SMED30022933
|
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., 2020SMED30022933 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30022933 aligns in the following genomic locations: Homology
BLAST of SMED30022933 vs. Planmine SMEST
Match: SMESG000063851.1 (SMESG000063851.1) HSP 1 Score: 184.111 bits (466), Expect = 1.996e-60 Identity = 89/115 (77.39%), Postives = 102/115 (88.70%), Query Frame = -3
Query: 1 KREPGRNPTREMRGQAEYLLARLERHQAETNRQVEQARRYLQRINENIAAGRIPSTDGYAPQYNVSYELDDPKLQERMTDMNVVVPRYILPRKMREEDRATEIRREHSYATERYI 345
KRE GR+P RE+RGQAE+LLARLE HQAETNRQVEQAR+YLQR+NE+IAAG IPSTDGYAPQYNVSYEL+DP+LQ RM +M V VPR+ILP++MR ED TE+ REHSYA ERYI
Sbjct: 69 KRESGRSPAREIRGQAEHLLARLEHHQAETNRQVEQARQYLQRVNEDIAAGWIPSTDGYAPQYNVSYELNDPRLQRRMPEMRVAVPRHILPKEMRNEDEITELHREHSYARERYI 183 HSP 2 Score: 65.855 bits (159), Expect = 1.996e-60 Identity = 30/35 (85.71%), Postives = 31/35 (88.57%), Query Frame = -2
Query: 341 AMWDAGFSISRVHETRGGTQGDSDEVDLPYVAIKK 445
AMWDAGFSIS V E RGGTQGDSDEV LPYVAIK+
Sbjct: 36 AMWDAGFSISPVREARGGTQGDSDEVYLPYVAIKR 70
BLAST of SMED30022933 vs. Planmine SMEST
Match: SMESG000013157.1 (SMESG000013157.1) HSP 1 Score: 184.496 bits (467), Expect = 6.243e-60 Identity = 88/113 (77.88%), Postives = 103/113 (91.15%), Query Frame = -3
Query: 7 KREPGRNPTREMRGQAEYLLARLERHQAETNRQVEQARRYLQRINENIAAGRIPSTDGYAPQYNVSYELDDPKLQERMTDMNVVVPRYILPRKMREEDRATEIRREHSYATER 345
KREPGR+P REMRGQAEYLLARLERHQAETNRQVEQAR+YL+R+NE+IAAGRIPSTDGYAPQYNVS+ELDDP+LQ +M++M V VPR+ILP++MR E+ E +REHSYA ER
Sbjct: 146 KREPGRSPAREMRGQAEYLLARLERHQAETNRQVEQARQYLRRVNEDIAAGRIPSTDGYAPQYNVSFELDDPRLQRQMSEMRVAVPRHILPKEMRNENDIAEPQREHSYARER 258 HSP 2 Score: 63.5438 bits (153), Expect = 6.243e-60 Identity = 29/35 (82.86%), Postives = 31/35 (88.57%), Query Frame = -2
Query: 341 AMWDAGFSISRVHETRGGTQGDSDEVDLPYVAIKK 445
AMWDAGFSI V ETRGGTQGDS+EVDL YVAIK+
Sbjct: 113 AMWDAGFSIFPVRETRGGTQGDSNEVDLSYVAIKR 147
BLAST of SMED30022933 vs. Planmine SMEST
Match: SMESG000065931.1 (SMESG000065931.1) HSP 1 Score: 147.517 bits (371), Expect = 2.074e-47 Identity = 68/113 (60.18%), Postives = 89/113 (78.76%), Query Frame = -3
Query: 7 KREPGRNPTREMRGQAEYLLARLERHQAETNRQVEQARRYLQRINENIAAGRIPSTDGYAPQYNVSYELDDPKLQERMTDMNVVVPRYILPRKMREEDRATEIRREHSYATER 345
KREPG N RE+RGQAE+LL RLE HQ ET RQ+ +ARRYL ++N++IA GRIPSTDGYAP YNVS+ELDDP L R+ MNV++PR +LPR++R + ++ R++HS+A R
Sbjct: 69 KREPGGNLAREIRGQAEFLLGRLEEHQKETERQIIKARRYLAQVNKDIAEGRIPSTDGYAPSYNVSFELDDPSLCNRLETMNVILPRRVLPRELRNVEENSDSRQDHSFARNR 181 HSP 2 Score: 58.9214 bits (141), Expect = 2.074e-47 Identity = 26/35 (74.29%), Postives = 30/35 (85.71%), Query Frame = -2
Query: 341 AMWDAGFSISRVHETRGGTQGDSDEVDLPYVAIKK 445
AMWDAGFSIS V ETR G QG S++V+LPYVAIK+
Sbjct: 36 AMWDAGFSISTVRETRFGNQGSSEDVELPYVAIKR 70
BLAST of SMED30022933 vs. Planmine SMEST
Match: SMESG000029442.1 (SMESG000029442.1) HSP 1 Score: 146.747 bits (369), Expect = 4.305e-46 Identity = 70/113 (61.95%), Postives = 89/113 (78.76%), Query Frame = -3
Query: 7 KREPGRNPTREMRGQAEYLLARLERHQAETNRQVEQARRYLQRINENIAAGRIPSTDGYAPQYNVSYELDDPKLQERMTDMNVVVPRYILPRKMREEDRATEIRREHSYATER 345
KREPGRNP E+RGQAE++LARLE HQ ETNRQ+ +ARRYL ++N +IA G+IPSTD YAP YNVS+ELDDP+L+ + MNVVVPR +LPR++R + + R +HSYA R
Sbjct: 33 KREPGRNPAWEIRGQAEFILARLEEHQKETNRQIAKARRYLAQVNADIAEGKIPSTDRYAPNYNVSFELDDPRLRGQTGAMNVVVPRRVLPRELRNVEEKPDHRYDHSYARSR 145 HSP 2 Score: 55.0694 bits (131), Expect = 4.305e-46 Identity = 24/34 (70.59%), Postives = 28/34 (82.35%), Query Frame = -2
Query: 341 MWDAGFSISRVHETRGGTQGDSDEVDLPYVAIKK 442
MW AGF ISRV ETR G QG S++V+LPYVAIK+
Sbjct: 1 MWVAGFLISRVRETRSGNQGSSEDVELPYVAIKR 34
BLAST of SMED30022933 vs. Planmine SMEST
Match: SMESG000023390.1 (SMESG000023390.1) HSP 1 Score: 144.436 bits (363), Expect = 9.807e-44 Identity = 72/112 (64.29%), Postives = 85/112 (75.89%), Query Frame = -3
Query: 10 KREPGRNPTREMRGQAEYLLARLERHQAETNRQVEQARRYLQRINENIAAGRIPSTDGYAPQYNVSYELDDPKLQERMTDMNVVVPRYILPRKMREEDRATEIRREHSYATE 345
KREPGRNP RE+RGQAE+LLARLE HQ +T RQV +ARR+L IN+ IA G IPSTD YAP YNVS+ LDDP L MNVVVPR IL R+M+++DR + +EHSYA E
Sbjct: 416 KREPGRNPAREIRGQAEFLLARLEEHQRQTKRQVNRARRHLAEINKAIATGDIPSTDRYAPPYNVSFNLDDPNLAGEAEAMNVVVPRRILTREMKDKDRRSNQDQEHSYARE 527 HSP 2 Score: 49.6766 bits (117), Expect = 9.807e-44 Identity = 20/35 (57.14%), Postives = 28/35 (80.00%), Query Frame = -2
Query: 341 AMWDAGFSISRVHETRGGTQGDSDEVDLPYVAIKK 445
+WDAGFS+S V E+R T+ D ++VDLP+VAIK+
Sbjct: 383 VLWDAGFSVSPVRESRTATRRDDEKVDLPFVAIKR 417 The following BLAST results are available for this feature:
BLAST of SMED30022933 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30022933 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30022933 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30022933 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30022933 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30022933 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30022933 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30022933 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30022933 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30022933 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30022933 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30022933 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30022933 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30022933 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 >SMED30022933 ID=SMED30022933|Name=SMED30022933|organism=Schmidtea mediterranea sexual|type=transcript|length=446bpback to top protein sequence of SMED30022933-orf-1 >SMED30022933-orf-1 ID=SMED30022933-orf-1|Name=SMED30022933-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp MRGQAEYLLARLERHQAETNRQVEQARRYLQRINENIAAGRIPSTDGYAPback to top Annotated Terms
The following terms have been associated with this transcript:
|
