SMED30030520
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., 2020SMED30030520 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Homology
BLAST of SMED30030520 vs. TrEMBL
Match: A0A355ABF2 (Uncharacterized protein OS=Flavobacteriaceae bacterium OX=1871037 GN=DDZ39_05755 PE=4 SV=1) HSP 1 Score: 63.929 bits (154), Expect = 5.976e-7 Identity = 29/53 (54.72%), Postives = 36/53 (67.92%), Query Frame = 1 Query: 1 MKQDVRQ*CNTCEICLTRRNTGHKIRVLLKPMPVPTAPMEMTTMDIVGPLPET 159 +K DV++ C TC ICL R+ R LLKP+ P+ PME T MDI+GPLPET Sbjct: 1872 LKDDVKEWCKTCNICLRRKGRAPS-RALLKPISSPSTPMETTAMDIMGPLPET 1923
BLAST of SMED30030520 vs. Planmine SMEST
Match: SMESG000032364.1 (SMESG000032364.1) HSP 1 Score: 154.451 bits (389), Expect = 4.713e-43 Identity = 76/93 (81.72%), Postives = 80/93 (86.02%), Query Frame = 2 Query: 167 YYRRKTISDPWLLTLVDRNFVRVHYENIYDEHPNKVELTIQNKSYLKFQNSTMGTSSDNNTYDIF-SQNRNKSLMINRTLYVLDSNDISCLFV 442 +Y RKTISDPW L LVDRNFVRV+YENIYDEH NKVELTI NKSYLKFQNS MGT SDNN YDI SQNR KSLMI TLYVLD+NDISC+FV Sbjct: 72 HYLRKTISDPWRLILVDRNFVRVYYENIYDEHANKVELTILNKSYLKFQNSAMGTPSDNNIYDIISSQNRKKSLMIKGTLYVLDNNDISCIFV 164
BLAST of SMED30030520 vs. Planmine SMEST
Match: SMESG000011497.1 (SMESG000011497.1) HSP 1 Score: 145.206 bits (365), Expect = 2.535e-41 Identity = 75/89 (84.27%), Postives = 80/89 (89.89%), Query Frame = 2 Query: 167 YYRRKTISDPWLLTLVDRNFVRVHYENIYDEHPNKVELTIQNKSYLKFQNSTMGTSSDNNTYDIF-SQNRNKSLMINRTLYVLDSNDIS 430 +YRRKTIS+ W LTLVDRNFVRV+YE I+DEH NKVE TIQNKSYLKFQNSTM TSSDNNTYDI SQNRNKSLMIN TLYVLD+NDIS Sbjct: 72 HYRRKTISNLWRLTLVDRNFVRVYYEKIHDEHQNKVEPTIQNKSYLKFQNSTMATSSDNNTYDIISSQNRNKSLMINGTLYVLDNNDIS 160
BLAST of SMED30030520 vs. Planmine SMEST
Match: SMESG000064337.1 (SMESG000064337.1) HSP 1 Score: 145.976 bits (367), Expect = 1.725e-38 Identity = 71/71 (100.00%), Postives = 71/71 (100.00%), Query Frame = 1 Query: 955 RSTYGIATSIDFIGSPFRGGNEHGILLFQVALAAIITTLKEAGWFLVVSADTSNETLSRSKQSDIKWSIYG 1167 RSTYGIATSIDFIGSPFRGGNEHGILLFQVALAAIITTLKEAGWFLVVSADTSNETLSRSKQSDIKWSIYG Sbjct: 401 RSTYGIATSIDFIGSPFRGGNEHGILLFQVALAAIITTLKEAGWFLVVSADTSNETLSRSKQSDIKWSIYG 471
BLAST of SMED30030520 vs. Planmine SMEST
Match: SMESG000064337.1 (SMESG000064337.1) HSP 1 Score: 145.976 bits (367), Expect = 2.079e-38 Identity = 71/71 (100.00%), Postives = 71/71 (100.00%), Query Frame = 1 Query: 955 RSTYGIATSIDFIGSPFRGGNEHGILLFQVALAAIITTLKEAGWFLVVSADTSNETLSRSKQSDIKWSIYG 1167 RSTYGIATSIDFIGSPFRGGNEHGILLFQVALAAIITTLKEAGWFLVVSADTSNETLSRSKQSDIKWSIYG Sbjct: 409 RSTYGIATSIDFIGSPFRGGNEHGILLFQVALAAIITTLKEAGWFLVVSADTSNETLSRSKQSDIKWSIYG 479
BLAST of SMED30030520 vs. Planmine SMEST
Match: SMESG000064344.1 (SMESG000064344.1) HSP 1 Score: 98.9821 bits (245), Expect = 4.153e-22 Identity = 45/71 (63.38%), Postives = 58/71 (81.69%), Query Frame = 1 Query: 955 RSTYGIATSIDFIGSPFRGGNEHGILLFQVALAAIITTLKEAGWFLVVSADTSNETLSRSKQSDIKWSIYG 1167 RS YG+A SIDF G FRG N HG++LFQ+ALAAII+ LK+ GW+L+VSADTSNET++ + ++IKWSIY Sbjct: 410 RSFYGVAYSIDFKGDAFRGSNLHGVILFQLALAAIISVLKDIGWYLLVSADTSNETMTVDENTEIKWSIYA 480 The following BLAST results are available for this feature:
BLAST of SMED30030520 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30030520 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30030520 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30030520 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30030520 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30030520 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30030520 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30030520 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of SMED30030520 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30030520 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30030520 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30030520 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30030520 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30030520 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 >SMED30030520 ID=SMED30030520|Name=SMED30030520|organism=Schmidtea mediterranea sexual|type=transcript|length=1389bpback to top protein sequence of SMED30030520-orf-1 >SMED30030520-orf-1 ID=SMED30030520-orf-1|Name=SMED30030520-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=138bp MYYRRKTISDPWLLTLVDRNFVRVHYENIYDEHPNKVELTIQNKSYLKFQback 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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