SMED30029447
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., 2020SMED30029447 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30029447 aligns in the following genomic locations:
Homology
BLAST of SMED30029447 vs. Planmine SMEST
Match: SMESG000055115.1 (SMESG000055115.1) HSP 1 Score: 322.783 bits (826), Expect = 1.933e-113 Identity = 180/233 (77.25%), Postives = 187/233 (80.26%), Query Frame = -3 Query: 704 CYHVLLPL*NFS*DKHLLSLSHPIYCRQQALSVEIENCLLTKMSSLSNLTRIPRLSPSFTAMYQRLETLEKDFATLKDKYQKLKGTWSPPEAPRNLNQNISRLS*ARDDLVIENRSQRITIAEQSAALCQIFTENELRARLSSRSWAQEINIIPAQHLPSNPAIIXXXXXXXXXXSDNQSEG-------------------SLLRIHERPEVPAGVNDPPPAYTEFEFPERDP 1345 CY +FS DKHLL+ +HPIY RQQALS+EIEN LL KMSSLSNL RIPRLSPSFTAM QRLETLEKDF TLKDKYQKLKGTWSPPEA RNL + ISRLS ARDDLVIENRSQRITIAEQSAALCQIFTENELRARLSS SW QEINIIPAQ LP NPA I STGPS SGPSDNQSEG SLLRIHERPEVPAGV +PPPAYTEFEFPE+DP Sbjct: 8 CYISATHTEDFSYDKHLLNSNHPIYSRQQALSIEIENRLLAKMSSLSNLPRIPRLSPSFTAMPQRLETLEKDFTTLKDKYQKLKGTWSPPEATRNLFKKISRLSRARDDLVIENRSQRITIAEQSAALCQIFTENELRARLSSHSWVQEINIIPAQQLPGNPATIQSTGPSVSGPSDNQSEGRRRRPNRNRRRWARRPAEASLLRIHERPEVPAGVIEPPPAYTEFEFPEKDP 240 HSP 2 Score: 107.842 bits (268), Expect = 1.933e-113 Identity = 71/82 (86.59%), Postives = 73/82 (89.02%), Query Frame = -1 Query: 433 LPP-SAYIDLVADELETPSLNLILEDLRLTPDEIAVLTGQVPSITRLGKEPSTSGQEPISLTTASPSRRPPKRRCLPVDIDL 675 LPP S YIDLVADELE PSLNLILEDLRLTPDEIAVLTGQVPS TRLG+EP TS +EP S TT SPSRRPPKRRCLPVDIDL Sbjct: 252 LPPLSVYIDLVADELENPSLNLILEDLRLTPDEIAVLTGQVPSNTRLGEEPLTSTREPTSPTTPSPSRRPPKRRCLPVDIDL 333
BLAST of SMED30029447 vs. Planmine SMEST
Match: SMESG000038618.1 (SMESG000038618.1) HSP 1 Score: 228.409 bits (581), Expect = 7.633e-81 Identity = 130/191 (68.06%), Postives = 142/191 (74.35%), Query Frame = -3 Query: 704 MSSLSNLTRIPRLSPSFTAMYQRLETLEKDFATLKDKYQKLKGTWSPPEAPRNLNQNISRLS*ARDDLVIENRSQRITIAEQSAALCQIFTENELRARLSSRSWAQEINIIPAQHLPSNPAIIXXXXXXXXXXSDNQS-------------------EGSLLRIHERPEVPAGVNDPPPAYTEFEFPERDP 1219 MS+LSNL RIPRLSPS TAM QRLETLE+DF LK KYQK+KGTWSPPEA RNL Q SRLS ARDDLVIENRSQRITIAE SAAL QIFTEN+LRA LSSRSWAQEINIIPAQHLP NP +PS G SG ++NQS + +LL+++ER P VNDPP AYTEFEFPE DP Sbjct: 1 MSNLSNLPRIPRLSPSVTAMSQRLETLERDFTALKTKYQKIKGTWSPPEATRNLYQKTSRLSRARDDLVIENRSQRITIAEHSAALRQIFTENKLRACLSSRSWAQEINIIPAQHLPINPGSLPSNGSPLSGTTENQSGVQRRRPNRNRRRRERRRAQANLLQVNERTGEPVEVNDPPFAYTEFEFPEMDP 191 HSP 2 Score: 92.8189 bits (229), Expect = 7.633e-81 Identity = 53/81 (65.43%), Postives = 60/81 (74.07%), Query Frame = -1 Query: 433 LPPSAYIDLVADELETPSLNLILEDLRLTPDEIAVLTGQVPSITRLGKEPSTSGQEPISLTTASPSRRPPKRRCLPVDIDL 675 LPP YIDL ADE ETP++NLILE LRLTPD+IA+L+GQVPS EPSTS QE S T + + R PKRR LPVDIDL Sbjct: 204 LPPPIYIDLEADEPETPNVNLILERLRLTPDKIALLSGQVPSNAYSAIEPSTSMQEDPSPTVSISNHRQPKRRYLPVDIDL 284 HSP 3 Score: 21.9422 bits (45), Expect = 7.633e-81 Identity = 12/17 (70.59%), Postives = 13/17 (76.47%), Query Frame = -2 Query: 660 PDIVYAPSLTAY-LPPP 707 P+IVYAPS Y LPPP Sbjct: 191 PEIVYAPSSIIYPLPPP 207
BLAST of SMED30029447 vs. Planmine SMEST
Match: SMESG000007654.1 (SMESG000007654.1) HSP 1 Score: 227.254 bits (578), Expect = 3.709e-69 Identity = 129/170 (75.88%), Postives = 134/170 (78.82%), Query Frame = -3 Query: 710 MYQRLETLEKDFATLKDKYQKLKGTWSPPEAPRNLNQNISRLS*ARDDLVIENRSQRITIAEQSAALCQIFTENELRARLSSRSWAQEINIIPAQHLPSNPAIIXXXXXXXXXXSDNQS-------------------EGSLLRIHERPEVPAGVNDPPPAYTEFEFPER 1162 M QRLETLEK+F LK KYQKLKGTWSPPEA RNL Q ISR S A+D+L+IENRSQRITIA+QSAAL QIFTENELRARLSSRSW QEINIIPAQHLP NPAIIPSTG S SGPSDNQS E SLLRIHER E PAGVNDPPPAYTEFEFPER Sbjct: 1 MSQRLETLEKNFTALKVKYQKLKGTWSPPEATRNLYQKISRFSRAKDNLIIENRSQRITIAKQSAALRQIFTENELRARLSSRSWPQEINIIPAQHLPVNPAIIPSTGLSVSGPSDNQSGMRRRRPNRNRRRQERRRAEASLLRIHERSEAPAGVNDPPPAYTEFEFPER 170
BLAST of SMED30029447 vs. Planmine SMEST
Match: SMESG000061002.1 (SMESG000061002.1) HSP 1 Score: 186.808 bits (473), Expect = 6.718e-66 Identity = 105/187 (56.15%), Postives = 128/187 (68.45%), Query Frame = -3 Query: 704 MSSLSNLTRIPRLSPSFTAMYQRLETLEKDFATLKDKYQKLKGTWSPPEAPRNLNQNISRLS*ARDDLVIENRSQRITIAEQSAALCQIFTENELRARLSSRSWAQEINIIPAQHLPSNPAIIXXXXXXXXXXSDNQS---------------EGSLLRIHERPEVPAGVNDPPPAYTEFEFPERDP 1219 M LS+L RIPRL PS T QRLE LE+DFATLK+KYQ++K TWS PEA ++L Q ISRLS A+DDLVIEN+ QRITIAEQSAAL +IFTENELRARL SRS A+EI++IPAQ L ++P I + + NQ+ E +LLR +ER + +DP PAYTEF+FP DP Sbjct: 38 MPGLSSLPRIPRLLPSATVTSQRLEILERDFATLKEKYQRVKSTWSSPEATKSLFQKISRLSRAKDDLVIENQGQRITIAEQSAALRRIFTENELRARLPSRSCAREIDVIPAQRLTNDPGSISPIILPANTATKNQTGAPRRRPNRNRRRLAEANLLRANERIQGLVPTSDPSPAYTEFDFPTADP 224 HSP 2 Score: 84.7297 bits (208), Expect = 6.718e-66 Identity = 48/82 (58.54%), Postives = 58/82 (70.73%), Query Frame = -1 Query: 427 PPSAYIDLVADELETPSLNLILEDLRLTPDEIAVLTGQVPSITRLGKEPSTSGQEPISLTTASPSRRPPKRRCLPVDIDLAN 672 PP YIDLV DE E P ++ +LE LTP+EIAVLTGQ+PS T +EPSTS QE + ++ P R PKRRCLPVDIDL + Sbjct: 238 PPQVYIDLVTDETELPDVSRVLETQLLTPEEIAVLTGQLPSTTH-PEEPSTSIQEAVHPNSSDPIPRRPKRRCLPVDIDLED 318
BLAST of SMED30029447 vs. Planmine SMEST
Match: SMESG000054095.1 (SMESG000054095.1) HSP 1 Score: 216.853 bits (551), Expect = 6.957e-65 Identity = 126/191 (65.97%), Postives = 140/191 (73.30%), Query Frame = -3 Query: 704 MSSLSNLTRIPRLSPSFTAMYQRLETLEKDFATLKDKYQKLKGTWSPPEAPRNLNQNISRLS*ARDDLVIENRSQRITIAEQSAALCQIFTENELRARLSSRSWAQEINIIPAQHLPSNPAIIXXXXXXXXXXSDNQS-------------------EGSLLRIHERPEVPAGVNDPPPAYTEFEFPERDP 1219 MS+LSN RIPRLSPS TAM RLETLE+DF LK KYQKLK WS PEA RNL Q ISRLS AR++LVIENRSQ+ITIAEQSAAL Q+FTENELRA LSSRSW+QEINIIPAQ+LP NP +P GPS SG ++N+S E +LLR +ER PA VNDPPPAYTEFEF E DP Sbjct: 1 MSNLSNQPRIPRLSPSLTAMSHRLETLERDFTALKVKYQKLKSNWSSPEATRNLYQKISRLSRARNNLVIENRSQQITIAEQSAALRQLFTENELRAHLSSRSWSQEINIIPAQYLPINPGSLPPNGPSLSGTTENRSGVQRRRPNRNRRHRERRRAEANLLRANERTGAPAEVNDPPPAYTEFEFLETDP 191 The following BLAST results are available for this feature:
BLAST of SMED30029447 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30029447 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30029447 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30029447 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30029447 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30029447 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30029447 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30029447 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30029447 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30029447 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30029447 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30029447 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30029447 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30029447 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 >SMED30029447 ID=SMED30029447|Name=SMED30029447|organism=Schmidtea mediterranea sexual|type=transcript|length=2646bpback to top protein sequence of SMED30029447-orf-1 >SMED30029447-orf-1 ID=SMED30029447-orf-1|Name=SMED30029447-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=110bp MTRPRLTPNLNFRRGTRHSVCPVPDSLPPSAYIDLVADELETPSLNLILEback to top Annotated Terms
The following terms have been associated with this transcript:
|