SMED30001295
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., 2020SMED30001295 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30001295 aligns in the following genomic locations:
Homology
BLAST of SMED30001295 vs. TrEMBL
Match: A0A448X8C9 (G_PROTEIN_RECEP_F1_2 domain-containing protein (Fragment) OS=Protopolystoma xenopodis OX=117903 GN=PXEA_LOCUS24171 PE=3 SV=1) HSP 1 Score: 77.7962 bits (190), Expect = 5.575e-12 Identity = 55/141 (39.01%), Postives = 88/141 (62.41%), Query Frame = -2 Query: 542 GSLANLIVILLFNINTSNGI-SNXXXXXXXXXXXXXXXXXIPATLMWTIWKIRSTDTLCKIHMIIKATIIPASLLVLVLIAVDRFLIICFMPSKIITKKSGSYILILIFLVSIGLAMPFGMAFGVRSDMM-KMEDDDVLLP 958 G + NL+VI F+ + S++ I +L DL+ICL+DIP TL +W +T LC++H +K IIP S +LVLIA++RFL+ICFMP + ++ Y+++ +F++ +GLAMP + RS ++ + D+LLP Sbjct: 58 GGVGNLLVIWAFSRQARRAVVSSLLIILLGITDLVICLVDIPVTLYLKVWFREATVVLCRLHGGLKGFIIPFSSGLLVLIALERFLLICFMPGTPLRPRATGYLIVGLFVICVGLAMPVSL----RSTLLERNSQGDLLLP 194
BLAST of SMED30001295 vs. TrEMBL
Match: A0A5J4NP51 (G_PROTEIN_RECEP_F1_2 domain-containing protein OS=Paragonimus westermani OX=34504 GN=DEA37_0011069 PE=3 SV=1) HSP 1 Score: 78.9518 bits (193), Expect = 3.104e-11 Identity = 49/121 (40.50%), Postives = 74/121 (61.16%), Query Frame = -2 Query: 599 GSLANLIVILLFNINTSNGI-SNXXXXXXXXXXXXXXXXXIPATLMWTIWKIRSTDTLCKIHMIIKATIIPASLLVLVLIAVDRFLIICFMPSKIITKKSGSYILILIFLVSIGLAMPFGM 958 G + N +V+ F + GI S++ I +LAC+D C + IP T+ IWK ++ D LC++HM K I+P S +LVLIA++RFL+ICF+P + + Y +LI V I LA+P G+ Sbjct: 44 GLIGNGLVVWAFRCQVTQGIVSSLLILLLACLDFTSCAVGIPTTIYLDIWKGQTVDWLCRLHMAFKGFIVPVSAFLLVLIALERFLLICFIPGIGLKRNHLRYAFVLILTVGILLAIPMGL 164
BLAST of SMED30001295 vs. TrEMBL
Match: A0A183WA62 (G_PROTEIN_RECEP_F1_2 domain-containing protein OS=Trichobilharzia regenti OX=157069 GN=TRE_LOCUS9015 PE=3 SV=1) HSP 1 Score: 76.6406 bits (187), Expect = 1.453e-10 Identity = 78/268 (29.10%), Postives = 134/268 (50.00%), Query Frame = -2 Query: 179 GSLANLIVILLFNINTSNGI-SNXXXXXXXXXXXXXXXXXIPATLMWTIWKIRSTDTLCKIHMIIKATIIPASLLVLVLIAVDRFLIICFMPSKIITKKSGSYILILIFLVSIGLAMPFGMAFGVRSDMMKMEDDDVLLPGLIXXXXXXXXXXXXXXXTITHYPLSVYIIPKTCEMNYEITSKMTIIRYQLSIFILFTVMMTXXXXXXXXXXXXVWKKQKRLLTKYATNEDGKYS-----NSLVSFQKP--PSQYTPMKSHHEFSTQQ 958 G++ N +V+ F S GI S + I +LAC DL ICLI IP TL IW +TD +C+IH+ +K ++P S +L+LIA++RFL+ICF+P + +K L++IF + + A+P G+ D K D+ + L L ++ ++ + +T K C+ + + +Q+ + ILF + Y IF++VW+ + + KY T++ K S ++ S +P P+ + P + F +Q Sbjct: 55 GTIGNSLVVWAFRKQVSQGIVSGLFILLLACNDLFICLIVIPCTLYLDIWTGDTTDWICRIHLSMKGFVVPISACILMLIAMERFLLICFIPGIQMKRKHIVIALVIIFCIGLLCALPMGLHVTA-IDACKEHDELLDLNTLKHSLSTFKSKEWFVQLRVT----------KRCDKDETYLNDNLYWYHQICVLILFIGLFIGTAGTYALIFLFVWRHESFMYEKYGTSKAAKGSWVRIHAAMNSSGEPCSPAIWNPFRKRLSFRHKQ 311
BLAST of SMED30001295 vs. TrEMBL
Match: A0A095AXD5 (G_PROTEIN_RECEP_F1_2 domain-containing protein OS=Schistosoma haematobium OX=6185 GN=MS3_07717 PE=3 SV=1) HSP 1 Score: 76.2554 bits (186), Expect = 2.054e-10 Identity = 32/86 (37.21%), Postives = 58/86 (67.44%), Query Frame = -2 Query: 581 PATLMWTIWKIRSTDTLCKIHMIIKATIIPASLLVLVLIAVDRFLIICFMPSKIITKKSGSYILILIFLVSIGLAMPFGMAFGVRS 838 P T+ +W+ R+ D +C++H+I+K+ + S L LV+IA+DR+L++CF+P I+TKK +++ +++ I A+P G+ GV S Sbjct: 205 PTTIFLIVWETRTYDFICRLHVILKSFTLTVSALFLVIIALDRWLLVCFIPCVIMTKKCMKRLIVGTYILGILWAIPMGLHHGVHS 290
BLAST of SMED30001295 vs. TrEMBL
Match: A0A430QLG1 (G_PROTEIN_RECEP_F1_2 domain-containing protein OS=Schistosoma bovis OX=6184 GN=DC041_0008792 PE=3 SV=1) HSP 1 Score: 76.2554 bits (186), Expect = 2.167e-10 Identity = 32/86 (37.21%), Postives = 58/86 (67.44%), Query Frame = -2 Query: 581 PATLMWTIWKIRSTDTLCKIHMIIKATIIPASLLVLVLIAVDRFLIICFMPSKIITKKSGSYILILIFLVSIGLAMPFGMAFGVRS 838 P T+ +W+ R+ D +C++H+I+K+ + S L LV+IA+DR+L++CF+P I+TKK +++ +++ I A+P G+ GV S Sbjct: 205 PTTIFLIVWETRTYDFICRLHVILKSFTLTVSALFLVIIALDRWLLVCFIPCVIMTKKCMKRLIVGTYILGILWAIPMGLHHGVHS 290
BLAST of SMED30001295 vs. Planmine SMEST
Match: SMESG000050757.1 (SMESG000050757.1) HSP 1 Score: 128.642 bits (322), Expect = 2.009e-31 Identity = 112/322 (34.78%), Postives = 186/322 (57.76%), Query Frame = -2 Query: 11 GSLANLIVILLFNINTSNGISNXXXXXXXXXXXXXXXXXIPATLMWTIWKIRSTDTLCKIHMIIKATIIPASLLVLVLIAVDRFLIICFMPSKIITKKSGSYILILIFLVSIGLAMPFGMAFGVRSDMMKMEDDDVLLPGLIXXXXXXXXXXXX-XXXTITHYPLSVYIIPK-TCEMNYEITSKMTIIRYQLSIFILFTVMMTXXXXXXXXXXXXVWKKQKRLLTKYATNEDGKYSNSLVSFQKPPSQYTPMKSHHEFSTQQHDCFDHQIQPRTKHIYCTIS----HPKRRNRAHVKTGQXXXXXXXXXXXSYLPYFLIVNN 958 G + N VI++F+ + +SN+ I LA ID++IC+IDIP TL +W+ S D +CK+H+ +KA +P S L+LV+IA+DRFLIICF+PS +I KKS IL+L+FL I LA+P G+ G++ K +DVL+P L N+N + + +K + P ++ +C ++ SK+ Y++++F+LFT +M +I++FY IFI++W K +++ + +N + ++ S M+S + ++ + H + + C+ + H RR + HVKT L I+ +FI+SYLPY LI N+ Sbjct: 44 GLIGNYFVIVVFSKHIKQAVSNLFITFLAIIDMIICVIDIPMTLYLVVWQKNSVDIVCKLHISLKAFCVPVSALILVMIAIDRFLIICFIPSILIRKKSAMIILLLVFLSGIVLAVPMGIHTGIKI-FFKTSINDVLMPPLSKNSNDTEDLFKVGNIDNAIERPAERHLFKSGSCGIDQSYISKLNFSYYKMALFVLFTFLMVLIIVFYSIIFIFLWSKHQKMKSYKNSNNRKNQKETSITLS---SNLLRMRSLN----KRKSSYKHSVDIDEPSLSCSSNLKRQHSHRRRKPHVKTAYTLALIAAAFIVSYLPYLLISND 357
BLAST of SMED30001295 vs. Planmine SMEST
Match: SMESG000062718.1 (SMESG000062718.1) HSP 1 Score: 60.4622 bits (145), Expect = 4.306e-9 Identity = 34/84 (40.48%), Postives = 57/84 (67.86%), Query Frame = -2 Query: 587 PATLMWTIWKIRSTDTLCKIHMIIKATIIPASLLVLVLIAVDRFLIICFMPSKIITKKSGSYILILIFLVSIGLAMPFGMAFGV 838 P +L+ IW++ + D CKI M + ++ S ++LVLIA+DRFLIICF+PSK ++ K +++ + L+SI +++P G+ GV Sbjct: 104 PTSLIVEIWRLPTYDIACKIVMAFRCFLLIFSPMLLVLIALDRFLIICFVPSKKMSLKQTLFVIGFMLLISISISIPSGLCTGV 187 The following BLAST results are available for this feature:
BLAST of SMED30001295 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30001295 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30001295 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30001295 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30001295 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30001295 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30001295 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30001295 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 5
BLAST of SMED30001295 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30001295 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30001295 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30001295 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30001295 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30001295 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 >SMED30001295 ID=SMED30001295|Name=SMED30001295|organism=Schmidtea mediterranea sexual|type=transcript|length=2612bpback to top protein sequence of SMED30001295-orf-1 >SMED30001295-orf-1 ID=SMED30001295-orf-1|Name=SMED30001295-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp MIRNRSTAIRTSTSKDAGMIVAFIIICILQSVSVERIFQIVHMSVAGMSIback to top protein sequence of SMED30001295-orf-2 >SMED30001295-orf-2 ID=SMED30001295-orf-2|Name=SMED30001295-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=360bp MNMSHNPVITYNYVDIIQADFQKYMPSLILLTILLITISLFGSLANLIVIback to top Annotated Terms
The following terms have been associated with this transcript:
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
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