SMED30021298
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., 2020SMED30021298 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30021298 aligns in the following genomic locations:
Homology
BLAST of SMED30021298 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1) HSP 1 Score: 229.95 bits (585), Expect = 1.313e-72 Identity = 154/308 (50.00%), Postives = 192/308 (62.34%), Query Frame = 1 Query: 286 MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATRELYKKIMRLSRARDDLSIESRGQRITILYQSSALRQIFTEKELQVQLPGRNMAQLLDIIPAHHLQINSSNLTNSEDPNASTTIPNSSAPXXXXXXXXXXXXXXXXXAETAALQANLRVIENPNLSRISETFLQEPVFMPNDTDLEIIPAPXXXXXXXXXXXXXXXXYQWIFALWRYQQTYKSSFLPGL---------PLRDVVPKISSGRSSPQIISVIEPQVRGNFDRVASNLSRTLSNFGPRRPKKRCLPIDIDEE 1182 MN+PRI +I+PAPS VA AQYL KLE EN L+EKY++LK TWCSPE TRE YKKI RLSRARDDL IE+R QRI I Y+ +A RQIFTEKE Q +LP RNM Q LDIIP HHL N N ++ + N T + S N+RH+ N+NRRRRQ+++AE A LQ+NL V EN +L I+E F +P+ + + DL +I APR + S Y + L + P RD ISSGRSSPQIISVIEP + N + + NL R S+ R PK++ LP+DIDEE Sbjct: 1 MNLPRIPKISPAPSAVAEAQYLEKLERENFTLREKYNRLKVTWCSPEITRERYKKINRLSRARDDLIIENRSQRIMISYECAAFRQIFTEKEKQARLPSRNMTQRLDIIPVHHLPTNPKNQRDNNNKNVPTKLTTPSTVNQRHRPNRNRRRRQRRKAENALLQSNLGVRENASLESITELFWPQPIALNDGEDLGVIDAPRQPDFSQPAPIPAQINITM--------DNYSAEMLINMQISIASRTTPDRDA---ISSGRSSPQIISVIEPTI--NRSQRSDNLPRAPSSSTTRPPKRKYLPVDIDEE 295
BLAST of SMED30021298 vs. Planmine SMEST
Match: SMESG000004294.1 (SMESG000004294.1) HSP 1 Score: 185.652 bits (470), Expect = 5.515e-57 Identity = 106/197 (53.81%), Postives = 124/197 (62.94%), Query Frame = 1 Query: 286 MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATRELYKKIMRLSRARDDLSIESRGQRITILYQSSALRQIFTEKELQVQLPGRNMAQLLDIIPAHHLQINSSNLTNSEDPNASTTIPNSSAPXXXXXXXXXXXXXXXXXAETAALQANLRVIENPNLSRISETFLQEPVFMPNDTDLEII 876 MN+PRI +I+P PS VAAAQYL KLE EN L+EKY+KLK TWCS EATRELYK I RLSRARDDL IE+R QRITI Q++ LRQIFTEKELQ +LP RNM Q LDII AHHL N N + PN P RAE +QANL V EN +L ++E F EP + + +L +I Sbjct: 1 MNLPRIPKISPPPSAVAAAQYLEKLERENFALREKYNKLKFTWCSTEATRELYKMITRLSRARDDLIIENRSQRITISDQNATLRQIFTEKELQARLPSRNMVQRLDIILAHHLSKNPENQRDYWPPNCRRCQPEIGV-----------------RAENTLIQANLGVRENASLGSVTELFGLEPTVLNDGENLGVI 180
BLAST of SMED30021298 vs. Planmine SMEST
Match: SMESG000062943.1 (SMESG000062943.1) HSP 1 Score: 176.022 bits (445), Expect = 8.029e-54 Identity = 92/132 (69.70%), Postives = 104/132 (78.79%), Query Frame = 1 Query: 286 MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATRELYKKIMRLSRARDDLSIESRGQRITILYQSSALRQIFTEKELQVQLPGRNMAQLLDIIPAHHLQINS-----SNLTNSEDP 666 MN+ RI RIAPAPS VAAAQY KL+ EN L+EKY+KLK TWCSPEAT+EL KKI LSRARDDL I++RGQRITI QS+ALRQIFTEKELQ +LP RNM Q LDIIPAHHL NS +N TN++ P Sbjct: 1 MNLRRIPRIAPAPSTVAAAQYAEKLKRENFTLREKYNKLKCTWCSPEATKELIKKITWLSRARDDLIIKNRGQRITISDQSAALRQIFTEKELQARLPSRNMTQRLDIIPAHHLPANSEGSKENNETNTQFP 132
BLAST of SMED30021298 vs. Planmine SMEST
Match: SMESG000021151.1 (SMESG000021151.1) HSP 1 Score: 178.333 bits (451), Expect = 5.537e-53 Identity = 136/297 (45.79%), Postives = 175/297 (58.92%), Query Frame = 1 Query: 286 MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATRELYKKIMRLSRARDDLSIESRGQRITILYQSSALRQIFTEKELQVQLPGRNMAQLLDIIPAHHLQINSSNLTNSEDPNASTTIPNSSAPXXXXXXXXXXXXXXXXXAETAALQANLRVIENPNLSRISETFLQEPVFMPNDTDLEIIPAPXXXXXXXXXXXXXXXXYQWIFALWRYQQTYKSSFLPGLPLRDVVPKISSGRSSPQIISVIEPQVRGNFDRVASNLSRTLSNFGPRRPKKRCLPIDID 1176 MN+P I+RI AP VA Q L LE EN I++EKY K+KGTWCSP+AT+EL+KKI LSR RDDL IE+R Q++TI QS+ALRQIFTEKELQ +LP RN+AQ ++IIPAHHL N+ N ++D ST S NRRHK N+NRR+RQ++RAE L ANLR E P+++ + ++ E + D EII AP I+ I R + SSGRSSP II V EP +++A + S+ R PK+RCLP+DID Sbjct: 1 MNLPSIIRIVRAPYAVAMNQRLESLERENFIIREKYEKIKGTWCSPDATKELHKKITSLSRDRDDLVIETRSQQVTISEQSAALRQIFTEKELQARLPSRNLAQQINIIPAHHLPTNAENQAINQD--NSTPEDGISHANRRHKPNRNRRQRQRRRAENTLLLANLRSDEYPDVTEVLDSTTIERAI--SGYDKEIIYAP----------LNPSPIHINIATTSRAMLEEEGQ--------------SSGRSSPLIILVTEPTAPQ--EQMAGFPQQPESHPTARCPKRRCLPVDID 267
BLAST of SMED30021298 vs. Planmine SMEST
Match: SMESG000021652.1 (SMESG000021652.1) HSP 1 Score: 167.162 bits (422), Expect = 1.591e-50 Identity = 86/136 (63.24%), Postives = 101/136 (74.26%), Query Frame = 1 Query: 286 MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATRELYKKIMRLSRARDDLSIESRGQRITILYQSSALRQIFTEKELQVQLPGRNMAQLLDIIPAHHLQINSSNLTNSEDPNASTTIPNS 693 M++P+I +I AP VV AAQ+L LENE ILKEKY+K+KG W S EAT ELYKKI R+SRA DDL IE+R QRITI QS+ALRQ FTEKELQ +LPGRN AQ L+ IPA+HL ++SSN E N TT P S Sbjct: 1 MHLPKIPKITQAPLVVTAAQHLPNLENEQRILKEKYAKMKGIWLSKEATSELYKKITRISRAHDDLIIENRSQRITIADQSAALRQTFTEKELQARLPGRNTAQPLNSIPAYHLLVDSSNYAEHEVSNIVTTTPTS 136 The following BLAST results are available for this feature:
BLAST of SMED30021298 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30021298 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30021298 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30021298 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30021298 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30021298 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30021298 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30021298 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30021298 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30021298 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30021298 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30021298 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30021298 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30021298 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 >SMED30021298 ID=SMED30021298|Name=SMED30021298|organism=Schmidtea mediterranea sexual|type=transcript|length=1243bpback to top protein sequence of SMED30021298-orf-1 >SMED30021298-orf-1 ID=SMED30021298-orf-1|Name=SMED30021298-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=302bp MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATRback to top protein sequence of SMED30021298-orf-2 >SMED30021298-orf-2 ID=SMED30021298-orf-2|Name=SMED30021298-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp RRFFHNEDKFYKPFKVSHPYSSSISIGRHLFLGRRGPKFESVRERLLATRback to top Annotated Terms
The following terms have been associated with this transcript:
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