SMED30016392
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Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ Neoblast 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
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., 2020SMED30016392 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30016392 aligns in the following genomic locations: Homology
BLAST of SMED30016392 vs. Planmine SMEST
Match: SMESG000042945.1 (SMESG000042945.1) HSP 1 Score: 159.844 bits (403), Expect = 8.393e-73 Identity = 80/103 (77.67%), Postives = 85/103 (82.52%), Query Frame = 1
Query: 478 QMNPNYHIPKLPKSKVNIVTQPSVQNDNHLLCQQRYNKLFAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR 786
+M+P Y IPK + + S NH LCQQ+YNKL AEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR
Sbjct: 108 KMHPGYKIPKSSRK-----SDTSALQLNHDLCQQKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR 205 HSP 2 Score: 133.265 bits (334), Expect = 8.393e-73 Identity = 95/100 (95.00%), Postives = 96/100 (96.00%), Query Frame = 2
Query: 785 DLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNXXXXXXXXAEGLTIXXXXXXXXXXXXXXXXXXHPEFVKEDDPAPTPKRSTESVLPTHAKETDE 1084
DLALKLNLIPA HLPETTQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFVK+DDPAPTPKRSTE VLP H KETDE
Sbjct: 210 DLALKLNLIPAGHLPETTQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFVKDDDPAPTPKRSTEPVLPIHVKETDE 309
BLAST of SMED30016392 vs. Planmine SMEST
Match: SMESG000059904.1 (SMESG000059904.1) HSP 1 Score: 152.14 bits (383), Expect = 1.049e-66 Identity = 84/133 (63.16%), Postives = 94/133 (70.68%), Query Frame = 1
Query: 406 IFFV*FLHSENVKKLVFIHSQENRQMNPNYHIPKLPKSKVNIVTQPS-VQND-----NHLLCQQRYNKLFAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR 786
+ F +E K++ + P HIP+ K++V P V+N NH CQQ+YNKLFAEHERTLGTWFAPEAVKILQDKIH LSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR
Sbjct: 48 VLIASFTKAELTKRIAGRDLAVKLNLIPPTHIPE--KNEVGQAKPPKPVKNATPLQLNHDFCQQKYNKLFAEHERTLGTWFAPEAVKILQDKIHELSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR 178 HSP 2 Score: 120.939 bits (302), Expect = 1.049e-66 Identity = 90/100 (90.00%), Postives = 92/100 (92.00%), Query Frame = 2
Query: 785 DLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNXXXXXXXXAEGLTIXXXXXXXXXXXXXXXXXXHPEFVKEDDPAPTPKRSTESVLPTHAKETDE 1084
DLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFVK+DD T KRS E +LP H KETDE
Sbjct: 183 DLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFVKKDDTTLTLKRSKEHMLPIHVKETDE 282 HSP 3 Score: 72.4034 bits (176), Expect = 3.126e-17 Identity = 36/50 (72.00%), Postives = 42/50 (84.00%), Query Frame = 1
Query: 637 EAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR 786
E VK L +IHRL+R R+DLI+ENRAQRIIINDQ VL+ASFT+AEL KR
Sbjct: 12 EFVKALHQQIHRLTRYRDDLISENRAQRIIINDQIPVLIASFTKAELTKR 61 HSP 4 Score: 34.6538 bits (78), Expect = 3.126e-17 Identity = 17/34 (50.00%), Postives = 22/34 (64.71%), Query Frame = 2
Query: 785 DLALKLNLIPANHLPETTQAGPAQTPRTSKKHHP 886
DLA+KLNLIP H+PE + G A+ P+ K P
Sbjct: 66 DLAVKLNLIPPTHIPEKNEVGQAKPPKPVKNATP 99
BLAST of SMED30016392 vs. Planmine SMEST
Match: SMESG000072638.1 (SMESG000072638.1) HSP 1 Score: 150.984 bits (380), Expect = 3.180e-66 Identity = 76/94 (80.85%), Postives = 81/94 (86.17%), Query Frame = 1
Query: 505 KLPKSKVNIVTQPSVQNDNHLLCQQRYNKLFAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR 786
K+PKS + S +H LCQ++YNKL AEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR
Sbjct: 195 KIPKSSRK--SDTSASQLDHDLCQRKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR 286 HSP 2 Score: 120.553 bits (301), Expect = 3.180e-66 Identity = 88/100 (88.00%), Postives = 89/100 (89.00%), Query Frame = 2
Query: 785 DLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNXXXXXXXXAEGLTIXXXXXXXXXXXXXXXXXXHPEFVKEDDPAPTPKRSTESVLPTHAKETDE 1084
DLALKLNLIPANHLPE QAGPAQ PRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFV EDDPA PK STE V+P KETDE
Sbjct: 291 DLALKLNLIPANHLPEIAQAGPAQIPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFVTEDDPASNPKGSTELVIPIQVKETDE 390
BLAST of SMED30016392 vs. Planmine SMEST
Match: SMESG000039380.1 (SMESG000039380.1) HSP 1 Score: 154.836 bits (390), Expect = 6.649e-65 Identity = 78/102 (76.47%), Postives = 83/102 (81.37%), Query Frame = 1
Query: 481 MNPNYHIPKLPKSKVNIVTQPSVQNDNHLLCQQRYNKLFAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR 786
M+ Y IPK + + S +H LCQQ+YNKL AEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR
Sbjct: 1 MHSGYKIPKSSRK-----SDTSALQLDHDLCQQKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR 97 HSP 2 Score: 112.464 bits (280), Expect = 6.649e-65 Identity = 86/100 (86.00%), Postives = 88/100 (88.00%), Query Frame = 2
Query: 785 DLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNXXXXXXXXAEGLTIXXXXXXXXXXXXXXXXXXHPEFVKEDDPAPTPKRSTESVLPTHAKETDE 1084
DLALKLNLIPA+HLPE TQAGPAQT RTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALV EQHPEFV ED PA PK STE V+P KETDE
Sbjct: 102 DLALKLNLIPASHLPEPTQAGPAQTLRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVTEQHPEFVTEDVPASNPKGSTELVMPIQVKETDE 201
BLAST of SMED30016392 vs. Planmine SMEST
Match: SMESG000028417.1 (SMESG000028417.1) HSP 1 Score: 156.377 bits (394), Expect = 4.258e-61 Identity = 79/102 (77.45%), Postives = 81/102 (79.41%), Query Frame = 1
Query: 481 MNPNYHIPKLPKSKVNIVTQPSVQNDNHLLCQQRYNKLFAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKR 786
M P Y IPKL I TQ +H CQQ+YNKLFAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSA LVASFTE EL KR
Sbjct: 1 MQPGYKIPKLSSKPSAINTQM-----DHSSCQQKYNKLFAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSADLVASFTEVELTKR 97 HSP 2 Score: 97.8265 bits (242), Expect = 4.258e-61 Identity = 75/100 (75.00%), Postives = 82/100 (82.00%), Query Frame = 2
Query: 785 DLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNXXXXXXXXAEGLTIXXXXXXXXXXXXXXXXXXHPEFVKEDDPAPTPKRSTESVLPTHAKETDE 1084
DL +KLNLIP NHLPE TQAGPAQTPRTSKKHHPSKN RRRERRRAEGLT+L+NAAQVLEEAA LVAEQHP+FVK D+ T +S E+ A ETDE
Sbjct: 102 DLVVKLNLIPVNHLPEETQAGPAQTPRTSKKHHPSKNCRRRERRRAEGLTLLSNAAQVLEEAAMLVAEQHPQFVKSDENPQTTAKSEENATLISADETDE 201 The following BLAST results are available for this feature:
BLAST of SMED30016392 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30016392 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30016392 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30016392 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30016392 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30016392 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30016392 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30016392 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30016392 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30016392 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30016392 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30016392 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30016392 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30016392 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 >SMED30016392 ID=SMED30016392|Name=SMED30016392|organism=Schmidtea mediterranea sexual|type=transcript|length=1085bpback to top protein sequence of SMED30016392-orf-1 >SMED30016392-orf-1 ID=SMED30016392-orf-1|Name=SMED30016392-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp MNPNYHIPKLPKSKVNIVTQPSVQNDNHLLCQQRYNKLFAEHERTLGTWFback to top Annotated Terms
The following terms have been associated with this transcript:
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