SMED30016347
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., 2020SMED30016347 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 10
Alignments
SMED30016347 aligns in the following genomic locations:
Homology
BLAST of SMED30016347 vs. Ensembl Nematostella
Match: EDO37470 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SFI6]) HSP 1 Score: 46.595 bits (109), Expect = 3.390e-6 Identity = 34/119 (28.57%), Postives = 56/119 (47.06%), Query Frame = 3 Query: 27 QSDRICHSDPQCPLYGDCCYGHQDNGKPGLLKDVLSCKPYNKLFPSAMW-VTNKC-KNPNHPLSDFCTKK----IFNPKNHLKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNC 365 Q + +C+ D C GDCC+ ++ + K LS KP K S + VTN C K + L C++ + P + L++ ++ I Y N+FCA+CN + +Y +C Sbjct: 53 QIETLCYCDSICLQIGDCCHDYRK-----VCKAKLSEKPQVKQVCSNHYIVTNSCPKGTDQYLDGLCSETHGEILRRPYDLLRNLHVFDHDKNISYRNVFCARCNGARNTSYWTTTADC 166
BLAST of SMED30016347 vs. Planmine SMEST
Match: SMESG000033614.1 (SMESG000033614.1) HSP 1 Score: 421.779 bits (1083), Expect = 2.749e-147 Identity = 202/212 (95.28%), Postives = 204/212 (96.23%), Query Frame = 3 Query: 6 RSGYNGSQSDRICHSDPQCPLYGDCCYGHQDNGKPGLLKDVLSCKPYNKLFPSAMWVTNKCKNPNHPLSDFCTKKIFNPKNHLKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTKLIQNKFVIDKCENGGKDYFVFRLQKYKNVFCCKCWNKNCFVRGK 641 RSGYNGSQSDRICHSDPQCPLYGDCCYGHQD+GKPGLLKDVLSCKPYNKLFPSAMW+ NKCKN NHPLSDFCTKKIF PK LKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTKLIQNKFVIDKCENG KDYFVFRLQKYKNVFCCKCWNKNCF R K Sbjct: 14 RSGYNGSQSDRICHSDPQCPLYGDCCYGHQDHGKPGLLKDVLSCKPYNKLFPSAMWLINKCKNLNHPLSDFCTKKIFYPKAPLKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTKLIQNKFVIDKCENGEKDYFVFRLQKYKNVFCCKCWNKNCFGRRK 225
BLAST of SMED30016347 vs. Planmine SMEST
Match: SMESG000033611.1 (SMESG000033611.1) HSP 1 Score: 144.821 bits (364), Expect = 2.659e-40 Identity = 75/196 (38.27%), Postives = 116/196 (59.18%), Query Frame = 3 Query: 42 CHSDPQCPLYGDCCYGHQDNGKPGLLKDVLSCKPYNKLFPSAMWVTNKCKN-PNHPLSDFCTKKIFNPKNHLKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTKLIQNKFVIDKCENGGKDYFVFRLQKYKNVFCCKCWNKNC 626 C+ D +C LYGDCC GH+ K G L+++L CK + +++V +KCKN H LS C K++ K +KS+IPVI+ +I++N FCAKCN E ++YL + ++C + I D ANQA+ + + CEI P ++R C+ ++I C+N+ + + KC NG + + V Y+N FCCKCW +C Sbjct: 29 CNCDDKCTLYGDCCSGHESFNKTGSLRNILKCKLFKPSVAESIYVVDKCKNNTKHILSKLCRKEVIFSKIPVKSFIPVINENGVIFENSFCAKCNNEDLYSYLNISISCPDVNITDIYDANQAIAKSRDSCEIQPEIESNIKRICKTKLIDFCSNSFEDIGENITGKCTNGPESFEVHGEILYRNTFCCKCWKIHC 224
BLAST of SMED30016347 vs. Planmine SMEST
Match: SMESG000033610.1 (SMESG000033610.1) HSP 1 Score: 124.79 bits (312), Expect = 5.083e-33 Identity = 72/204 (35.29%), Postives = 105/204 (51.47%), Query Frame = 3 Query: 18 NGSQSDRICHSDPQCPLYGDCCYGHQDNGKPGLLKDVLSCKPYNKLFPSAMWVTNKCKNPNHPLSDFCTKKIFNPKNHLKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTKLIQNKFVIDKCENGGKDYFVFRLQKYKNVFCCKCWNKNCF 629 N +SD+ C D C +GDCC GH+ + G L+ + SCK + K M V NKC N NH S +CTK++ +PK +KS+ V+ K+IY+N +CA+CN + Y + V+C I ++ N+ +I +P C I P + LQR+C + C + V D C NG D Y+N CC C N +CF Sbjct: 19 NCRKSDQYCQCDKICVQFGDCCPGHEKFQQTGSLESISSCKVFAKNSYENMRVINKCVNDNHYYSKYCTKELMDPKLPIKSFAAVMGENKLIYENYYCARCNNIKRYQYFSLSVSCFGHNITNFKQVNEIMIKSPYSCSILPLIDSELQRTCFINLTRLCQEPLSKRFDNVSDMCLNGKLDIVSDGRNFYRNDHCCSCRNISCF 222
BLAST of SMED30016347 vs. Planmine SMEST
Match: SMESG000067292.1 (SMESG000067292.1) HSP 1 Score: 51.2174 bits (121), Expect = 1.491e-7 Identity = 54/206 (26.21%), Postives = 87/206 (42.23%), Query Frame = 3 Query: 30 SDRICHSDPQCPLYGDCCYGHQDNGKPGLLKDVLSCKPYNKLFPSAMWVTNKC--KNPNHPLSDFCTKKIFNPKNHLKSWIPVISNRK---IIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTK------LIQNKFVIDKCENGGKDYFVFRLQK-YKNVFCCKC 611 S+ C+ D QC ++GDCC+ HQ + +P + SC +V +KC K+ + L D C +K N+L +P N + + + N FCA CN + F + V+ + L+ + N+ FP + QR C +I C + L +N+ EN G +QK Y+N +C C Sbjct: 32 SETHCYCDDQCSMFGDCCHKHQQHHEP-----IASCHD-------GYYVIDKCLYKSTDGNLKDKCERKSEISVNNLLYHVPTYGNYENVSLTFKNAFCAVCNGKNQFEFARVEKHKTSLK-----RKKDNTTEKSNYKYTFP---KEFQRICHENVIITCDDDSEDALKLLCRNQPTFYVTENRG------MVQKIYRNAYCFLC 211 The following BLAST results are available for this feature:
BLAST of SMED30016347 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30016347 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30016347 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30016347 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30016347 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30016347 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30016347 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30016347 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30016347 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30016347 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30016347 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30016347 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 1
BLAST of SMED30016347 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30016347 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 4
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30016347 ID=SMED30016347|Name=SMED30016347|organism=Schmidtea mediterranea sexual|type=transcript|length=641bpback to top protein sequence of SMED30016347-orf-1 >SMED30016347-orf-1 ID=SMED30016347-orf-1|Name=SMED30016347-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=158bp MWVTNKCKNPNHPLSDFCTKKIFNPKNHLKSWIPVISNRKIIYDNLFCAKback to top Annotated Terms
The following terms have been associated with this transcript:
|