SMED30008381
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., 2020SMED30008381 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Homology
BLAST of SMED30008381 vs. TrEMBL
Match: A0A0L8GX06 (GIY-YIG domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22026335mg PE=4 SV=1) HSP 1 Score: 41.9726 bits (97), Expect = 1.232e-6 Identity = 47/172 (27.33%), Postives = 72/172 (41.86%), Query Frame = 1 Query: 211 KNEKQSIANRCTKGKENYEQQLQFDKVLRRNRYHKENIERMDSKPKIPMDRTQKKDT---FI*RSHLS--VTRSTSRSGKSSITLAFQFVYHTSLGY*GKHWQTTQKKRTFA*WKIARHQRKCASEKTLQKC---------------IM*NACKEIYIGSTLRNLHQRIKEH 666 +NE I +C+K ++ F +L+ NRY + + ++ P+ P RT +K + F+ H S +TRS R+ + L Q H+ G +A+ Q K +S+ TL C I N C + Y+GST R LH IKEH Sbjct: 62 RNELAHIQGKCSKTEDKVTHTTCFLDILKTNRYPRSIVNQL-KYPRRPTHRTHRKPSNTCFLKIPHFSKRITRSIRRAIRRE-GLDIQLA-HSGPSLRG---------------HLAKKQAKDSSQCTLANCPIRDTDLCQRVNVYRIQCNKCNKFYVGSTTRPLHVHIKEH 215 HSP 2 Score: 40.0466 bits (92), Expect = 1.232e-6 Identity = 22/56 (39.29%), Postives = 35/56 (62.50%), Query Frame = 2 Query: 35 DIKFEIEYPDENGSLNLLDLRIKIDVDTPT-*GFYKKSARKEIFMHQKLLLPIYSK 199 +IKF +EY GSL+LLDL++ I + FY+K+A K++F+ LP+ +K Sbjct: 2 NIKFTLEYSSITGSLSLLDLKLNITEEGEIHIEFYRKAASKDMFVQYNSALPLGAK 57
BLAST of SMED30008381 vs. TrEMBL
Match: A0A0L8GYC4 (GIY-YIG domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22026335mg PE=4 SV=1) HSP 1 Score: 41.5874 bits (96), Expect = 1.428e-6 Identity = 47/172 (27.33%), Postives = 72/172 (41.86%), Query Frame = 1 Query: 211 KNEKQSIANRCTKGKENYEQQLQFDKVLRRNRYHKENIERMDSKPKIPMDRTQKKDT---FI*RSHLS--VTRSTSRSGKSSITLAFQFVYHTSLGY*GKHWQTTQKKRTFA*WKIARHQRKCASEKTLQKC---------------IM*NACKEIYIGSTLRNLHQRIKEH 666 +NE I +C+K ++ F +L+ NRY + + ++ P+ P RT +K + F+ H S +TRS R+ + L Q H+ G +A+ Q K +S+ TL C I N C + Y+GST R LH IKEH Sbjct: 62 RNELAHIQGKCSKTEDKVTHTTCFLDILKTNRYPRSIVNQL-KYPRRPTHRTHRKPSNTCFLKIPHFSKRITRSIRRAIRRE-GLDIQLA-HSGPSLRG---------------HLAKKQAKDSSQCTLANCPIRDTDLCQRVNVYRIQCNKCNKFYVGSTTRPLHVHIKEH 215 HSP 2 Score: 40.0466 bits (92), Expect = 1.428e-6 Identity = 22/56 (39.29%), Postives = 35/56 (62.50%), Query Frame = 2 Query: 35 DIKFEIEYPDENGSLNLLDLRIKIDVDTPT-*GFYKKSARKEIFMHQKLLLPIYSK 199 +IKF +EY GSL+LLDL++ I + FY+K+A K++F+ LP+ +K Sbjct: 2 NIKFTLEYSSITGSLSLLDLKLNITEEGEIHIEFYRKAASKDMFVQYNSALPLGAK 57
BLAST of SMED30008381 vs. TrEMBL
Match: A0A3M6TYW2 (GIY-YIG domain-containing protein OS=Pocillopora damicornis OX=46731 GN=pdam_00017828 PE=4 SV=1) HSP 1 Score: 50.447 bits (119), Expect = 4.674e-6 Identity = 28/75 (37.33%), Postives = 41/75 (54.67%), Query Frame = 3 Query: 360 QNTKKRYFYLKIPFIGYTLDFKIGKELNHTGFPIRVSHKSWILRQALANNTKKENICIMENCQTSK-KMCFRKNV 581 Q K + YLKIP I L+ KI P+R++HKS+ +RQAL++NT E C NC + +C ++N Sbjct: 414 QTQTKEWHYLKIPCISDQLNRKITGIFKRGNIPVRIAHKSYTMRQALSHNT-TERKCNRPNCPIADTNLCLQRNT 487 HSP 2 Score: 29.6462 bits (65), Expect = 4.674e-6 Identity = 13/21 (61.90%), Postives = 14/21 (66.67%), Query Frame = 1 Query: 604 ACKEIYIGSTLRNLHQRIKEH 666 AC E YIGS + LH R KEH Sbjct: 495 ACGEYYIGSMTQFLHDRTKEH 515
BLAST of SMED30008381 vs. Planmine SMEST
Match: SMESG000069853.1 (SMESG000069853.1) HSP 1 Score: 110.923 bits (276), Expect = 7.803e-28 Identity = 75/149 (50.34%), Postives = 88/149 (59.06%), Query Frame = 2 Query: 2 EIFHIFNVAHPDIKFEIEYPDENGSLNLLDLRIKIDVDTPT*GFYKKSARKEIFMHQKLLLPIYSKGML*RTRSR--A*PIGVLKEKRIMNNNYNSIKS---YAETDTTRRTSKEWIQNQKYLWTEHKKKILLSKDPIYRLHARLQDRE 433 EIFHI N AHP+IKFEIEYPDENGSLNLLDLRIKIDVDTPT FYK SA +EIFMHQ+ LP K + R + A +K+ N+N + S Y D SK + T+ K++ILLSK PI H R D E Sbjct: 162 EIFHISNAAHPNIKFEIEYPDENGSLNLLDLRIKIDVDTPTFEFYKISAHEEIFMHQRSSLPYLQKVYVIRNEKQRIANRCTEVKDNYKQQLNFNVVLSKNGYHNEDIETMNSKPKTPIDR---TQKKEEILLSKHPI---HQRDSDLE 304
BLAST of SMED30008381 vs. Planmine SMEST
Match: SMESG000049225.1 (SMESG000049225.1) HSP 1 Score: 103.605 bits (257), Expect = 1.100e-24 Identity = 62/118 (52.54%), Postives = 74/118 (62.71%), Query Frame = 2 Query: 2 EIFHIFNVAHPDIKFEIEYPDENGSLNLLDLRIKIDVDTPT*GFYKKSARKEIFMHQKLLLPIYSK-GML*RTRSRA*PIGVLKEKRIMNNN-YNSIKSYAETDTTRRTSKEWIQNQK 349 EIFHIFN HP+IKFEIEYPD NGSLNLLDLRIKIDVDTPT KKSA +EIFMHQ+ LP K + + R + +K+ N YNS + A ++ S+E I QK Sbjct: 170 EIFHIFNEDHPEIKFEIEYPDINGSLNLLDLRIKIDVDTPTYELCKKSAGEEIFMHQRSALPNLQKVNFIKNDKQRIANRSLFDQKKFNRNAMYNSYTNLATSNKMEAFSREDILKQK 287 The following BLAST results are available for this feature:
BLAST of SMED30008381 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30008381 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30008381 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30008381 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30008381 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30008381 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30008381 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30008381 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 3
BLAST of SMED30008381 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30008381 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30008381 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30008381 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30008381 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30008381 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 2
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30008381 ID=SMED30008381|Name=SMED30008381|organism=Schmidtea mediterranea sexual|type=transcript|length=959bpback to top protein sequence of SMED30008381-orf-1 >SMED30008381-orf-1 ID=SMED30008381-orf-1|Name=SMED30008381-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=139bp MNNNYNSIKSYAETDTTRRTSKEWIQNQKYLWTEHKKKILLSKDPIYRLHback to top Annotated Terms
The following terms have been associated with this transcript:
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