SMED30013979
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., 2020SMED30013979 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30013979 aligns in the following genomic locations:
Homology
BLAST of SMED30013979 vs. TrEMBL
Match: A0A564YTW6 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=WMSIL1_LOCUS9512 PE=4 SV=1) HSP 1 Score: 75.485 bits (184), Expect = 1.783e-12 Identity = 41/95 (43.16%), Postives = 59/95 (62.11%), Query Frame = 3 Query: 375 RQKISFLDKYEWRLIKNKYLERAKYPFIPREHPVGLDVPISRNKSIFIEIDEMKPEYIVPKEFDP-QLKPYVSWRAKLIKQDKLEPESLFSLTYG 656 RQKI++ Y+W L +K +RA+YP+IPRE P + N + EI EM E++VP D +LKPYV+WRA +++Q +L ESLF + Y Sbjct: 23 RQKIAYATSYKWLLDVHKSRQRARYPWIPREPPTSCII----NGEVK-EIPEMHVEFVVPLNLDKCELKPYVTWRASVVQQPELTAESLFEIRYA 112
BLAST of SMED30013979 vs. TrEMBL
Match: A0A430Q8E5 (Large subunit ribosomal protein L41 OS=Schistosoma bovis OX=6184 GN=DC041_0010175 PE=4 SV=1) HSP 1 Score: 75.0998 bits (183), Expect = 2.832e-12 Identity = 51/130 (39.23%), Postives = 75/130 (57.69%), Query Frame = 3 Query: 333 QHCRSFHVSIL-LERRQKISFLDKYEWRLIKNKYLERAKYPFIPREHPVGLDVPISRNKSIFIEIDEMKPEYIVPKEFDP-QLKPYVSWRAKLIKQDKLEPESLFSLTYGSKLP-----SVSSEEVEKFV 701 Q R+ +V++ L RQKI+F +Y W L K RAKYP+IPRE ++ I K IF EM ++IVP D +LKPYVSW++KLI+++ L E LF+ Y K+ S+EE+ +++ Sbjct: 17 QTIRTINVAMGPLRSRQKIAFKTRYHWMLDLKKSKARAKYPWIPREPTTSME--IYGQKIIF---PEMYLDFIVPNNLDKCELKPYVSWQSKLIEEEPLTAEVLFNNRYSQKITEMFKNGASNEEIMEYL 141
BLAST of SMED30013979 vs. TrEMBL
Match: A0A094ZXJ0 (39S ribosomal protein L41, mitochondrial (Fragment) OS=Schistosoma haematobium OX=6185 GN=MS3_06259 PE=4 SV=1) HSP 1 Score: 74.7146 bits (182), Expect = 3.784e-12 Identity = 51/130 (39.23%), Postives = 74/130 (56.92%), Query Frame = 3 Query: 333 QHCRSFHVSIL-LERRQKISFLDKYEWRLIKNKYLERAKYPFIPREHPVGLDVPISRNKSIFIEIDEMKPEYIVPKEFDP-QLKPYVSWRAKLIKQDKLEPESLFSLTYGSKLP-----SVSSEEVEKFV 701 Q R+ +V++ L RQKI+F +Y W L K RAKYP+IPRE ++ I K IF EM ++IVP D +LKPYVSW++KLI++ L E LF+ Y K+ S+EE+ +++ Sbjct: 17 QSIRTINVAMGPLRSRQKIAFKTRYHWMLDLKKSKARAKYPWIPREPTTSME--IYGQKIIF---PEMYLDFIVPNNLDKCELKPYVSWQSKLIEEGPLTAEVLFNNRYSQKITEMFRNGASNEEIMEYL 141
BLAST of SMED30013979 vs. TrEMBL
Match: A0A183KLD6 (Uncharacterized protein OS=Schistosoma curassoni OX=6186 GN=SCUD_LOCUS15850 PE=4 SV=1) HSP 1 Score: 74.7146 bits (182), Expect = 3.895e-12 Identity = 51/130 (39.23%), Postives = 74/130 (56.92%), Query Frame = 3 Query: 333 QHCRSFHVSIL-LERRQKISFLDKYEWRLIKNKYLERAKYPFIPREHPVGLDVPISRNKSIFIEIDEMKPEYIVPKEFDP-QLKPYVSWRAKLIKQDKLEPESLFSLTYGSKLP-----SVSSEEVEKFV 701 Q R+ +V++ L RQKI+F +Y W L K RAKYP+IPRE ++ I K IF EM ++IVP D +LKPYVSW++KLI++ L E LF+ Y K+ S+EE+ +++ Sbjct: 17 QSIRTINVAMGPLRSRQKIAFKTRYHWMLDLKKSKARAKYPWIPREPTTSME--IYGQKIIF---PEMYLDFIVPNNLDKCELKPYVSWQSKLIEEGPLTAEVLFNNRYSQKITEMFKNGASNEEIMEYL 141
BLAST of SMED30013979 vs. TrEMBL
Match: A0A183L9N8 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS513 PE=4 SV=1) HSP 1 Score: 74.3294 bits (181), Expect = 5.679e-12 Identity = 49/130 (37.69%), Postives = 74/130 (56.92%), Query Frame = 3 Query: 333 QHCRSFHVSIL-LERRQKISFLDKYEWRLIKNKYLERAKYPFIPREHPVGLDVPISRNKSIFIEIDEMKPEYIVPKEFDP-QLKPYVSWRAKLIKQDKLEPESLFSLTYGSKLP-----SVSSEEVEKFV 701 Q R+ +V++ L RQKI+F +Y W L K RAKYP+IPRE ++ I K +F EM ++IVP D +LKPYVSW++KL+++ L E LF+ Y K+ S+EE+ +++ Sbjct: 17 QSIRTINVAMGPLRSRQKIAFKTRYHWMLDLKKSKARAKYPWIPREPTTSME--IYGQKIVF---PEMYLDFIVPNNLDKCELKPYVSWKSKLVEEGPLTAEVLFNNRYSQKITEMFKNGASNEEIMEYL 141
BLAST of SMED30013979 vs. Planmine SMEST
Match: SMESG000035951.1 (SMESG000035951.1) HSP 1 Score: 314.309 bits (804), Expect = 6.193e-105 Identity = 158/159 (99.37%), Postives = 158/159 (99.37%), Query Frame = 3 Query: 288 MIMKFLNISISKFCFQHCRSFHVSILLERRQKISFLDKYEWRLIKNKYLERAKYPFIPREHPVGLDVPISRNKSIFIEIDEMKPEYIVPKEFDPQLKPYVSWRAKLIKQDKLEPESLFSLTYGSKLPSVSSEEVEKFVDEYSHKKLPDSEILPLNKLRK 764 MIMKFLNISISKFCFQH RSFHVSILLERRQKISFLDKYEWRLIKNKYLERAKYPFIPREHPVGLDVPISRNKSIFIEIDEMKPEYIVPKEFDPQLKPYVSWRAKLIKQDKLEPESLFSLTYGSKLPSVSSEEVEKFVDEYSHKKLPDSEILPLNKLRK Sbjct: 1 MIMKFLNISISKFCFQHSRSFHVSILLERRQKISFLDKYEWRLIKNKYLERAKYPFIPREHPVGLDVPISRNKSIFIEIDEMKPEYIVPKEFDPQLKPYVSWRAKLIKQDKLEPESLFSLTYGSKLPSVSSEEVEKFVDEYSHKKLPDSEILPLNKLRK 159
BLAST of SMED30013979 vs. Planmine SMEST
Match: SMESG000035951.1 (SMESG000035951.1) HSP 1 Score: 310.842 bits (795), Expect = 1.250e-103 Identity = 156/157 (99.36%), Postives = 156/157 (99.36%), Query Frame = 3 Query: 294 MKFLNISISKFCFQHCRSFHVSILLERRQKISFLDKYEWRLIKNKYLERAKYPFIPREHPVGLDVPISRNKSIFIEIDEMKPEYIVPKEFDPQLKPYVSWRAKLIKQDKLEPESLFSLTYGSKLPSVSSEEVEKFVDEYSHKKLPDSEILPLNKLRK 764 MKFLNISISKFCFQH RSFHVSILLERRQKISFLDKYEWRLIKNKYLERAKYPFIPREHPVGLDVPISRNKSIFIEIDEMKPEYIVPKEFDPQLKPYVSWRAKLIKQDKLEPESLFSLTYGSKLPSVSSEEVEKFVDEYSHKKLPDSEILPLNKLRK Sbjct: 1 MKFLNISISKFCFQHSRSFHVSILLERRQKISFLDKYEWRLIKNKYLERAKYPFIPREHPVGLDVPISRNKSIFIEIDEMKPEYIVPKEFDPQLKPYVSWRAKLIKQDKLEPESLFSLTYGSKLPSVSSEEVEKFVDEYSHKKLPDSEILPLNKLRK 157
BLAST of SMED30013979 vs. Planmine SMEST
Match: SMESG000061492.1 (SMESG000061492.1) HSP 1 Score: 81.6481 bits (200), Expect = 7.255e-18 Identity = 37/48 (77.08%), Postives = 40/48 (83.33%), Query Frame = -2 Query: 2 MISNINYRGRCQVNRMKFQTGKPRHVMDRIGKYPILFIKSEKCRIMGC 145 MISNINYRGRC+V MKF GKP+HV+DR GKYPIL KS KCRIMGC Sbjct: 1 MISNINYRGRCEVTGMKFPAGKPQHVVDRSGKYPILLFKSGKCRIMGC 48
BLAST of SMED30013979 vs. Planmine SMEST
Match: SMESG000064388.1 (SMESG000064388.1) HSP 1 Score: 85.8853 bits (211), Expect = 1.485e-17 Identity = 38/48 (79.17%), Postives = 42/48 (87.50%), Query Frame = -2 Query: 2 MISNINYRGRCQVNRMKFQTGKPRHVMDRIGKYPILFIKSEKCRIMGC 145 MISNINYRGRC+V MKF TGKP+HV+DR GKYPILF KS KCR+MGC Sbjct: 1 MISNINYRGRCEVTGMKFPTGKPQHVVDRSGKYPILFFKSGKCRVMGC 48
BLAST of SMED30013979 vs. Planmine SMEST
Match: SMESG000013399.1 (SMESG000013399.1) HSP 1 Score: 79.7221 bits (195), Expect = 3.615e-17 Identity = 37/48 (77.08%), Postives = 41/48 (85.42%), Query Frame = -2 Query: 2 MISNINYRGRCQVNRMKFQTGKPRHVMDRIGKYPILFIKSEKCRIMGC 145 MISNINYRGRC+V MKF TGKP+HV++R GKYPILF K KCRIMGC Sbjct: 1 MISNINYRGRCEVTGMKFPTGKPQHVVNRSGKYPILFFKRGKCRIMGC 48 The following BLAST results are available for this feature:
BLAST of SMED30013979 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30013979 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30013979 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30013979 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30013979 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30013979 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30013979 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30013979 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 5
BLAST of SMED30013979 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30013979 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30013979 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30013979 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30013979 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30013979 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 >SMED30013979 ID=SMED30013979|Name=SMED30013979|organism=Schmidtea mediterranea sexual|type=transcript|length=1859bpback to top protein sequence of SMED30013979-orf-1 >SMED30013979-orf-1 ID=SMED30013979-orf-1|Name=SMED30013979-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=160bp MIMKFLNISISKFCFQHCRSFHVSILLERRQKISFLDKYEWRLIKNKYLEback to top Annotated Terms
The following terms have been associated with this transcript:
|