Glucosylceramidase 4

Overview
NameGlucosylceramidase 4
Smed IDSMED30009768
Length (bp)991
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 Glucosylceramidase 4 (SMED30009768) t-SNE clustered cells

Violin plots show distribution of expression levels for Glucosylceramidase 4 (SMED30009768) 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 Glucosylceramidase 4 (SMED30009768) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Glucosylceramidase 4 (SMED30009768) 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




SMED30009768

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
X2 cellSMED30009768 SmedASXL_056761SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
parenchymaSMED30009768 dd_Smed_v4_40050_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Glucosylceramidase 4 vs. TrEMBL
Match: A0A158P527 (DDE_3 domain-containing protein OS=Tetranychus urticae OX=32264 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 4.870e-8
Identity = 36/119 (30.25%), Postives = 57/119 (47.90%), Query Frame = 3
Query:  561 MWL*VSENRIGDHVFLEIPNSVNAQFYQEHYLRRGLISFINKHHSEYDVLFWLDPVSAHYANNTPSVLRFFLLRKSTILQTSTN----GAIENFWSFLKSKVYQAGWGLSQFPNKRCKL 905
            +W+ +S+       F+    ++NA  Y    +R+ L  FI K++ E   +FW D  S HYA  T   L    ++     Q   N      IE FW+ LK KVY+ GW  S +P+ + ++
Sbjct:  196 VWIAISKKGHSQPFFIPAKCALNADSYSSECIRKRLFPFIQKNYQEKRYIFWPDGASCHYARTTIDTLNELGIKFIEKEQNPPNIPQLRPIERFWAHLKQKVYEGGWSASSYPSLKARI 314          
BLAST of Glucosylceramidase 4 vs. TrEMBL
Match: T2MJF3 (WD repeat-containing protein 64 (Fragment) OS=Hydra vulgaris OX=6087 GN=WDR64 PE=2 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 6.221e-6
Identity = 41/142 (28.87%), Postives = 65/142 (45.77%), Query Frame = 3
Query:  558 MMWL*VSENRIGDHVFLEIPNSVNAQFYQEHYLRRGLISFINKHHSEYDVLFWLDPVSAHYANNTPSVLRF----FLLRKSTILQTSTNGAIENFWSFLKSKVYQAG----WGL----------SQF-PNKRCKL*KYCKTC 926
            ++WL  S   +    F+    +VN   Y+ + +R+ L+ FIN +H++ + +FW D  S+HYA    S        F+ +            IE+FW+ LK KVY++     +GL           QF P  RC+     KTC
Sbjct:  167 LVWLAASNKGVSKPFFIPSGLAVNKAIYEMNCIRKRLVPFINAYHADGNYIFWPDLASSHYAKTVTSCYETHNINFIKKVDNPPAVPECRPIEDFWAILKGKVYESAPRSPYGLITEHRGRAFNRQFTPPNRCR-----KTC 303          
BLAST of Glucosylceramidase 4 vs. TrEMBL
Match: A0A443RZ87 (Uncharacterized protein OS=Leptotrombidium deliense OX=299467 GN=B4U80_05270 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 6.446e-6
Identity = 33/112 (29.46%), Postives = 55/112 (49.11%), Query Frame = 3
Query:  546 PQE*MMWL*VSENRIGDHVFLEIPNSVNAQFYQEHYLRRGLISFINKHHSEYDVLFWLDPVSAHYANNTPSVLRF----FLLRKSTILQTSTNGAIENFWSFLKSKVYQAGW 869
            P++ ++WL +S N I    F++   ++N Q Y ++ + R L  FI K H     +FW D  S+HY + T   L+     ++ +    +       IE FW+ LK  VY  G+
Sbjct:  188 PEKVLVWLAISRNGISKPYFMKSKGAMNMQIYSKYCISRRLSKFIKKLHYNDKFIFWPDNASSHYGSVTLKTLKKLNIPYIPKSHNPVNVPQLRPIERFWAILKRNVYANGY 299          
BLAST of Glucosylceramidase 4 vs. Planmine SMEST
Match: SMESG000081253.1 (SMESG000081253.1)

HSP 1 Score: 83.9593 bits (206), Expect = 3.938e-20
Identity = 39/40 (97.50%), Postives = 39/40 (97.50%), Query Frame = 3
Query:   42 MKPGSVGHSELELVDGLTTDFVYPSDKTREISTAVPLGHA 161
            MKPGSVGHSELELVDGLTTD VYPSDKTREISTAVPLGHA
Sbjct:    1 MKPGSVGHSELELVDGLTTDLVYPSDKTREISTAVPLGHA 40          
The following BLAST results are available for this feature:
BLAST of Glucosylceramidase 4 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 Glucosylceramidase 4 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 Glucosylceramidase 4 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 Glucosylceramidase 4 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 Glucosylceramidase 4 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 Glucosylceramidase 4 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 Glucosylceramidase 4 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 Glucosylceramidase 4 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A158P5274.870e-830.25DDE_3 domain-containing protein OS=Tetranychus urt... [more]
T2MJF36.221e-628.87WD repeat-containing protein 64 (Fragment) OS=Hydr... [more]
A0A443RZ876.446e-629.46Uncharacterized protein OS=Leptotrombidium deliens... [more]
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BLAST of Glucosylceramidase 4 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 Glucosylceramidase 4 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 Glucosylceramidase 4 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 Glucosylceramidase 4 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 Glucosylceramidase 4 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 Glucosylceramidase 4 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000081253.13.938e-2097.50SMESG000081253.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009768 ID=SMED30009768|Name=Glucosylceramidase 4|organism=Schmidtea mediterranea sexual|type=transcript|length=991bp
TTCGCTATAAATCACTTTGTGAGTGAAAGTCAAGATGTGTAATGAAGCCT
GGAAGTGTAGGGCACAGTGAGCTAGAACTGGTCGATGGCTTAACAACAGA
CTTTGTATATCCCTCAGACAAGACGCGAGAAATATCGACTGCAGTACCTT
TAGGTCACGCGCCTCAAACTACGCCTCTTTCTCTGAATACATCTTTGCAA
TCAACTTCGAATTCATCTCTGCCATCAACTTCGAATCCATCTCTGTCATC
AACTTCGAATCAATTTCTGCTACAAACTCTGAGTTCATCTCTGCCATCAA
CTCAGGATTCATTTCCGTTATTTAGTGTATCATAACCATGCACAGTATCA
TTCACGATCGTGGAATATCACAAGAGAAGGAAAGCTCCTTAGTAAACAAA
GGACCAAAAAAACGAGCAAAGATACGAGTACGAAAATTACTTCGAGTTTT
GGCCGAGCGATACATTGGACTCTTACTTTATGTCTTTGATTATTTGCCGA
GTAATGATCACTTCTACACCTTTTGTGTTCAGTCTGCTACTTTGACCACA
AGAGTAGATGATGTGGCTCTGAGTGTCCGAAAATCGCATTGGTGATCATG
TATTCTTGGAGATTCCCAACAGTGTGAATGCCCAGTTTTATCAGGAACAT
TACCTAAGACGTGGTTTGATTTCATTTATTAATAAGCACCATAGTGAATA
TGATGTTCTCTTCTGGCTAGACCCGGTATCTGCACATTACGCCAACAACA
CTCCAAGTGTTTTGAGATTTTTTTTGTTGAGAAAGAGTACGATCCTCCAA
ACATCTACTAATGGGGCCATCGAGAATTTCTGGAGTTTTTTAAAGTCCAA
AGTGTATCAGGCAGGTTGGGGGCTCAGTCAGTTCCCAAACAAAAGATGCA
AATTATAAAAATATTGTAAAACATGCACCAGTCATCGCGTATGTAGATTT
TCGTAGAATCAATAAGCGCCTACGGTCCTTAAACCGTGATG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 49..71