SMED30023764

Overview
NameSMED30023764
Smed IDSMED30023764
Length (bp)563
Neoblast Clusters

Zeng et. al., 2018



 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We 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



Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30023764

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
reproductive organSMED30023764SMESG000073231.1 Contig11047newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30023764SMESG000073231.1 Contig11047uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023764 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000262:113393..114029 -2326
v31.013286:15276..15915 +2287
v31.002026:67945..68593 -2184
v31.010858:929..1543 +2181
Homology
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BLAST of SMED30023764 vs. Planmine SMEST
Match: SMESG000080316.1 (SMESG000080316.1)

HSP 1 Score: 266.929 bits (681), Expect = 2.303e-89
Identity = 154/170 (90.59%), Postives = 163/170 (95.88%), Query Frame = 3 
Query:   57 NGRLYNQLIKCFTNYGYKIIMLDITDQINMDRIQQLGVNQIIIMAPQAATIEILDKNPALLEYLCLIYGPTDFTRFLSLNGKIENIFFIKDNLVINNTNIENVISESSSYEQRXXXXXXXXXXXXXXXXXELKSILKNQTCSNS-FDINSFEIKINKMVLDSIELEIWNT 563
            NGRLYNQLIKCFTNYGYK+IMLDITDQINMDRIQQLGVNQIIIMAPQAATIEILDKNPALLEYLCLIYGPTDFTRFLSLNGKIENIFFIKDNLVINNTNIENVISESSSYEQRINILNLLDIILAVNNNLELK    NQTCSN+ F  N+FEIK+NK+V+++I+LEIWNT
Sbjct:  110 NGRLYNQLIKCFTNYGYKLIMLDITDQINMDRIQQLGVNQIIIMAPQAATIEILDKNPALLEYLCLIYGPTDFTRFLSLNGKIENIFFIKDNLVINNTNIENVISESSSYEQRINILNLLDIILAVNNNLELKIFFTNQTCSNNFFSKNNFEIKLNKIVVENIKLEIWNT 279
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BLAST of SMED30023764 vs. Planmine SMEST
Match: SMESG000073231.1 (SMESG000073231.1)

HSP 1 Score: 213.386 bits (542), Expect = 1.539e-67
Identity = 127/140 (90.71%), Postives = 136/140 (97.14%), Query Frame = 3 
Query:  144 MDRIQQLGVNQIIIMAPQAATIEILDKNPALLEYLCLIYGPTDFTRFLSLNGKIENIFFIKDNLVINNTNIENVISESSSYEQRXXXXXXXXXXXXXXXXXELKSILKNQTCSNSFDINSFEIKINKMVLDSIELEIWNT 563
            MDRIQQLGVNQIIIMAPQAATIEILDKNPALLEY CLIYGPTDFTRFLSLNGKIENIFFIKDNLVINNTNIENVISESSSYE+RINILNLLDI+LAVNNNLELK+IL+NQTCSN+FD  +FEIKI K+VL+SI+LEIWNT
Sbjct:    1 MDRIQQLGVNQIIIMAPQAATIEILDKNPALLEYFCLIYGPTDFTRFLSLNGKIENIFFIKDNLVINNTNIENVISESSSYEKRINILNLLDIMLAVNNNLELKNILRNQTCSNNFD--NFEIKIKKIVLESIKLEIWNT 138
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BLAST of SMED30023764 vs. Planmine SMEST
Match: SMESG000073189.1 (SMESG000073189.1)

HSP 1 Score: 63.929 bits (154), Expect = 5.528e-12
Identity = 55/183 (30.05%), Postives = 103/183 (56.28%), Query Frame = 3 
Query:   30 LFLNFLHYGNGRLYNQLIKCFTNYGYKIIMLDITDQINMDRIQQLGVNQIIIMAPQAATIEILDKNPALLEYLCLIYGPTDFTRFLSLNGKIENIFFIKD--NLVINNTNIENVISESSSYEQRXXXXXXXXXXXXXXXXXELKSILKNQTCSNSFDIN----SFEIKINKMVLDSIELEIWN 560
            L +  L   N  ++N+ ++CF N+GYK+ +++    INM+ I++   NQI ++A Q+       +N  L EY  LIYG +D + F +L     NI+ + +  + +I    ++ ++     YE++ N+L L+D+I+ +NNN EL  I  N TC  S  ++    SF+  + K+++ + ++EI+ 
Sbjct:  110 LIVYILGCDNLMVFNETLRCFMNFGYKVSIINAGGSINMETIRKFQGNQIFLIANQSLITTFFLENTELSEYNFLIYGLSDISEFFALTKTTNNIYIMNEFNSYIIE--KVQEIVQSVMKYEEKKNLLKLIDLIVTINNNSELFWIAGNGTCLESSSLHPSVYSFDDLLTKLLVVNAKVEIFG 290
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BLAST of SMED30023764 vs. Planmine SMEST
Match: SMESG000080378.1 (SMESG000080378.1)

HSP 1 Score: 58.5362 bits (140), Expect = 1.967e-10
Identity = 31/82 (37.80%), Postives = 48/82 (58.54%), Query Frame = 3 
Query:   36 LNFLHYGNGRLYNQLIKCFTNYGYKIIMLDITDQINMDRIQQLGVNQIIIMAPQAATIEILDKNPALLEYLCLIYGPTDFTR 281
            LNF       + ++L+ CFT++GYK+++ DI +    + I QLGVNQI +M  Q+ T+ + + N      + LIYGP DF  
Sbjct:   68 LNFYQINTWDINDELLTCFTDFGYKLLLFDINNTNKTNNIFQLGVNQIFMMVNQSTTLSLFNNNQIFKGNIYLIYGPKDFNH 149
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BLAST of SMED30023764 vs. Planmine SMEST
Match: SMESG000080367.1 (SMESG000080367.1)

HSP 1 Score: 46.2098 bits (108), Expect = 6.555e-6
Identity = 27/108 (25.00%), Postives = 54/108 (50.00%), Query Frame = 3 
Query:    3 KIVFHRFDILFLNFLHYGNGRLYNQLIKCFTNYGYKIIMLDITDQINMDRIQQLGVNQIIIMAPQAATIEILDKNPALLEYLCLIYGPTDFTRFLSLNGKIENIFFIK 326
            K +F + +IL +    Y +  ++N++I  F   GY++ +    +Q N+D   + G+ QII++A  + T  +L+       +  +++   +   F       ENIF+IK
Sbjct:  135 KTIFTKREILIIYSQIYRDWNIFNKIISNFPTEGYQLFLSKFNNQPNLDSNIKYGIEQIILLATPSETATVLNMKSTFHSFAWIVFWGENLEFFNPKFQNRENIFYIK 242
The following BLAST results are available for this feature:
BLAST of SMED30023764 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023764 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000080316.12.303e-8990.59SMESG000080316.1[more]
SMESG000073231.11.539e-6790.71SMESG000073231.1[more]
SMESG000073189.15.528e-1230.05SMESG000073189.1[more]
SMESG000080378.11.967e-1037.80SMESG000080378.1[more]
SMESG000080367.16.555e-625.00SMESG000080367.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023764 ID=SMED30023764|Name=SMED30023764|organism=Schmidtea mediterranea sexual|type=transcript|length=563bp
GGAAAATTGTATTTCATCGTTTTGATATTTTATTTTTGAATTTTCTACAT
TATGGAAATGGGCGATTGTATAATCAATTAATAAAATGTTTCACAAATTA
CGGATACAAAATAATAATGCTAGACATAACGGATCAGATTAATATGGACA
GAATTCAGCAGTTGGGGGTCAATCAAATAATTATCATGGCCCCTCAGGCG
GCTACAATAGAAATTTTAGACAAAAATCCAGCTCTGTTGGAATATCTCTG
TTTGATCTACGGCCCGACTGATTTCACCCGGTTTTTGTCATTAAATGGGA
AAATAGAAAATATATTCTTCATCAAAGACAATTTAGTAATAAACAATACC
AACATAGAAAATGTTATAAGTGAATCATCGAGTTATGAGCAAAGGATAAA
TATTTTAAATCTCTTAGATATAATTTTGGCAGTTAATAATAATTTGGAAT
TGAAAAGCATTTTAAAAAATCAAACTTGTTCAAACAGTTTTGATATTAAC
AGTTTTGAAATTAAAATAAACAAGATGGTTCTGGATAGTATAGAACTTGA
AATATGGAACACA
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protein sequence of SMED30023764-orf-1

>SMED30023764-orf-1 ID=SMED30023764-orf-1|Name=SMED30023764-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=187bp
KIVFHRFDILFLNFLHYGNGRLYNQLIKCFTNYGYKIIMLDITDQINMDR
IQQLGVNQIIIMAPQAATIEILDKNPALLEYLCLIYGPTDFTRFLSLNGK
IENIFFIKDNLVINNTNIENVISESSSYEQRINILNLLDIILAVNNNLEL
KSILKNQTCSNSFDINSFEIKINKMVLDSIELEIWNT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ