SMED30001401
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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., 2020SMED30001401 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30001401 aligns in the following genomic locations: Homology
BLAST of SMED30001401 vs. Planmine SMEST
Match: SMESG000042945.1 (SMESG000042945.1) HSP 1 Score: 487.263 bits (1253), Expect = 2.420e-172 Identity = 276/289 (95.50%), Postives = 280/289 (96.89%), Query Frame = 2
Query: 308 QENXXXXXXXXXXXRVSKIKIPILKMQPGYKIPKSSRKSDISALQLNHDLCQQKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNXXXXXXXXAEGLTIXXXXXXXXXXXXXXXXXXHPEFVKEDDPTPTPKRSTESVLPTHAKETDEVRICLDISPVENSITTMRERSPTLASRWMDEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE 1174
QENLKKI PKILIKRVSKIKIP LKM PGYKIPKSSRKSD SALQLNHDLCQQKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPA HLPETTQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFVK+DDP PTPKRSTE VLP H KETDE+++CLDISPVENSITTMRERSPTLASRWMDEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE
Sbjct: 84 QENLKKILPKILIKRVSKIKIPFLKMHPGYKIPKSSRKSDTSALQLNHDLCQQKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPAGHLPETTQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFVKDDDPAPTPKRSTEPVLPIHVKETDEMQMCLDISPVENSITTMRERSPTLASRWMDEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE 372
BLAST of SMED30001401 vs. Planmine SMEST
Match: SMESG000039380.1 (SMESG000039380.1) HSP 1 Score: 427.172 bits (1097), Expect = 2.557e-150 Identity = 237/264 (89.77%), Postives = 243/264 (92.05%), Query Frame = 2
Query: 383 MQPGYKIPKSSRKSDISALQLNHDLCQQKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNXXXXXXXXAEGLTIXXXXXXXXXXXXXXXXXXHPEFVKEDDPTPTPKRSTESVLPTHAKETDEVRICLDISPVENSITTMRERSPTLASRWMDEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE 1174
M GYKIPKSSRKSD SALQL+HDLCQQKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPA+HLPE TQAGPAQT RTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALV EQHPEFV ED P PK STE V+P KETDE+ ICLDISPVENS TT +ERSPTL S WM+EFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE
Sbjct: 1 MHSGYKIPKSSRKSDTSALQLDHDLCQQKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPASHLPEPTQAGPAQTLRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVTEQHPEFVTEDVPASNPKGSTELVMPIQVKETDEIPICLDISPVENSTTTTKERSPTLTSCWMNEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE 264
BLAST of SMED30001401 vs. Planmine SMEST
Match: SMESG000072638.1 (SMESG000072638.1) HSP 1 Score: 428.328 bits (1100), Expect = 6.383e-148 Identity = 237/260 (91.15%), Postives = 242/260 (93.08%), Query Frame = 2
Query: 395 YKIPKSSRKSDISALQLNHDLCQQKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNXXXXXXXXAEGLTIXXXXXXXXXXXXXXXXXXHPEFVKEDDPTPTPKRSTESVLPTHAKETDEVRICLDISPVENSITTMRERSPTLASRWMDEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE 1174
YKIPKSSRKSD SA QL+HDLCQ+KYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPE QAGPAQ PRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFV EDDP PK STE V+P KETDE +ICL ISPVENS TTM+ERSPTLAS WMDEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE
Sbjct: 194 YKIPKSSRKSDTSASQLDHDLCQRKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPEIAQAGPAQIPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFVTEDDPASNPKGSTELVIPIQVKETDERQICLGISPVENSTTTMKERSPTLASCWMDEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE 453
BLAST of SMED30001401 vs. Planmine SMEST
Match: SMESG000059904.1 (SMESG000059904.1) HSP 1 Score: 404.445 bits (1038), Expect = 4.341e-140 Identity = 225/246 (91.46%), Postives = 231/246 (93.90%), Query Frame = 2
Query: 437 LQLNHDLCQQKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNXXXXXXXXAEGLTIXXXXXXXXXXXXXXXXXXHPEFVKEDDPTPTPKRSTESVLPTHAKETDEVRICLDISPVENSITTMRERSPTLASRWMDEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE 1174
LQLNHD CQQKYNKL AEHERTLGTWFAPEAVKILQDKIH LSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFVK+DD T T KRS E +LP H KETDE++ICLDISP+EN TT +ERSPTLAS WMDEFGEELCHTVPQVGT PFQPLRNKRKFPVDIDE
Sbjct: 100 LQLNHDFCQQKYNKLFAEHERTLGTWFAPEAVKILQDKIHELSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFVKKDDTTLTLKRSKEHMLPIHVKETDEMQICLDISPIENPSTTTKERSPTLASCWMDEFGEELCHTVPQVGTIPFQPLRNKRKFPVDIDE 345 HSP 2 Score: 112.849 bits (281), Expect = 1.115e-27 Identity = 56/88 (63.64%), Postives = 68/88 (77.27%), Query Frame = 2
Query: 524 EAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPETTQAGPAQTPRTSKKHHP 787
E VK L +IHRL+R R+DLI+ENRAQRIIINDQ VL+ASFT+AEL KR+AGRDLA+KLNLIP H+PE + G A+ P+ K P
Sbjct: 12 EFVKALHQQIHRLTRYRDDLISENRAQRIIINDQIPVLIASFTKAELTKRIAGRDLAVKLNLIPPTHIPEKNEVGQAKPPKPVKNATP 99
BLAST of SMED30001401 vs. Planmine SMEST
Match: SMESG000042352.1 (SMESG000042352.1) HSP 1 Score: 358.221 bits (918), Expect = 8.543e-119 Identity = 202/238 (84.87%), Postives = 212/238 (89.08%), Query Frame = 2
Query: 461 QQKYNKLLAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNXXXXXXXXAEGLTIXXXXXXXXXXXXXXXXXXHPEFVKEDDPTPTPKRSTESVLPTHAKETDEVRICLDISPVENSITTMRERSPTLASRWMDEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE 1174
QQKYNKLLAEHERTLGTWFAPEAVKIL KIHRL RCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDL LKLNLIPANHLPET QAGPAQTPRTSKKHHPSKNRRRRERRRAEGLT+LNNAAQVLEEAAALVAEQHPEFVK+DD P P ES L + ETDE++ICLD+ V NS T +ERSPTL S W+D+FGEEL H+VPQVGTTPFQPLRNKRKFPVDIDE
Sbjct: 346 QQKYNKLLAEHERTLGTWFAPEAVKILHGKIHRLPRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLTLKLNLIPANHLPETNQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTMLNNAAQVLEEAAALVAEQHPEFVKKDDFIPNPANPVESALQIYTDETDEMQICLDVLTVNNSTTKTKERSPTLVSYWVDDFGEELHHSVPQVGTTPFQPLRNKRKFPVDIDE 583 The following BLAST results are available for this feature:
BLAST of SMED30001401 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30001401 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30001401 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30001401 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30001401 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30001401 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30001401 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30001401 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30001401 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30001401 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30001401 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30001401 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30001401 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30001401 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 >SMED30001401 ID=SMED30001401|Name=SMED30001401|organism=Schmidtea mediterranea sexual|type=transcript|length=1266bpback to top protein sequence of SMED30001401-orf-1 >SMED30001401-orf-1 ID=SMED30001401-orf-1|Name=SMED30001401-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=265bp MQPGYKIPKSSRKSDISALQLNHDLCQQKYNKLLAEHERTLGTWFAPEAVback to top Annotated Terms
The following terms have been associated with this transcript:
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