SMED30030778

Overview
NameSMED30030778
Smed IDSMED30030778
Length (bp)430
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




SMED30030778

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
cephalic gangliaSMED30030778SMESG000054106.1 dd_Smed_v4_1782_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30030778SMESG000054106.1 dd_Smed_v4_1782_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
prepharyngeal regionSMED30030778SMESG000054106.1 dd_Smed_v6_1782_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30030778SMESG000054106.1 OX_Smed_1.0.04544ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030778 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000401:97890..98411 -2085
Homology
BLAST of SMED30030778 vs. Planmine SMEST
Match: SMESG000054106.1 (SMESG000054106.1)

HSP 1 Score: 151.369 bits (381), Expect = 1.948e-48
Identity = 93/94 (98.94%), Postives = 93/94 (98.94%), Query Frame = 3
Query:  102 MNFXXXXXXXXXXXXXXXXDFIGVGVVRNGKQYVTITGVEYSADSQRNILIGTGDKCVLCKIVPGKNKTNPTYNCLEPIKVISASGKVMYKSQC 383
            MNFILILTLILLSISLISSDFIGVGVVRNGKQYVTITGVEYSADSQRNILIGTGDKC LCKIVPGKNKTNPTYNCLEPIKVISASGKVMYKSQC
Sbjct:    1 MNFILILTLILLSISLISSDFIGVGVVRNGKQYVTITGVEYSADSQRNILIGTGDKCNLCKIVPGKNKTNPTYNCLEPIKVISASGKVMYKSQC 94          
BLAST of SMED30030778 vs. Planmine SMEST
Match: SMESG000054105.1 (SMESG000054105.1)

HSP 1 Score: 69.707 bits (169), Expect = 2.920e-16
Identity = 35/76 (46.05%), Postives = 46/76 (60.53%), Query Frame = 3
Query:  159 DFIGVGVVRNGKQYVTITGVEYSADSQRNILIGTGDKCVLCKIVPGKNKT-NPTYNCLEPIKVISASGKVMYKSQC 383
            D  G G  R GKQYV + G EYSAD + ++ IGTGDKC+ C I P K+   N T+ C +P+   + +G V Y S C
Sbjct:   20 DTNGRGFWRKGKQYVVLNGTEYSADLKASVNIGTGDKCIYCSITPSKSANQNSTFYCQDPMTTKTITGYVTYYSFC 95          
BLAST of SMED30030778 vs. Planmine SMEST
Match: SMESG000020860.1 (SMESG000020860.1)

HSP 1 Score: 63.5438 bits (153), Expect = 7.736e-14
Identity = 33/74 (44.59%), Postives = 43/74 (58.11%), Query Frame = 3
Query:  165 IGVGVVRNGKQYVTITGVEYSADSQRNILIGTGDKCVLCKIVPGKNKTN-PTYNCLEPIKVISASGKVMYKSQC 383
             G G  R+GK YV I GVEY A+    I  G GD+CV+C     K+K   PTY+C  P  ++   GK+ Y+SQC
Sbjct:   20 FGRGYFRDGKGYVKINGVEYLAEEDGEIQYGEGDRCVVCNYFASKDKVKPPTYSCYGPSPMM-IDGKLTYRSQC 92          
BLAST of SMED30030778 vs. Planmine SMEST
Match: SMESG000055805.1 (SMESG000055805.1)

HSP 1 Score: 51.9878 bits (123), Expect = 1.500e-9
Identity = 27/74 (36.49%), Postives = 37/74 (50.00%), Query Frame = 3
Query:  165 IGVGVVRNGKQYVTITGVEYSADSQRNILIGTGDKCVLCKIVPGKN-KTNPTYNCLEPIKVISASGKVMYKSQC 383
             G G  ++GK +V I+  EY AD    + +G GD C LC I P  +  TNPT+ C  P       G+ +Y   C
Sbjct:   22 FGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPA-EIDGETIYLPVC 94          
BLAST of SMED30030778 vs. Planmine SMEST
Match: SMESG000039587.1 (SMESG000039587.1)

HSP 1 Score: 48.521 bits (114), Expect = 3.586e-8
Identity = 25/68 (36.76%), Postives = 38/68 (55.88%), Query Frame = 3
Query:  183 RNGKQYVTITGVEYSADSQRNILIGTGDKCVLCKIVPGKNKTN-PTYNCLEPIKVISASGKVMYKSQC 383
            R G  YV I G+ +SA   RN+  G G  C++C I   K++++ P + C +    +S +GK  YKS C
Sbjct:   31 RKGNPYVIIKGIVFSATRSRNVRFGEGVNCIICNIYAPKSRSDLPRFEC-QGASPVSLNGKQAYKSPC 97          
The following BLAST results are available for this feature:
BLAST of SMED30030778 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 SMED30030778 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 SMED30030778 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 SMED30030778 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 SMED30030778 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 SMED30030778 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 SMED30030778 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 SMED30030778 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 SMED30030778 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 SMED30030778 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 SMED30030778 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 SMED30030778 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 SMED30030778 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 SMED30030778 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000054106.11.948e-4898.94SMESG000054106.1[more]
SMESG000054105.12.920e-1646.05SMESG000054105.1[more]
SMESG000020860.17.736e-1444.59SMESG000020860.1[more]
SMESG000055805.11.500e-936.49SMESG000055805.1[more]
SMESG000039587.13.586e-836.76SMESG000039587.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030778 ID=SMED30030778|Name=SMED30030778|organism=Schmidtea mediterranea sexual|type=transcript|length=430bp
GAGAGTAGATTAAACATAAGCTAAAACGACATATGTTTCTACTTTTCATT
ATTTATACGTGGGGAAATATCAGGATTTCGTTCTTCACGGTATTAAAAAT
TATGAATTTTATATTAATTTTGACGTTGATTTTGTTGAGTATTTCCTTAA
TTTCGTCTGATTTCATAGGAGTTGGAGTTGTAAGAAATGGAAAGCAGTAC
GTAACGATCACCGGCGTCGAGTACAGTGCCGATTCTCAAAGAAATATTTT
AATAGGAACGGGGGACAAATGTGTTTTGTGTAAAATTGTGCCAGGAAAAA
ATAAAACGAATCCAACCTACAACTGTCTAGAGCCCATAAAGGTAATTTCT
GCAAGTGGGAAAGTTATGTACAAATCACAATGTTGATGATAAATAATTAA
ATTTTATTTTAATACATATTTTATTTTGGC
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protein sequence of SMED30030778-orf-1

>SMED30030778-orf-1 ID=SMED30030778-orf-1|Name=SMED30030778-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=118bp
MFLLFIIYTWGNIRISFFTVLKIMNFILILTLILLSISLISSDFIGVGVV
RNGKQYVTITGVEYSADSQRNILIGTGDKCVLCKIVPGKNKTNPTYNCLE
PIKVISASGKVMYKSQC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000419prepharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 15..37