267bp MIIRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRIback 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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