SMED30023417
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., 2020SMED30023417 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30023417 aligns in the following genomic locations:
Homology
BLAST of SMED30023417 vs. TrEMBL
Match: C3Y2Y3 (Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_124611 PE=4 SV=1) HSP 1 Score: 62.003 bits (149), Expect = 7.311e-6 Identity = 73/271 (26.94%), Postives = 115/271 (42.44%), Query Frame = 2 Query: 92 NIVSLQHDIVKHKDTISE----AFHLF---PPSRPALLDIFCDIIVDKYVGSYIHQRNNYTNELEEIITSLTNEVNIILDKEFESNDYVLTAVNTKVSHYSGYGFVVYACQWVLQVLAKITMKYDQILAFNEPLSVNDKLK-WTQVPVIINLLDILCKTLKSKMVGHET---VSIIMKNVAQHRNHLLWVIKFIGERHPSGIVDKIIDCILSEF-------IPTQEYEKLQSCMVVLSSLGAHHARQLQSALYKKLKAAI-EGSFE--TVP 841 V +H HK T+ E A L P +R A+L+ F I D+ V S+I Q I + + V LD + VL KV+ + ++ A W + +L +I+ KY S+N+ L+ W L+DI + L + M G V ++ QH H WV+ IG P+ I+ +++ C L +F + KL S + +L L AHHA+ ++ AL + ++ EG E TVP Sbjct: 26 TFVQGKHATFGHKLTLEEHARSALSLLRNVPAARSAVLE-FLQGIFDEAVNSHILQ----------IESEGSGTVGPNLDPVIQEVCSVLLGF-VKVN-PQAWAPLISA--WSIDLLGQISTKYAGRRGVPHSSSLNELLQLWMTCKATRTLMDIYTQCLAA-MTGSSADLCVDALLDTSVQHSPHFDWVVAHIGSSFPNTIITRVLSCGLKDFCSHSSSQVTESHVPKLASVVGILGHLAAHHAQDIREALLQLFHVSLSEGKQEQYTVP 280
BLAST of SMED30023417 vs. TrEMBL
Match: A0A224XJD9 (Putative integrator complex subunit 5-like isoform x1 (Fragment) OS=Panstrongylus lignarius OX=156445 PE=4 SV=1) HSP 1 Score: 62.003 bits (149), Expect = 8.485e-6 Identity = 61/262 (23.28%), Postives = 115/262 (43.89%), Query Frame = 2 Query: 158 FPPSRPALLDIFCDIIVDKYVGSYIHQRN-NYTNELEEIITSLTNEVNIILDKEFESNDYVLTAVNTKVSHYSGYGFVVYACQWVLQVLAKITMKYDQILAFNEPLSVNDKLK-WTQVPVIINLLDILCKTLKSKMVGHET----VSIIMKNVAQHRNHLLWVIKFIGERHPSGIVDKIIDCILSEFI--P--TQEYEKLQSCMVVLSSLGAHHARQLQSALYKKLKAAIEGSFETVPKQKIINYQTLIYFTLLLASRSDVF 913 P SR A+ + Y+G+ + N+ ELE +L N N D E + ++NT +++ + V +W + L ++ KY S++D L+ W LLDI LK +++G++ +S ++ +H H WV+ +IG +P +V +++ C L EF P + KL+S + +L L H +++ A+ ++E + ++ I + + + L LAS + V Sbjct: 39 LPASRDAVFE---------YLGTVFEKSTLNHMQELENRNKALNNSSNSFDDSIIEE---INASLNTFLTNQP-LAWAVIVSKWAFEHLGSLSSKYSSRGKSPVNGSLSDSLQQWMSCNATSALLDITTNCLK-RLIGNDEARNCISFLLDTCVKHSPHFDWVVAYIGSCYPEMVVIRVLSCGLQEFSCNPGNAAKIPKLKSVVGILIHLSGSHRAEIKKAMSDLFNWSMEENSRNEDREIIREKNSAVPYLLQLASLAPVL 286
BLAST of SMED30023417 vs. Planmine SMEST
Match: SMESG000027258.1 (SMESG000027258.1) HSP 1 Score: 1961.81 bits (5081), Expect = 0.000e+0 Identity = 978/980 (99.80%), Postives = 979/980 (99.90%), Query Frame = 2 Query: 56 MTSVELSWKKLVNIVSLQHDIVKHKDTISEAFHLFPPSRPALLDIFCDIIVDKYVGSYIHQRNNYTNELEEIITSLTNEVNIILDKEFESNDYVLTAVNTKVSHYSGYGFVVYACQWVLQVLAKITMKYDQILAFNEPLSVNDKLKWTQVPVIINLLDILCKTLKSKMVGHETVSIIMKNVAQHRNHLLWVIKFIGERHPSGIVDKIIDCILSEFIPTQEYEKLQSCMVVLSSLGAHHARQLQSALYKKLKAAIEGSFETVPKQKIINYQTLIYFTLLLASRSDVFELTNASISMIGRIICQFTPKQLEQFFLHQNFGDNILRSYYHMTLNILLNSHDLEIGRVLEFIIHHTHSTITGRTGVSCCSANFSQMCMNIIANVSVKLLIQCHSAGLSKPSNNRTMALAILNYVMQHLEFWIQRVVKDGSCVAAKLLSCLVLNDFKSIGDDLLLTIVTNDPQTPTEVNGHKKALVLFFRLVDEFESVSYNILEEVTTRSLCVAQSYQPSRQMRYLSTLYSMLVYEARMQSQRRRLARAINSNIDXXXXXXXTNKXXXXXXXXXXXXXXXXXXXXEKYSVPISSPYLCKTDTRFKAWPIFVASRVVRCISVMLSILIESLNANNPSSVILIRRLTDFLVNFLRTTDPRHTISAVQIIFREFLRSSWIDTNNRFVFKKTLKPGWFNGKLVHDYPPTDSKTGRLNNTNQSPIIRNRYSPIQEKHWEVLIMTLCHFHRQHDVNSTSAYQVIQWICRQCLSPSYYLLINADLNTIPKDLNYITIFWKRFNQSELFWGLFYMLSRKAPQTFQPPYQTLEALMSACQHLWSTSDCPRKRLIRNVPDSEIFISDSHDPIILHKQRFYELINSNSNLYRATVFLFECLSSQMALTDELKLMLPYLSCSEVQTILFHLAYIWNKKVQKPPTVPAPVNEIDADGNVVSVSMVPIEDTQPKNTFSWETLLPALVHARIHFKSLYDQFCRLLFISCE 2995 MTSVELSWKKLVNIVSLQHDIVKHKDTISEAFHLFPPSRPALLDIFCDIIVDKYVGSYIHQRNNYTNELEEIITSLTNEVNIILDKEFESNDYVLTAVNTKVSHYSGYGFVVYACQWVLQVLAKITMKYDQILAFNEPLSVNDKLKWTQVPVIINLLDILCKTLKSKMVGHETVSIIMKNVAQHRNHLLWVIKFIGERHPSGIVDKIIDCILSEFIPTQEYEKLQSCMVVLSSLGAHHARQLQSALYKKLKAAIEGSFETVPKQKIINYQTLIYFTLLLASRSDVFELTNASISMIGRIICQFTPKQLEQFFLHQNFGDNILRSYYHMTLNILLNSHDLEIGRVLEF+IHHTHSTITGRTGVSCCSANFSQMCMNIIANVSVKLLIQCHSAGLSKPSNNRTMALAILNYVMQHLEFWIQRVVKDGSCVAAKLLSCLVLNDFKSIGDDLLLTIVTNDPQTPTEVNGHKKALVLFFRLVDEFESVSYNILEEVTTRSLCVAQSYQPSRQMRYLSTLYSMLVYEARMQSQRRRLARAINSNIDLLLLLVVTNKSLPIIKISISILSKIDVVSDEKYSVPISSPYLCKTDTRFKAWPIFVASRVVRCISVMLSILIESLNANNPSSVILIRRLTDFLVNFLRTTDPRHTISAVQIIFREFLRSSWIDTNNRFVFKKTLKPGWFNGKLVHDYPPTDSKTGRLNNTNQSPIIRNRYSPIQEKHWEVLIMTLCHFHRQHDVNSTSAYQVIQWICRQCLSPSYYLLINADLNTIPKDLNYITIFWKRFNQSELFW LFYMLSRKAPQTFQPPYQTLEALMSACQHLWSTSDCPRKRLIRNVPDSEIFISDSHDPIILHKQRFYELINSNSNLYRATVFLFECLSSQMALTDELKLMLPYLSCSEVQTILFHLAYIWNKKVQKPPTVPAPVNEIDADGNVVSVSMVPIEDTQPKNTFSWETLLPALVHARIHFKSLYDQFCRLLFISCE Sbjct: 1 MTSVELSWKKLVNIVSLQHDIVKHKDTISEAFHLFPPSRPALLDIFCDIIVDKYVGSYIHQRNNYTNELEEIITSLTNEVNIILDKEFESNDYVLTAVNTKVSHYSGYGFVVYACQWVLQVLAKITMKYDQILAFNEPLSVNDKLKWTQVPVIINLLDILCKTLKSKMVGHETVSIIMKNVAQHRNHLLWVIKFIGERHPSGIVDKIIDCILSEFIPTQEYEKLQSCMVVLSSLGAHHARQLQSALYKKLKAAIEGSFETVPKQKIINYQTLIYFTLLLASRSDVFELTNASISMIGRIICQFTPKQLEQFFLHQNFGDNILRSYYHMTLNILLNSHDLEIGRVLEFMIHHTHSTITGRTGVSCCSANFSQMCMNIIANVSVKLLIQCHSAGLSKPSNNRTMALAILNYVMQHLEFWIQRVVKDGSCVAAKLLSCLVLNDFKSIGDDLLLTIVTNDPQTPTEVNGHKKALVLFFRLVDEFESVSYNILEEVTTRSLCVAQSYQPSRQMRYLSTLYSMLVYEARMQSQRRRLARAINSNIDLLLLLVVTNKSLPIIKISISILSKIDVVSDEKYSVPISSPYLCKTDTRFKAWPIFVASRVVRCISVMLSILIESLNANNPSSVILIRRLTDFLVNFLRTTDPRHTISAVQIIFREFLRSSWIDTNNRFVFKKTLKPGWFNGKLVHDYPPTDSKTGRLNNTNQSPIIRNRYSPIQEKHWEVLIMTLCHFHRQHDVNSTSAYQVIQWICRQCLSPSYYLLINADLNTIPKDLNYITIFWKRFNQSELFWSLFYMLSRKAPQTFQPPYQTLEALMSACQHLWSTSDCPRKRLIRNVPDSEIFISDSHDPIILHKQRFYELINSNSNLYRATVFLFECLSSQMALTDELKLMLPYLSCSEVQTILFHLAYIWNKKVQKPPTVPAPVNEIDADGNVVSVSMVPIEDTQPKNTFSWETLLPALVHARIHFKSLYDQFCRLLFISCE 980 The following BLAST results are available for this feature:
BLAST of SMED30023417 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30023417 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30023417 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30023417 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30023417 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30023417 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30023417 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30023417 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 2
BLAST of SMED30023417 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30023417 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30023417 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30023417 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30023417 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30023417 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 1
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30023417 ID=SMED30023417|Name=SMED30023417|organism=Schmidtea mediterranea sexual|type=transcript|length=3050bpback to top protein sequence of SMED30023417-orf-1 >SMED30023417-orf-1 ID=SMED30023417-orf-1|Name=SMED30023417-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=126bp MIWTAEIVCLGSVVRRKFTRKSVRRRIRMTEEGLLAFRDSIKIDSITEMHback to top protein sequence of SMED30023417-orf-2 >SMED30023417-orf-2 ID=SMED30023417-orf-2|Name=SMED30023417-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=981bp MTSVELSWKKLVNIVSLQHDIVKHKDTISEAFHLFPPSRPALLDIFCDIIback 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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