SMED30022446

Overview
NameSMED30022446
Smed IDSMED30022446
Length (bp)608
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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Alignments
SMED30022446 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008008:12126..12724 +2974
v31.028020:8653..9252 -2973
Homology
BLAST of SMED30022446 vs. TrEMBL
Match: A0A4Y2MLP2 (MULE domain-containing protein OS=Araneus ventricosus OX=182803 GN=AVEN_190515_1 PE=4 SV=1)

HSP 1 Score: 169.088 bits (427), Expect = 3.140e-46
Identity = 92/191 (48.17%), Postives = 122/191 (63.87%), Query Frame = -3
Query:    1 FKKICKTHPSVFFIDKDFTEMKAIRDIFSSATVLLCKFHVIKYIKGLVSTAYNSQIDEKKEILDAFKKCLYAQSXXXXXEQKKKFLDICKYIKVIAGTKDKYVTLEEQFLKNWDSCKEMWVHYFRKHLPLMGDTTTNRIERSFWTLKQYIQTKYHRLPTIYLCIKELIEFIDSRIKNKLAKNEQKVFKIMD 573
            F+KIC    S+F +DKDF E+  ++++F  A +LLC FHV+KY+K L++TA    ++ K +I+  FKK L A + + YEE KK  L   K ++V      KYV+LE+QF+ NWDSCKEMWV YFRK L  +GD T NRIE SFWTLKQ I  K+  LP I   I  LI F D RI  +++ +  K  KI D
Sbjct:  265 FRKICTQPSSIFIVDKDFNEISVLKEVFGRAIILLCYFHVLKYVKNLITTA-PVIVEVKSDIMTKFKKMLDAGTEDIYEEHKKDSLTTVKTVQV--RVNKKYVSLEDQFINNWDSCKEMWVAYFRKCLATLGDNTNNRIEISFWTLKQSIHVKFPTLPVIEKSIIHLISFCDQRINEEISDSNLKSLKIFD 452          
BLAST of SMED30022446 vs. TrEMBL
Match: W2L6E3 (SWIM-type domain-containing protein OS=Phytophthora parasitica OX=4792 GN=L917_08816 PE=4 SV=1)

HSP 1 Score: 97.0561 bits (240), Expect = 8.618e-20
Identity = 54/142 (38.03%), Postives = 75/142 (52.82%), Query Frame = -3
Query:  115 FFIDKDFTEMKAIRDIFSSATVLLCKFHVIKYIKGLVSTAYNSQIDEKKEILDAFKKCLYAQSXXXXXEQKKKFLDICKYIKVIAGTKDKYVTLEEQFLKNWDSCKEMWVHYFRKHLPLMGDTTTNRIERSFWTLKQYIQTK 540
            F IDK F E + + + F +A VLLC+FH I Y K LVS  +   + E+  +   F K LY+ S   +E   K+F   C      AG   +Y  +   F KNW  C+EMW ++ R      G+TTTNRIE ++  LKQ +  K
Sbjct:  391 FVIDKHFVEWRVLEECFPTAKVLLCQFHAIMYWKKLVSNRFGLVLAEQDTVQHYFAKMLYSTSLSAFERTYKQFCSFC------AG---RYPNVRSYFDKNWKECREMWSNHLRNKYFSAGNTTTNRIESNWHLLKQLLGKK 523          
BLAST of SMED30022446 vs. TrEMBL
Match: W2VRC2 (Uncharacterized protein OS=Phytophthora parasitica CJ01A1 OX=1317063 GN=F441_22626 PE=4 SV=1)

HSP 1 Score: 97.0561 bits (240), Expect = 8.749e-20
Identity = 54/142 (38.03%), Postives = 75/142 (52.82%), Query Frame = -3
Query:  115 FFIDKDFTEMKAIRDIFSSATVLLCKFHVIKYIKGLVSTAYNSQIDEKKEILDAFKKCLYAQSXXXXXEQKKKFLDICKYIKVIAGTKDKYVTLEEQFLKNWDSCKEMWVHYFRKHLPLMGDTTTNRIERSFWTLKQYIQTK 540
            F IDK F E + + + F +A VLLC+FH I Y K LVS  +   + E+  +   F K LY+ S   +E   K+F   C      AG   +Y  +   F KNW  C+EMW ++ R      G+TTTNRIE ++  LKQ +  K
Sbjct:  381 FVIDKHFVEWRVLEECFPTAKVLLCQFHAIMYWKKLVSNRFGLVLAEQDTVQHYFAKMLYSTSLSAFERTYKQFCSFC------AG---RYPNVRSYFDKNWKECREMWSNHLRNKYFSAGNTTTNRIESNWRLLKQLLGKK 513          
BLAST of SMED30022446 vs. TrEMBL
Match: V9DRV1 (SWIM-type domain-containing protein OS=Phytophthora parasitica P1569 OX=1317065 GN=F443_23259 PE=4 SV=1)

HSP 1 Score: 96.6709 bits (239), Expect = 1.177e-19
Identity = 54/142 (38.03%), Postives = 75/142 (52.82%), Query Frame = -3
Query:  115 FFIDKDFTEMKAIRDIFSSATVLLCKFHVIKYIKGLVSTAYNSQIDEKKEILDAFKKCLYAQSXXXXXEQKKKFLDICKYIKVIAGTKDKYVTLEEQFLKNWDSCKEMWVHYFRKHLPLMGDTTTNRIERSFWTLKQYIQTK 540
            F IDK F E + + + F +A VLLC+FH I Y K LVS  +   + E+  +   F K LY+ S   +E   K+F   C      AG   +Y  +   F KNW  C+EMW ++ R      G+TTTNRIE ++  LKQ +  K
Sbjct:  371 FVIDKHFVEWRVLEECFPTAKVLLCQFHAIMYWKKLVSNRFGLVLAEQDTVQHYFAKMLYSTSLSAFERTYKQFCSFC------AG---RYPNVRSYFDKNWKECREMWSNHLRNKYFSAGNTTTNRIESNWRLLKQLLGKK 503          
BLAST of SMED30022446 vs. TrEMBL
Match: V9F4K1 (Uncharacterized protein OS=Phytophthora parasitica P1569 OX=1317065 GN=F443_09147 PE=4 SV=1)

HSP 1 Score: 96.2857 bits (238), Expect = 2.136e-19
Identity = 53/142 (37.32%), Postives = 76/142 (53.52%), Query Frame = -3
Query:  115 FFIDKDFTEMKAIRDIFSSATVLLCKFHVIKYIKGLVSTAYNSQIDEKKEILDAFKKCLYAQSXXXXXEQKKKFLDICKYIKVIAGTKDKYVTLEEQFLKNWDSCKEMWVHYFRKHLPLMGDTTTNRIERSFWTLKQYIQTK 540
            F IDK F E + + + F +A VLLC+FH I Y K LVS  +   + E+  +   F K LY++S   +E   K+F   C      AG   +Y  +   F KNW  C++MW ++ R      G+TTTNRIE ++  LKQ +  K
Sbjct:  624 FVIDKHFVEWRVLEECFPTAKVLLCQFHSIMYWKKLVSNRFGLVVAEQDTVQRYFAKMLYSKSLSAFERTYKQFCSFC------AG---RYPNVRSYFDKNWKECRKMWSNHLRNKYFSAGNTTTNRIESNWHLLKQLLGKK 756          
BLAST of SMED30022446 vs. Planmine SMEST
Match: SMESG000037896.1 (SMESG000037896.1)

HSP 1 Score: 173.326 bits (438), Expect = 5.748e-53
Identity = 92/92 (100.00%), Postives = 92/92 (100.00%), Query Frame = -3
Query:  325 SAFKYCMNEFKKICKTHPSVFFIDKDFTEMKAIRDIFSSATVLLCKFHVIKYIKGLVSTAYNSQIDEKKEILDAFKKCLYAQSXXXXXEQKK 600
            SAFKYCMNEFKKICKTHPSVFFIDKDFTEMKAIRDIFSSATVLLCKFHVIKYIKGLVSTAYNSQIDEKKEILDAFKKCLYAQSYEEYEEQKK
Sbjct:  251 SAFKYCMNEFKKICKTHPSVFFIDKDFTEMKAIRDIFSSATVLLCKFHVIKYIKGLVSTAYNSQIDEKKEILDAFKKCLYAQSYEEYEEQKK 342          
BLAST of SMED30022446 vs. Planmine SMEST
Match: SMESG000013507.1 (SMESG000013507.1)

HSP 1 Score: 84.7297 bits (208), Expect = 1.248e-19
Identity = 39/39 (100.00%), Postives = 39/39 (100.00%), Query Frame = -3
Query:  484 SAFKYCMNEFKKICKTHPSVFFIDKDFTEMKAIRDIFSS 600
            SAFKYCMNEFKKICKTHPSVFFIDKDFTEMKAIRDIFSS
Sbjct:  267 SAFKYCMNEFKKICKTHPSVFFIDKDFTEMKAIRDIFSS 305          
The following BLAST results are available for this feature:
BLAST of SMED30022446 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 SMED30022446 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 SMED30022446 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 SMED30022446 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 SMED30022446 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 SMED30022446 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 SMED30022446 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 SMED30022446 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4Y2MLP23.140e-4648.17MULE domain-containing protein OS=Araneus ventrico... [more]
W2L6E38.618e-2038.03SWIM-type domain-containing protein OS=Phytophthor... [more]
W2VRC28.749e-2038.03Uncharacterized protein OS=Phytophthora parasitica... [more]
V9DRV11.177e-1938.03SWIM-type domain-containing protein OS=Phytophthor... [more]
V9F4K12.136e-1937.32Uncharacterized protein OS=Phytophthora parasitica... [more]
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BLAST of SMED30022446 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 SMED30022446 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 SMED30022446 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 SMED30022446 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 SMED30022446 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 SMED30022446 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000037896.15.748e-53100.00SMESG000037896.1[more]
SMESG000013507.11.248e-19100.00SMESG000013507.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022446 ID=SMED30022446|Name=SMED30022446|organism=Schmidtea mediterranea sexual|type=transcript|length=608bp
ATCCATAATTTTAAAAACTTTTTGTTCATTTTTGGCTAATTTATTCTTTA
TTCTTGAATCAATAAACTCTATAAGCTCTTTAATACATAAATAAATTGTC
GGCAATCTATGATATTTAGTTTGTATGTATTGCTTAAGAGTCCAAAATGA
TCGTTCAATTCTGTTTGTTGTCGTATCTCCCATTAGTGGCAAATGTTTTC
TAAAATAATGTACCCACATTTCTTTACAGCTGTCCCAATTTTTAAGAAAT
TGCTCTTCAAGAGTCACGTATTTATCTTTTGTTCCTGCAATAACTTTTAT
ATACTTGCAAATGTCTAGGAATTTTTTTTTCTGCTCTTCGTATTCTTCAT
ATGATTGAGCATATAAACATTTCTTGAACGCATCCAATATTTCCTTTTTT
TCATCAATTTGGCTATTGTAGGCAGTAGAAACTAGCCCCTTAATATATTT
AATGACATGAAATTTACAAAGTAAAACGGTTGCACTAGAAAAAATGTCTC
TGATAGCTTTCATTTCGGTAAAATCTTTGTCAATGAAAAAAACGGATGGG
TGGGTCTTACAAATTTTTTTAAATTCATTCATACAATATTTGAATGCGGA
GATCGGAA
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protein sequence of SMED30022446-orf-1

>SMED30022446-orf-1 ID=SMED30022446-orf-1|Name=SMED30022446-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=202bp
PISAFKYCMNEFKKICKTHPSVFFIDKDFTEMKAIRDIFSSATVLLCKFH
VIKYIKGLVSTAYNSQIDEKKEILDAFKKCLYAQSYEEYEEQKKKFLDIC
KYIKVIAGTKDKYVTLEEQFLKNWDSCKEMWVHYFRKHLPLMGDTTTNRI
ERSFWTLKQYIQTKYHRLPTIYLCIKELIEFIDSRIKNKLAKNEQKVFKI
MD
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland