Protein LLP homolog

Overview
NameProtein LLP homolog
Smed IDSMED30007534
Length (bp)486
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 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




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of Protein LLP homolog (SMED30007534) t-SNE clustered cells

Violin plots show distribution of expression levels for Protein LLP homolog (SMED30007534) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of Protein LLP homolog (SMED30007534) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Protein LLP homolog (SMED30007534) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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




SMED30007534

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30007534SMESG000010838.1 SmedASXL_004261SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
pharynxSMED30007534SMESG000010838.1 dd_Smed_v4_5414_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30007534SMESG000010838.1 dd_Smed_v4_5414_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30007534SMESG000010838.1 dd_Smed_v4_5414_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007534SMESG000010838.1 dd_Smed_v4_5414_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007534SMESG000010838.1 dd_Smed_v4_5414_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30007534SMESG000010838.1 dd_Smed_v4_5414_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30007534SMESG000010838.1 dd_Smed_v4_5414_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007534SMESG000010838.1 Contig50394newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007534SMESG000010838.1 Contig50394uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
gutSMED30007534SMESG000010838.1 SMED30007534smed_20140614PMID:26457503
Tu et al., 2015
whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30007534SMESG000010838.1 SMED30007534smed_20140614PMID:26457503
Tu et al., 2015
whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Protein LLP homolog vs. Ensembl Mouse
Match: Llph (LLP homolog, long-term synaptic facilitation (Aplysia) [Source:MGI Symbol;Acc:MGI:1913475])

HSP 1 Score: 45.4394 bits (106), Expect = 2.410e-6
Identity = 38/105 (36.19%), Postives = 51/105 (48.57%), Query Frame = 1
Query:   31 MAKGLRSKSKRKVKAIRRIENAPIIRQTLLKTLSVDSSKLK------YPFITSKSFEESKSNEDVQEKNCXXXXXXXXXXXXXTNTKI-VKNLKNEHGNYPIWMN 324
            MAK LRSK KRK++A +R +NAP     L   L VD   L          + +K  +E    E   E  C+   E   ++  ET  K   K L ++HG YP+WMN
Sbjct:    1 MAKSLRSKWKRKMRAEKRKKNAPRELNRLKSILRVDGDALMKDVEEIATVVVAKPRQEKMQCE---EGRCDGADEEKDDMKMETEIKRNRKTLLDQHGQYPVWMN 102          
BLAST of Protein LLP homolog vs. Ensembl Mouse
Match: Llph (LLP homolog, long-term synaptic facilitation (Aplysia) [Source:MGI Symbol;Acc:MGI:1913475])

HSP 1 Score: 45.4394 bits (106), Expect = 2.410e-6
Identity = 38/105 (36.19%), Postives = 51/105 (48.57%), Query Frame = 1
Query:   31 MAKGLRSKSKRKVKAIRRIENAPIIRQTLLKTLSVDSSKLK------YPFITSKSFEESKSNEDVQEKNCXXXXXXXXXXXXXTNTKI-VKNLKNEHGNYPIWMN 324
            MAK LRSK KRK++A +R +NAP     L   L VD   L          + +K  +E    E   E  C+   E   ++  ET  K   K L ++HG YP+WMN
Sbjct:    1 MAKSLRSKWKRKMRAEKRKKNAPRELNRLKSILRVDGDALMKDVEEIATVVVAKPRQEKMQCE---EGRCDGADEEKDDMKMETEIKRNRKTLLDQHGQYPVWMN 102          
BLAST of Protein LLP homolog vs. TrEMBL
Match: A0A3S5ASF5 (Uncharacterized protein OS=Protopolystoma xenopodis OX=117903 GN=PXEA_LOCUS30091 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 7.149e-8
Identity = 38/98 (38.78%), Postives = 49/98 (50.00%), Query Frame = 1
Query:   31 MAKGLRSKSKRKVKAIRRIENAPIIRQTLLKTLSVDSSKLKYPFITSKSFEESKSNEDVQEKNCXXXXXXXXXXXXXTNTKIVKNLKNEHGNYPIWMN 324
            MAK  RSK KR  +A+RRI+  P     L K  S++ S L  P +  K  +E   ++DV              L    N +I   L+NEHGNYPIWMN
Sbjct:    1 MAKSKRSKVKRHFRALRRIKRIPFELNRLKKIESINLSSLSMPSVNQKIIDEQCESKDVNP-------YSSDPLKSLENPQIKARLQNEHGNYPIWMN 91          
BLAST of Protein LLP homolog vs. Planmine SMEST
Match: SMESG000010838.1 (SMESG000010838.1)

HSP 1 Score: 164.466 bits (415), Expect = 4.519e-53
Identity = 97/98 (98.98%), Postives = 97/98 (98.98%), Query Frame = 1
Query:   31 MAKGLRSKSKRKVKAIRRIENAPIIRQTLLKTLSVDSSKLKYPFITSKSFEESKSNEDVQEKNCXXXXXXXXXXXXXTNTKIVKNLKNEHGNYPIWMN 324
            MAKGLRSKSKRKVKAIRRIENAPIIRQTLLKTLSVDSSK KYPFITSKSFEESKSNEDVQEKNCEVPIEVVPELIEETNTKIVKNLKNEHGNYPIWMN
Sbjct:    1 MAKGLRSKSKRKVKAIRRIENAPIIRQTLLKTLSVDSSKSKYPFITSKSFEESKSNEDVQEKNCEVPIEVVPELIEETNTKIVKNLKNEHGNYPIWMN 98          
The following BLAST results are available for this feature:
BLAST of Protein LLP homolog 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 Protein LLP homolog 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 Protein LLP homolog 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 Protein LLP homolog 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 Protein LLP homolog 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 Protein LLP homolog vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 2
Match NameE-valueIdentityDescription
Llph2.410e-636.19LLP homolog, long-term synaptic facilitation (Aply... [more]
Llph2.410e-636.19LLP homolog, long-term synaptic facilitation (Aply... [more]
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BLAST of Protein LLP homolog 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 Protein LLP homolog vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A3S5ASF57.149e-838.78Uncharacterized protein OS=Protopolystoma xenopodi... [more]
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BLAST of Protein LLP homolog 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 Protein LLP homolog 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 Protein LLP homolog 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 Protein LLP homolog 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 Protein LLP homolog 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 Protein LLP homolog vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000010838.14.519e-5398.98SMESG000010838.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007534 ID=SMED30007534|Name=Protein LLP homolog|organism=Schmidtea mediterranea sexual|type=transcript|length=486bp
TTTAATATTCACAATTATTAACAATAAATCATGGCTAAAGGATTACGTAG
TAAATCAAAAAGGAAAGTTAAGGCAATTAGAAGAATTGAAAATGCTCCTA
TTATTCGACAAACTTTATTAAAAACACTTTCAGTAGATTCATCAAAATTG
AAGTATCCTTTTATTACATCAAAATCTTTTGAGGAATCAAAGTCTAATGA
AGATGTACAAGAAAAGAATTGTGAAGTACCAATAGAAGTTGTACCAGAAT
TAATTGAAGAAACTAATACCAAAATTGTTAAAAATCTTAAAAATGAACAT
GGAAACTACCCAATTTGGATGAACAAAAGAGCAATCAGGAAGCTTAAAAA
TAAAAAGAAAATTTTTTATTAAATAAAGTGTTAACCCATTTATTTAGTTA
ATAGTAGTTTTGAATTAAATAAACCAAAGCTAGTTTGTAATGAAAATATT
AATTTTATAATGTTCAATGTAGCGTTTATTTTAAAC
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protein sequence of SMED30007534-orf-1

>SMED30007534-orf-1 ID=SMED30007534-orf-1|Name=SMED30007534-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp
MAKGLRSKSKRKVKAIRRIENAPIIRQTLLKTLSVDSSKLKYPFITSKSF
EESKSNEDVQEKNCEVPIEVVPELIEETNTKIVKNLKNEHGNYPIWMNKR
AIRKLKNKKKIFY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0001099basal RNA polymerase II transcription machinery binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0005694chromosome
GO:0005730nucleolus
Vocabulary: biological process
TermDefinition
GO:0060999positive regulation of dendritic spine development
GO:0097484dendrite extension
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000429neoblast
PLANA:0002032epidermal cell
PLANA:0002109X1 cell
PLANA:0002142parenchyma
Vocabulary: INTERPRO
TermDefinition
IPR018784LAPS18-like
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR018784Learning associated protein 18-likePFAMPF10169Lapscoord: 3..110
e-value: 2.7E-14
score: 53.8
IPR018784Learning associated protein 18-likePANTHERPTHR34253FAMILY NOT NAMEDcoord: 1..110
NoneNo IPR availablePANTHERPTHR34253:SF1PROTEIN LLP HOMOLOGcoord: 1..110