SMED30030913
Overview
Neoblast Clusters
Zeng et. al., 2018
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 AppEmbryonic 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., 2020SMED30030913 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 5
Alignments
SMED30030913 aligns in the following genomic locations:
Homology
BLAST of SMED30030913 vs. TrEMBL
Match: A0A0L8H6T8 (Uncharacterized protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22021012mg PE=4 SV=1) HSP 1 Score: 75.485 bits (184), Expect = 1.857e-11 Identity = 68/239 (28.45%), Postives = 114/239 (47.70%), Query Frame = 3 Query: 63 MRCGSNAF--RKNLIYFVMVNNIC--YTPT-AASAQSTLISNENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNF-RSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNSSDNISSWFILDNVLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCHIDVGVLMIFDAPDVCEYGLAWIVQLNKYPQIIYAVKNGMPALYNDNVRQAKSLEI 761 + C S A + I + V+++C Y+P + ST SNE + R + + + + G+G +N P + V++ G + NF R +LD WS L + I + +V ++ N++ + SWF L+ L S PW L + N FS+ G R F++ S YGGC D G ++I +A +C Y QL+ YPQ++Y+ +N L++ N + S+ I Sbjct: 63 LECASIALNSQSEFITYNNVSHVCKNYSPKNLMTVVSTNDSNEISFYRNTQWIKVYALSMGAGSKVYDSFANKGSPSSWNVEKCIGTFCPNFFRHPILDVWSHLPIDEAKLVIYENQTAVVNMVFDGRNTT--LESWFSLE-TLKSSPWPD--LHQQPVNIFSLFG--AAIRRFYVSSEYGGCVGDWGWMLIAEARHMCYYE-----QLSSYPQLLYSKRNSR-TLWDSNQGKGDSIAI 288
BLAST of SMED30030913 vs. TrEMBL
Match: C3ZNM0 (Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_100697 PE=4 SV=1) HSP 1 Score: 67.3958 bits (163), Expect = 4.637e-9 Identity = 44/130 (33.85%), Postives = 67/130 (51.54%), Query Frame = 3 Query: 312 SMNFRSILLDEWSTLRPSYMNVTIKD-VDDVIVGWLYFVVNSSDNISSWFILDNVLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCHIDVGVLMIFDAPDVCEYGLAWIVQLNKYPQIIYA 698 + +F+S L+ EW TL + ++ V L F + +S WF + +++S PW LKT+T N FSI+GD T RSFFI+ YGGC D G L++ D C W + + P I+++ Sbjct: 61 AAHFKSPLVQEWETLGIQLVKGSLYSYRQGTEVRELIFDGRDTTKVS-WFSHERLISS-PW--TDLKTETNNIFSIIGDSTYHRSFFINRNYGGCEKDAGWLVVPDGGTAC----GWETRDKRVPHILFS 182
BLAST of SMED30030913 vs. TrEMBL
Match: C3YAE7 (Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_72548 PE=4 SV=1) HSP 1 Score: 65.855 bits (159), Expect = 6.268e-8 Identity = 43/114 (37.72%), Postives = 59/114 (51.75%), Query Frame = 3 Query: 318 NFRSILLDEWSTLRPSYMNVTI----KDVDDVIVGWLYFVVNSSDNISSWFILDNVLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCHIDVGVLMIFDAPDVCEY 647 ++RS LD WS+L + + VT+ + D+I F + D + +WF D +L+S PW LKT FFSI GD R FFIH YGGC D G L++ D C + Sbjct: 324 HYRSPDLDRWSSLHVTKVKVTLVAQHQHTRDII-----FNAHGCD-MDNWFTKDRLLSS-PWTD--LKTAPTKFFSIRGDNQYNRRFFIHRSYGGCANDRGWLIVLDPGAECPW 428
BLAST of SMED30030913 vs. TrEMBL
Match: K1PKR8 (Uncharacterized protein OS=Crassostrea gigas OX=29159 GN=CGI_10014564 PE=4 SV=1) HSP 1 Score: 63.5438 bits (153), Expect = 1.561e-7 Identity = 46/171 (26.90%), Postives = 82/171 (47.95%), Query Frame = 3 Query: 210 LLRIVNGSGV-YPPGYLSNMIYPPQYE--VKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNSSDN-ISSWFILDNVLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCHIDVGVLMIFDAPDVCEYGLAWIVQLNKYPQIIYAVKNG 710 + R G G+ +L N+I P + + + + S ++R+ +D W +L S + + + + + + D+ I +WF +LNS W +N+ + YN+FSI G RSFF++++Y C +D G +++ D P C W NK PQ Y+ +G Sbjct: 94 MFRATPGVGLSVKDSWLGNIIPPTAQDTCISMKNTSCSTHYRNPRVDIWESLSISQVTLELYKHGSKVA---FIAFDGKDSTIENWFNSSRILNS-SW-SNVTPSTIYNYFSIKGHSECSRSFFVNTHYHNCSVDTGYMVVVDPPTAC---CPWENVPNK-PQFFYSAADG 255
BLAST of SMED30030913 vs. TrEMBL
Match: A0A0L8I848 (Uncharacterized protein (Fragment) OS=Octopus bimaculoides OX=37653 GN=OCBIM_22028930mg PE=4 SV=1) HSP 1 Score: 61.2326 bits (147), Expect = 1.977e-7 Identity = 36/121 (29.75%), Postives = 67/121 (55.37%), Query Frame = 3 Query: 306 NYSMN-FRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNSSDNISSWFILDNVLNSFPWDTNMLKTKTYNFFSIVGDRTLF-RSFFIHSYYGGCHIDVGVLMIFDAPD--VCEYGLA 656 NYS++ F+S L++ W++L + ++ + ++V ++ N +WF L+ ++ S PW LKT + FSI+G+ +++ R F+I+ YG C DVG L++ D VC + + Sbjct: 36 NYSLSVFKSSLIENWASLHVQEVKFVLEQDNQIVVSMIF--DGKQSNKMNWFCLNRLIKSSPWTD--LKTNKPSIFSIIGEDSIYKRRFYINKEYGRCKKDVGWLLVRDDKKGMVCSFAAS 152
BLAST of SMED30030913 vs. Planmine SMEST
Match: SMESG000034462.1 (SMESG000034462.1) HSP 1 Score: 468.774 bits (1205), Expect = 8.471e-168 Identity = 228/229 (99.56%), Postives = 229/229 (100.00%), Query Frame = 3 Query: 111 MVNNICYTPTAASAQSTLISNENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNSSDNISSWFILDNVLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCHIDVGVLMIFDAPDVCEYGLAWIVQLNKYPQIIYAVKNGMPALYNDNVRQAKSLEIIGVYSQNVEIYS 797 MVNNICYTPTAASAQSTLISNENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNSSDNISSWFILDN+LNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCHIDVGVLMIFDAPDVCEYGLAWIVQLNKYPQIIYAVKNGMPALYNDNVRQAKSLEIIGVYSQNVEIYS Sbjct: 1 MVNNICYTPTAASAQSTLISNENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNSSDNISSWFILDNLLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCHIDVGVLMIFDAPDVCEYGLAWIVQLNKYPQIIYAVKNGMPALYNDNVRQAKSLEIIGVYSQNVEIYS 229
BLAST of SMED30030913 vs. Planmine SMEST
Match: SMESG000034379.1 (SMESG000034379.1) HSP 1 Score: 458.759 bits (1179), Expect = 7.915e-164 Identity = 223/229 (97.38%), Postives = 225/229 (98.25%), Query Frame = 3 Query: 111 MVNNICYTPTAASAQSTLISNENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNSSDNISSWFILDNVLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCHIDVGVLMIFDAPDVCEYGLAWIVQLNKYPQIIYAVKNGMPALYNDNVRQAKSLEIIGVYSQNVEIYS 797 MVNNICYTPTAASAQSTLISNENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVN+SDNISSWFIL N+LNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGC DVGVLMIFDAPD CEYGLAWIVQLNKYPQIIYAVKNGMPALYNDNVRQAKSLEIIGVYSQNVEIYS Sbjct: 1 MVNNICYTPTAASAQSTLISNENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNASDNISSWFILGNLLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCDADVGVLMIFDAPDACEYGLAWIVQLNKYPQIIYAVKNGMPALYNDNVRQAKSLEIIGVYSQNVEIYS 229
BLAST of SMED30030913 vs. Planmine SMEST
Match: SMESG000076267.1 (SMESG000076267.1) HSP 1 Score: 298.13 bits (762), Expect = 5.963e-100 Identity = 148/264 (56.06%), Postives = 182/264 (68.94%), Query Frame = 3 Query: 6 KLFLAFSFATGMMVDPTGYMRCGSNAFRKNLIYFVMVNNICYTPTAASAQSTLIS-NENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNSSDNISSWFILDNVLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCHIDVGVLMIFDAPDVCEYGLAWIVQLNKYPQIIYAVKNGMPALYNDNVRQAKSLEIIGVYSQNVEIY 794 ++F+ F + +G DP MRCG AF +N+IYF MVN CY P A SAQ T S + IY+R+ N +T+LRIVNGSGVYPP +LS + P Y+VK+ + NYS NFRS++LDEWSTLRPS MNVTI+ V+ IVGWL F V++ DNI SWF L N+L+SFPWD N+LK Y FFS+ GDR RSFFI Y GC D GVLM+FD D C Y L WI YPQI YAV NG PA++ + +R AKSLEIIG Y ++ IY Sbjct: 5 EIFVLFVWFSGKKGDPLDEMRCGLKAFDRNIIYFAMVNKSCYIPKAISAQPTQSSPTKIIYQRIENTITVLRIVNGSGVYPPDFLSKLSNPSTYKVKDIQNNYSENFRSVILDEWSTLRPSGMNVTIRAVNKAIVGWLNFRVSAQDNIISWFTLGNLLDSFPWDINVLKNSLYKFFSVTGDRKGLRSFFISIRYNGCTGDAGVLMMFDGSDACSYNLKWITSAINYPQIFYAVLNGSPAIFYNYIRSAKSLEIIGSYPSDILIY 268
BLAST of SMED30030913 vs. Planmine SMEST
Match: SMESG000034377.1 (SMESG000034377.1) HSP 1 Score: 268.085 bits (684), Expect = 5.548e-88 Identity = 138/280 (49.29%), Postives = 177/280 (63.21%), Query Frame = 3 Query: 6 KLFLAFSFATGMMVDPTGYMRCGSNAFRKNLIYFVMVNNICYTPTAASAQSTLISN-----------------ENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNSSDNISSWFILDNVLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCHIDVGVLMIFDAPDVCEYGLAWIVQLNKYPQIIYAVKNGMPALYNDNVRQAKSLEIIGVYSQNVEIY 794 K F+ + + G D + C F+K L YF +V+N+C+TPT + + + +YR++ N L LLRIVNGSGVYPP YL+N P Y VK+ K N+S NFRSILLD+W +PS +NVTI+DV DV VGWLYF V DNI SWF N+++SFPW+ N+LK TYN+FSI GD+T RSF ++S YGGC DVGVLM+FD +VC Y L W+ +YPQIIYA NG P+ YN+ VR AKSLEIIG Y N+ I+ Sbjct: 5 KFFILLALSVGFG-DSVEFADCILQTFQKKLTYFSIVDNLCFTPTQPTQPTKSTQPTQSTQTTQSTQSTFTTTKAVYRKMGNTLILLRIVNGSGVYPPDYLANTTNPSPYGVKDYKRNFSENFRSILLDDWKRYQPSNLNVTIRDVSDVEVGWLYFSVFPKDNILSWFASTNLIDSFPWNINVLKNSTYNYFSINGDKTYNRSFLVNSQYGGCPNDVGVLMVFDGHNVCNYQLMWLTSATEYPQIIYAELNGSPSNYNNYVRVAKSLEIIGTYPSNIGIF 283
BLAST of SMED30030913 vs. Planmine SMEST
Match: SMESG000076443.1 (SMESG000076443.1) HSP 1 Score: 267.7 bits (683), Expect = 9.036e-88 Identity = 138/280 (49.29%), Postives = 177/280 (63.21%), Query Frame = 3 Query: 6 KLFLAFSFATGMMVDPTGYMRCGSNAFRKNLIYFVMVNNICYTPTAASAQSTLISN-----------------ENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNSSDNISSWFILDNVLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCHIDVGVLMIFDAPDVCEYGLAWIVQLNKYPQIIYAVKNGMPALYNDNVRQAKSLEIIGVYSQNVEIY 794 K F+ + + G D + C F+K L YF +V+N+C+TPT + + + +YR++ N L LLRIVNGSGVYPP YL+N P Y VK+ K N+S NFRSILLD+W +PS +NVTI+DV DV VGWLYF V DNI SWF N+++SFPW+ N+LK TYN+FSI GD+T RSF ++S YGGC DVGVLM+FD +VC Y L W+ +YPQIIYA NG P+ YN+ VR AKSLEIIG Y N+ I+ Sbjct: 5 KFFILLALSVGFG-DSVEFADCILQTFQKKLTYFSIVDNLCFTPTQPTQPTKSTQPTQSTQTTQSTQSTFTTTKAVYRKMGNTLILLRIVNGSGVYPPDYLANTTNPSPYGVKDYKRNFSENFRSILLDDWKRYQPSNLNVTIRDVSDVEVGWLYFSVFPKDNILSWFASTNLIDSFPWNINVLKNSTYNYFSINGDKTYNRSFLVNSQYGGCPNDVGVLMMFDGHNVCNYRLTWLTSATEYPQIIYAELNGSPSNYNNYVRVAKSLEIIGTYPSNIGIF 283 The following BLAST results are available for this feature:
BLAST of SMED30030913 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30030913 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30030913 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30030913 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30030913 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30030913 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30030913 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30030913 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 5
BLAST of SMED30030913 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30030913 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30030913 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30030913 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30030913 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30030913 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 >SMED30030913 ID=SMED30030913|Name=SMED30030913|organism=Schmidtea mediterranea sexual|type=transcript|length=1178bpback to top protein sequence of SMED30030913-orf-1 >SMED30030913-orf-1 ID=SMED30030913-orf-1|Name=SMED30030913-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=266bp LKLFLAFSFATGMMVDPTGYMRCGSNAFRKNLIYFVMVNNICYTPTAASAback 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
|