SMED30008334
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., 2020SMED30008334 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 21Note: Hover over icons to view figure legend
Homology
BLAST of SMED30008334 vs. Planmine SMEST
Match: SMESG000068971.1 (SMESG000068971.1) HSP 1 Score: 211.846 bits (538), Expect = 1.817e-63 Identity = 124/165 (75.15%), Postives = 140/165 (84.85%), Query Frame = 3 Query: 27 STILKSPTLVAANQXXXXXXXXXXXXXXXXXXXXEDPPRKNERSYKIIIKCSFTDEVYTTDYNNPTSAKYIDFKGRQFVKWQAALNAKLIRLIEIIINSLTSGSVKADMSLNVASTSALSTTDIQNTVTQAAQAAYGNSLQILSISAKQTSAAPKTQSWLATAFL 521 +TILKSPTLVAANQTTTVS TATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDE Y DY PTSA+YI+FK R KW+AAL KL+RLIEIIINSL+SGSVKADM +N+AS S++ST D+QNTVTQAAQAAYG+SLQ+ SI+A A+ QSW+A A L Sbjct: 677 ATILKSPTLVAANQTTTVSLTATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDETYYDDYKTPTSARYINFKARHHAKWKAALIFKLLRLIEIIINSLSSGSVKADMEMNIASNSSISTADLQNTVTQAAQAAYGSSLQVFSITATSLDASSTDQSWIAAAVL 841
BLAST of SMED30008334 vs. Planmine SMEST
Match: SMESG000068971.1 (SMESG000068971.1) HSP 1 Score: 211.846 bits (538), Expect = 1.929e-63 Identity = 124/165 (75.15%), Postives = 140/165 (84.85%), Query Frame = 3 Query: 27 STILKSPTLVAANQXXXXXXXXXXXXXXXXXXXXEDPPRKNERSYKIIIKCSFTDEVYTTDYNNPTSAKYIDFKGRQFVKWQAALNAKLIRLIEIIINSLTSGSVKADMSLNVASTSALSTTDIQNTVTQAAQAAYGNSLQILSISAKQTSAAPKTQSWLATAFL 521 +TILKSPTLVAANQTTTVS TATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDE Y DY PTSA+YI+FK R KW+AAL KL+RLIEIIINSL+SGSVKADM +N+AS S++ST D+QNTVTQAAQAAYG+SLQ+ SI+A A+ QSW+A A L Sbjct: 689 ATILKSPTLVAANQTTTVSLTATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDETYYDDYKTPTSARYINFKARHHAKWKAALIFKLLRLIEIIINSLSSGSVKADMEMNIASNSSISTADLQNTVTQAAQAAYGSSLQVFSITATSLDASSTDQSWIAAAVL 853
BLAST of SMED30008334 vs. Planmine SMEST
Match: SMESG000068971.1 (SMESG000068971.1) HSP 1 Score: 211.46 bits (537), Expect = 2.045e-63 Identity = 124/165 (75.15%), Postives = 140/165 (84.85%), Query Frame = 3 Query: 27 STILKSPTLVAANQXXXXXXXXXXXXXXXXXXXXEDPPRKNERSYKIIIKCSFTDEVYTTDYNNPTSAKYIDFKGRQFVKWQAALNAKLIRLIEIIINSLTSGSVKADMSLNVASTSALSTTDIQNTVTQAAQAAYGNSLQILSISAKQTSAAPKTQSWLATAFL 521 +TILKSPTLVAANQTTTVS TATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDE Y DY PTSA+YI+FK R KW+AAL KL+RLIEIIINSL+SGSVKADM +N+AS S++ST D+QNTVTQAAQAAYG+SLQ+ SI+A A+ QSW+A A L Sbjct: 665 ATILKSPTLVAANQTTTVSLTATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDETYYDDYKTPTSARYINFKARHHAKWKAALIFKLLRLIEIIINSLSSGSVKADMEMNIASNSSISTADLQNTVTQAAQAAYGSSLQVFSITATSLDASSTDQSWIAAAVL 829
BLAST of SMED30008334 vs. Planmine SMEST
Match: SMESG000068935.1 (SMESG000068935.1) HSP 1 Score: 85.1149 bits (209), Expect = 2.077e-19 Identity = 81/218 (37.16%), Postives = 118/218 (54.13%), Query Frame = 3 Query: 3 MTAVIITNSTILKSPTLVAANQXXXXXXXXXXXXXXXX----XXXXEDPPR----------KNERSYKIIIKCSFTDEVYTTDYNNPTSAKYIDFKGRQFVKWQAALNAKLIRLIEIIINSL--TSGSVKADMSLNVASTSALSTTDIQNTVTQAAQAAYGNSLQI------------------LSISAKQTSAAPKTQSWLATAFLXXXXXXXXGLD 554 MTAV+I+NSTILK PTLV AN TTT P ++ + T+ L P+ E S + ++ F++ Y ++N TS++ + F + ++L + IR++ ++NS+ +GSVKA ++ VA A++ + N A +AY + + I ++ISAKQTSAAPKTQSWLATA LVPVVVVIVGLD Sbjct: 132 MTAVVISNSTILKEPTLVGANLTTTALPASSATSVATSQITTLLTTTIIPKVPIVIGMAAQPGEYSASLYLQILFSNRTYIQAFSNVTSSESVSFFNEYYRNINSSLMSNKIRVVSAVVNSMRFVNGSVKAVYTIEVAMNGAMTDESLSNNFINATNSAYSSVVIITNSTVLQTSTLVTSTTAPITISAKQTSAAPKTQSWLATAVLVPVVVVIVGLD 349
BLAST of SMED30008334 vs. Planmine SMEST
Match: SMESG000067876.1 (SMESG000067876.1) HSP 1 Score: 66.2402 bits (160), Expect = 1.645e-12 Identity = 42/115 (36.52%), Postives = 62/115 (53.91%), Query Frame = 3 Query: 129 EDPPRKNERSYKIIIKCSFTDEVYTTDYNNPTSAKYIDFKGRQFVKWQAALNAKLIRLIEIIINSLTSGSVKADMSLNVASTSALSTTDIQNTVTQAAQAAYGNSLQILSISAKQ 473 E P E ++ + CS+T E Y ++Y N S Y F + F + +L KL+RLIEII +SL GSV A+M+ +AS S L +++ V AA A NS+ + I+ Q Sbjct: 843 EKPAAPGEFQSQVEMGCSYTSEKYNSNYKNKDSDDYKVFTNKIFTSMKISLLQKLLRLIEIIFHSLDEGSVVANMTFVMASASPLVGSNLSALVIAAAVDASNNSIVVNKITVIQ 957 The following BLAST results are available for this feature:
BLAST of SMED30008334 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30008334 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30008334 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30008334 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30008334 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30008334 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30008334 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30008334 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30008334 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30008334 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30008334 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30008334 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30008334 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30008334 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 >SMED30008334 ID=SMED30008334|Name=SMED30008334|organism=Schmidtea mediterranea sexual|type=transcript|length=652bpback to top protein sequence of SMED30008334-orf-1 >SMED30008334-orf-1 ID=SMED30008334-orf-1|Name=SMED30008334-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=185bp MTAVIITNSTILKSPTLVAANQTTTVSPTATTSLPITTLSIIEDPPRKNEback 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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