Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

Overview
NameBeta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase
Smed IDSMED30005462
Length (bp)433
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase (SMED30005462) t-SNE clustered cells

Violin plots show distribution of expression levels for Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase (SMED30005462) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30005462

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30005462h1SMcG0014465 SmedASXL_001294SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30005462h1SMcG0014465 dd_Smed_v4_14356_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30005462h1SMcG0014465 Contig42881newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30005462h1SMcG0014465 Contig42881uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30005462h1SMcG0014465 Contig43172uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30005462h1SMcG0014465 Contig43172newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30005462h1SMcG0014465 dd_Smed_v4_14356_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase vs. Planmine SMEST
Match: SMESG000009072.1 (SMESG000009072.1)

HSP 1 Score: 138.658 bits (348), Expect = 2.828e-40
Identity = 82/82 (100.00%), Postives = 82/82 (100.00%), Query Frame = 3 
Query:  186 MSKSVLKKAEDWQFPANEAFSDSQMYQRILNNCSSFLSYQKYFFTPPSNEERXXXXXXXXXXXXXXXQVERLLRMIYRPWNY 431
            MSKSVLKKAEDWQFPANEAFSDSQMYQRILNNCSSFLSYQKYFFTPPSNEERKFKIAFSIISFKSASQVERLLRMIYRPWNY
Sbjct:    1 MSKSVLKKAEDWQFPANEAFSDSQMYQRILNNCSSFLSYQKYFFTPPSNEERKFKIAFSIISFKSASQVERLLRMIYRPWNY 82
[Close]
BLAST of Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase vs. Planmine SMEST
Match: SMESG000043055.1 (SMESG000043055.1)

HSP 1 Score: 93.9745 bits (232), Expect = 1.775e-24
Identity = 54/94 (57.45%), Postives = 68/94 (72.34%), Query Frame = 3 
Query:  150 STLHCSKYFEWNMSKSVLKKAEDWQFPANEAFSDSQMYQRILNNCSSFLSYQKYFFTPPSNEERXXXXXXXXXXXXXXXQVERLLRMIYRPWNY 431
            S  +C +YF+ N SK ++  A  W  P N+ F+DSQ+ + I  NC+ FL  QKYFF  PSNEE+ F IAFSI+ FK+ASQVERLLRMIYRPWN+
Sbjct:    3 SEFNCYEYFQHNASKELINTATLWHIPPNQTFTDSQITEEIQRNCTEFLDQQKYFFQEPSNEEKSFPIAFSIMVFKTASQVERLLRMIYRPWNF 96
[Close]
BLAST of Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase vs. Planmine SMEST
Match: SMESG000008805.1 (SMESG000008805.1)

HSP 1 Score: 93.9745 bits (232), Expect = 1.775e-24
Identity = 54/94 (57.45%), Postives = 68/94 (72.34%), Query Frame = 3 
Query:  150 STLHCSKYFEWNMSKSVLKKAEDWQFPANEAFSDSQMYQRILNNCSSFLSYQKYFFTPPSNEERXXXXXXXXXXXXXXXQVERLLRMIYRPWNY 431
            S  +C +YF+ N SK ++  A  W  P N+ F+DSQ+ + I  NC+ FL  QKYFF  PSNEE+ F IAFSI+ FK+ASQVERLLRMIYRPWN+
Sbjct:    3 SEFNCYEYFQHNASKELINTATLWHIPPNQTFTDSQITEEIQRNCTEFLDQQKYFFQEPSNEEKSFPIAFSIMVFKTASQVERLLRMIYRPWNF 96
[Close]
BLAST of Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase vs. Planmine SMEST
Match: SMESG000008883.1 (SMESG000008883.1)

HSP 1 Score: 83.5741 bits (205), Expect = 1.436e-19
Identity = 53/131 (40.46%), Postives = 80/131 (61.07%), Query Frame = 3 
Query:   48 IILLIMISICVLFIYFNSIIRLFHV---EFDTLFNQSSTLHCSKYFEWNMSKSVLKKAEDWQFPANEAFSDSQMYQRILNNCSSFLSYQKYFFTPPSNEERXXXXXXXXXXXXXXXQVERLLRMIYRPWNY 431
            +    +++IC++  YF S++   +     F  L  QSS   C +  + N+    L+ AE W  P N+  +DSQ+ Q I ++C +FLS + Y    PS EE+ F ++FSI++FKS+SQ+ERLLR IYRPWNY
Sbjct:   10 LFFFTLLAICIIVGYFRSVLSPANQIVQSFKNLSIQSSEPDCYELLKPNVENKSLQDAEKWVVPLNDTLTDSQLLQNIHSSCDTFLSNKNYASNHPSKEEKNFPLSFSILAFKSSSQIERLLRTIYRPWNY 140
[Close]
BLAST of Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase vs. Planmine SMEST
Match: SMESG000043052.1 (SMESG000043052.1)

HSP 1 Score: 80.4925 bits (197), Expect = 7.331e-19
Identity = 50/95 (52.63%), Postives = 67/95 (70.53%), Query Frame = 3 
Query:  150 STLHCSKYFEWNMSKSVLKKAEDWQFPANEAFSDSQMYQRILNNCSSFLSYQKYFFT-PPSNEERXXXXXXXXXXXXXXXQVERLLRMIYRPWNY 431
            +T+ C+     N+++  L+ A+ WQ   NE+F+DSQMYQ I  NCS+FL  Q YF   P + EE  F+IAF+I++FKS SQ+ERLLR IYRPWNY
Sbjct:   64 NTIDCTALLHSNVNQKKLEYAKTWQPLRNESFTDSQMYQNIHQNCSNFLENQNYFLQFPNTTEEENFRIAFTIVTFKSGSQIERLLRTIYRPWNY 158
The following BLAST results are available for this feature:
BLAST of Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 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 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000009072.12.828e-40100.00SMESG000009072.1[more]
SMESG000043055.11.775e-2457.45SMESG000043055.1[more]
SMESG000008805.11.775e-2457.45SMESG000008805.1[more]
SMESG000008883.11.436e-1940.46SMESG000008883.1[more]
SMESG000043052.17.331e-1952.63SMESG000043052.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005462 ID=SMED30005462|Name=Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase|organism=Schmidtea mediterranea sexual|type=transcript|length=433bp
TATGTCTAATGCTTAAAATATTAAGAAAGGTAATTTATAAAAGAAAAATT
ATTTTATTAATAATGATATCTATATGTGTATTGTTTATTTATTTTAATTC
AATAATTCGTCTATTTCATGTCGAATTCGACACACTTTTTAATCAATCTT
CGACGTTACATTGCTCGAAATATTTTGAATGGAATATGAGTAAAAGTGTC
TTGAAAAAAGCCGAGGATTGGCAATTTCCGGCAAATGAAGCTTTTTCGGA
TTCTCAAATGTATCAACGAATTTTGAATAACTGCTCCTCATTTTTATCAT
ATCAAAAGTATTTTTTCACTCCACCCAGTAATGAGGAAAGAAAATTCAAA
ATTGCTTTTAGTATTATATCATTTAAAAGCGCCTCTCAAGTCGAAAGATT
GTTGCGAATGATTTATCGACCTTGGAATTATTA
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protein sequence of SMED30005462-orf-1

>SMED30005462-orf-1 ID=SMED30005462-orf-1|Name=SMED30005462-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp
CLMLKILRKVIYKRKIILLIMISICVLFIYFNSIIRLFHVEFDTLFNQSS
TLHCSKYFEWNMSKSVLKKAEDWQFPANEAFSDSQMYQRILNNCSSFLSY
QKYFFTPPSNEERKFKIAFSIISFKSASQVERLLRMIYRPWNY
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: molecular function
TermDefinition
GO:0016740transferase activity
GO:0016757transferase activity, transferring glycosyl groups
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000136whole organism
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePANTHERPTHR19297GLYCOSYLTRANSFERASE 14 FAMILY MEMBERcoord: 33..143
NoneNo IPR availableTMHMMTMhelixcoord: 16..38