SMED30033429

Overview
NameSMED30033429
Smed IDSMED30033429
Length (bp)492
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




SMED30033429

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
cement glandSMED30033429 GDAG01023926.1SmedSxl_ww_GDAG01.fsa_ntPMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30033429 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001957:38954..39438 +2425
Homology
BLAST of SMED30033429 vs. Planmine SMEST
Match: SMESG000057736.1 (SMESG000057736.1)

HSP 1 Score: 242.662 bits (618), Expect = 7.107e-84
Identity = 118/118 (100.00%), Postives = 118/118 (100.00%), Query Frame = 1
Query:   88 MNRQRTFLSIVISVLLFSKTRSAESGCNENFEDGDVPLYPIDRVRLALSKFKNAFPQSEYDRIVCILNRVKENKELVLKAMTMTSFGKGKVIDTQKLFKSLVKKNYPGESLESLYHSK 441
            MNRQRTFLSIVISVLLFSKTRSAESGCNENFEDGDVPLYPIDRVRLALSKFKNAFPQSEYDRIVCILNRVKENKELVLKAMTMTSFGKGKVIDTQKLFKSLVKKNYPGESLESLYHSK
Sbjct:    1 MNRQRTFLSIVISVLLFSKTRSAESGCNENFEDGDVPLYPIDRVRLALSKFKNAFPQSEYDRIVCILNRVKENKELVLKAMTMTSFGKGKVIDTQKLFKSLVKKNYPGESLESLYHSK 118          
BLAST of SMED30033429 vs. Planmine SMEST
Match: SMESG000005262.1 (SMESG000005262.1)

HSP 1 Score: 65.4698 bits (158), Expect = 3.146e-14
Identity = 30/85 (35.29%), Postives = 49/85 (57.65%), Query Frame = 1
Query:   88 MNRQRTFLSIVISVLLFSKTRSAESGCNENFEDGDVPLYPIDRVRLALSKFKNAFPQSEYDRIVCILNRVKENKELVLKAMTMTS 342
            M  Q  FL +VI++ +    +  E GC ++F+DGD+P  PI     A++  K   P+ +YD++VC +NR+K+NK   +  M   S
Sbjct:    1 MKHQINFLGVVIAIFISLLLQFTE-GCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKKNKAKYINVMKTLS 84          
BLAST of SMED30033429 vs. Planmine SMEST
Match: SMESG000005261.1 (SMESG000005261.1)

HSP 1 Score: 63.929 bits (154), Expect = 9.930e-14
Identity = 29/81 (35.80%), Postives = 48/81 (59.26%), Query Frame = 1
Query:   88 MNRQRTFLSIVISVLLFSKTRSAESGCNENFEDGDVPLYPIDRVRLALSKFKNAFPQSEYDRIVCILNRVKENKELVLKAM 330
            M  Q  FL +VI++ +    +  E GC ++F+DGD+P  PI     A++  K   P+ +YD++VC +NR+K NK   +K +
Sbjct:    1 MKHQINFLGVVIAIFISLLLQFTE-GCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKNNKADYIKVV 80          
BLAST of SMED30033429 vs. Planmine SMEST
Match: SMESG000048416.1 (SMESG000048416.1)

HSP 1 Score: 62.003 bits (149), Expect = 5.624e-13
Identity = 26/71 (36.62%), Postives = 46/71 (64.79%), Query Frame = 1
Query:   88 MNRQRTFLSIVISVLLFSKTRSAESGCNENFEDGDVPLYPIDRVRLALSKFKNAFPQSEYDRIVCILNRVK 300
            M  Q   +S+ I + LFS TR + + C++ F+DGD+P  P  ++   L+ FK+ + +++YD+++CI N VK
Sbjct:    1 MGYQMALVSVAI-LTLFSVTRQSSAACSDKFKDGDIPGMPAKKIAKYLTVFKSVYNKADYDKLICIWNEVK 70          
BLAST of SMED30033429 vs. Planmine SMEST
Match: SMESG000057720.1 (SMESG000057720.1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.905e-12
Identity = 31/118 (26.27%), Postives = 55/118 (46.61%), Query Frame = 1
Query:   88 MNRQRTFLSIVISVLLFSKTRSAESGCNENFEDGDVPLYPIDRVRLALSKFKNAFPQSEYDRIVCILNRVKENKELVLKAMTMTSFGKGKVIDTQKLFKSLVKKNYPGESLESLYHSK 441
            MN    F S+ +S+  F+  +   + C+E F  GD+P  P+      L+KFK     SEYD +VC  N +K  K      ++ + F   +    +    S++ K + G++ +  +  K
Sbjct:    1 MNYLIAFFSVALSIFCFTVAQPVSTKCSEEFMAGDIPRIPLKNFLYGLNKFKKVLNASEYDSVVCDFNAIKAMKVFYSLKISASDFRISEFYYIEGHLNSMMDKYFSGQNPKRFFFEK 118          
The following BLAST results are available for this feature:
BLAST of SMED30033429 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 SMED30033429 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 SMED30033429 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 SMED30033429 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 SMED30033429 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 SMED30033429 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 SMED30033429 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 SMED30033429 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 SMED30033429 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 SMED30033429 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 SMED30033429 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 SMED30033429 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 SMED30033429 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 SMED30033429 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000057736.17.107e-84100.00SMESG000057736.1[more]
SMESG000005262.13.146e-1435.29SMESG000005262.1[more]
SMESG000005261.19.930e-1435.80SMESG000005261.1[more]
SMESG000048416.15.624e-1336.62SMESG000048416.1[more]
SMESG000057720.11.905e-1226.27SMESG000057720.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033429 ID=SMED30033429|Name=SMED30033429|organism=Schmidtea mediterranea sexual|type=transcript|length=492bp
GAATTATCCTAAAAAAAATACAATTTGACATAGTTATACAAGAGTTGCAT
AAATAACCAAAAACAATTTGTACTCGGAAAATCATTCATGAATCGCCAAA
GGACCTTCCTATCGATTGTCATCTCGGTATTACTGTTTTCAAAGACGCGA
TCAGCCGAATCGGGTTGCAATGAGAACTTTGAAGACGGAGACGTCCCGCT
TTATCCGATAGATAGAGTTAGACTTGCGTTGAGTAAATTCAAAAATGCCT
TTCCACAATCCGAATATGATCGAATCGTATGCATTTTAAACAGAGTCAAG
GAAAATAAAGAATTAGTTTTAAAGGCTATGACGATGACCTCTTTTGGTAA
AGGTAAGGTCATCGACACGCAGAAACTATTCAAATCATTGGTTAAAAAGA
ATTACCCCGGAGAATCGTTGGAATCACTTTATCATTCTAAATAACATAAT
TTTTTATTTAATTATCAATTAAATTTTATTTTTGAAAAAAAA
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protein sequence of SMED30033429-orf-1

>SMED30033429-orf-1 ID=SMED30033429-orf-1|Name=SMED30033429-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=119bp
MNRQRTFLSIVISVLLFSKTRSAESGCNENFEDGDVPLYPIDRVRLALSK
FKNAFPQSEYDRIVCILNRVKENKELVLKAMTMTSFGKGKVIDTQKLFKS
LVKKNYPGESLESLYHSK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000224cement gland
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..22
score: 0.773