Sec16_C domain-containing protein

Overview
NameSec16_C domain-containing protein
Smed IDSMED30000482
Length (bp)661
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 Sec16_C domain-containing protein (SMED30000482) t-SNE clustered cells

Violin plots show distribution of expression levels for Sec16_C domain-containing protein (SMED30000482) 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 Sec16_C domain-containing protein (SMED30000482) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Sec16_C domain-containing protein (SMED30000482) 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.
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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



SMED30000482

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
epidermisSMED30000482SMESG000023280.1 dd_Smed_v4_1873_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30000482SMESG000023280.1 dd_Smed_v4_1873_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
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BLAST of Sec16_C domain-containing protein vs. TrEMBL
Match: A0A267EDE7 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig026211g1 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 5.312e-7
Identity = 40/153 (26.14%), Postives = 70/153 (45.75%), Query Frame = 2 
Query:  209 QQMTYYVQNLCIYLRAQHPKIFENLMPFIA----ANNDDDMGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQ-EGGTITISDEIYXXXXXXXXXXDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENGV 652
            QQ  YY Q      + ++ + F  L  F A    ++  +  GR TP+KF+  H+   L  PG+  QV  +   + E   + + D        +      YPGPL    T + ++ ++L  ++    +  +  DW+   LLI FL+ L++ NG+
Sbjct:  171 QQADYYRQQ-----KQEYRQYFAQLGVFTAWGDTSSEAEPAGRCTPLKFSLPHARLSLSCPGLAVQVPPSRPDEGEPARVHLFDSACLAADWDRVDFSAYPGPLVPGETLKSEVRAFLNAKLVEMHERLADTDWEDAALLIGFLDFLVRNNGI 318
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BLAST of Sec16_C domain-containing protein vs. TrEMBL
Match: A0A3P8CE09 (Uncharacterized protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS132 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 5.652e-7
Identity = 26/57 (45.61%), Postives = 39/57 (68.42%), Query Frame = 2 
Query:  491 YPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENGVRFF 661
            YPGPL+   T +  +  +L+D+++ E+QD  P DW+S  LLI+FLE ++K NGV  F
Sbjct:  415 YPGPLSRTGTLKADVLVFLRDKLA-EIQDRLPTDWESAGLLISFLEFMVKNNGVSVF 470
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BLAST of Sec16_C domain-containing protein vs. TrEMBL
Match: A0A182ZZJ7 (Uncharacterized protein OS=Echinostoma caproni OX=27848 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 5.706e-7
Identity = 26/57 (45.61%), Postives = 39/57 (68.42%), Query Frame = 2 
Query:  491 YPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENGVRFF 661
            YPGPL+   T +  +  +L+D+++ E+QD  P DW+S  LLI+FLE ++K NGV  F
Sbjct:  415 YPGPLSRTGTLKADVLVFLRDKLA-EIQDRLPTDWESAGLLISFLEFMVKNNGVSVF 470
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BLAST of Sec16_C domain-containing protein vs. TrEMBL
Match: A0A4E0QVP3 (Protein transport protein Sec16A OS=Fasciola hepatica OX=6192 GN=D915_010838 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 6.821e-7
Identity = 25/55 (45.45%), Postives = 40/55 (72.73%), Query Frame = 2 
Query:  491 YPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENGVR 655
            YPGPL+   T +  +  +L+D+++ E+QD  P+DW+S  LLI++LE ++K NGVR
Sbjct:  247 YPGPLSRSGTLKADVLVFLRDKLA-EIQDRLPIDWESAGLLISYLEFMVKNNGVR 300
[Close]
BLAST of Sec16_C domain-containing protein vs. TrEMBL
Match: A0A267EBN5 (Sec16_C domain-containing protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig018066g1 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 7.825e-7
Identity = 47/158 (29.75%), Postives = 76/158 (48.10%), Query Frame = 2 
Query:  209 QQMTYYVQNLCIYLRAQHPKIFENLMPFIA-ANNDDD--------MGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQ-EGGTITISDEIYXXXXXXXXXXDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENGV 652
            Q   Y+ Q      R ++   F N M ++  A  D D         GR TP+KF   H+   LD PG++ QV +    + E   + + +       +E+     +PGPL   +T + ++ +YL  ++  +LQD    DWDS  LLI +L+ LI+ NG+
Sbjct: 1318 QNAAYFHQQ-----RQEYRNYFLNYMNYVQQAQYDGDGDGDYAQPSGRCTPLKFNLPHARLGLDAPGLVVQVPAARPDEGEPARVHLLESSCVVSEAEKLEFVSFPGPLVRGKTLKSEVRAYLNGKLQ-QLQDRLAGDWDSATLLIGYLDFLIRNNGI 1469
[Close]
BLAST of Sec16_C domain-containing protein vs. Planmine SMEST
Match: SMESG000023280.1 (SMESG000023280.1)

HSP 1 Score: 386.726 bits (992), Expect = 4.054e-127
Identity = 212/212 (100.00%), Postives = 212/212 (100.00%), Query Frame = 2 
Query:   14 MDKESDSNLTEEGSFSVISNEEVTRRHYDVPNSQYRDRQGQNILNNQMFLXXXXXXXXXXXXXXDQQMTYYVQNLCIYLRAQHPKIFENLMPFIAANNDDDMGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQEGGTITISDEIYXXXXXXXXXXDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENG 649
            MDKESDSNLTEEGSFSVISNEEVTRRHYDVPNSQYRDRQGQNILNNQMFLHGHNNQNSNGQNISDQQMTYYVQNLCIYLRAQHPKIFENLMPFIAANNDDDMGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQEGGTITISDEIYSQQLSEESLSDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENG
Sbjct:    1 MDKESDSNLTEEGSFSVISNEEVTRRHYDVPNSQYRDRQGQNILNNQMFLHGHNNQNSNGQNISDQQMTYYVQNLCIYLRAQHPKIFENLMPFIAANNDDDMGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQEGGTITISDEIYSQQLSEESLSDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENG 212
[Close]
BLAST of Sec16_C domain-containing protein vs. Planmine SMEST
Match: SMESG000023280.1 (SMESG000023280.1)

HSP 1 Score: 386.726 bits (992), Expect = 6.841e-127
Identity = 212/212 (100.00%), Postives = 212/212 (100.00%), Query Frame = 2 
Query:   14 MDKESDSNLTEEGSFSVISNEEVTRRHYDVPNSQYRDRQGQNILNNQMFLXXXXXXXXXXXXXXDQQMTYYVQNLCIYLRAQHPKIFENLMPFIAANNDDDMGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQEGGTITISDEIYXXXXXXXXXXDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENG 649
            MDKESDSNLTEEGSFSVISNEEVTRRHYDVPNSQYRDRQGQNILNNQMFLHGHNNQNSNGQNISDQQMTYYVQNLCIYLRAQHPKIFENLMPFIAANNDDDMGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQEGGTITISDEIYSQQLSEESLSDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENG
Sbjct:    1 MDKESDSNLTEEGSFSVISNEEVTRRHYDVPNSQYRDRQGQNILNNQMFLHGHNNQNSNGQNISDQQMTYYVQNLCIYLRAQHPKIFENLMPFIAANNDDDMGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQEGGTITISDEIYSQQLSEESLSDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENG 212
[Close]
BLAST of Sec16_C domain-containing protein vs. Planmine SMEST
Match: SMESG000023280.1 (SMESG000023280.1)

HSP 1 Score: 380.178 bits (975), Expect = 1.757e-124
Identity = 210/219 (95.89%), Postives = 210/219 (95.89%), Query Frame = 2 
Query:   14 MDKESDSNLTEEGSFSVISNEEVTRRHYDVPNSQYRDRQGQNILNNQMFLXXXXXXXX-------XXXXXXDQQMTYYVQNLCIYLRAQHPKIFENLMPFIAANNDDDMGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQEGGTITISDEIYXXXXXXXXXXDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENG 649
            MDKESDSNLTEEGSFSVISNEEVTRRHYDVPNSQYRDRQGQNILNNQMFLHGHNNQNS         QNISDQQMTYYVQNLCIYLRAQHPKIFENLMPFIAANNDDDMGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQEGGTITISDEIYSQQLSEESLSDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENG
Sbjct:    1 MDKESDSNLTEEGSFSVISNEEVTRRHYDVPNSQYRDRQGQNILNNQMFLHGHNNQNSNDWNWMTQSQNISDQQMTYYVQNLCIYLRAQHPKIFENLMPFIAANNDDDMGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQEGGTITISDEIYSQQLSEESLSDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDSGQLLINFLELLIKENG 219
The following BLAST results are available for this feature:
BLAST of Sec16_C domain-containing protein 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 Sec16_C domain-containing protein 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 Sec16_C domain-containing protein 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 Sec16_C domain-containing protein 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 Sec16_C domain-containing protein 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 Sec16_C domain-containing protein 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 Sec16_C domain-containing protein 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 Sec16_C domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267EDE75.312e-726.14Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A3P8CE095.652e-745.61Uncharacterized protein OS=Echinostoma caproni OX=... [more]
A0A182ZZJ75.706e-745.61Uncharacterized protein OS=Echinostoma caproni OX=... [more]
A0A4E0QVP36.821e-745.45Protein transport protein Sec16A OS=Fasciola hepat... [more]
A0A267EBN57.825e-729.75Sec16_C domain-containing protein OS=Macrostomum l... [more]
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BLAST of Sec16_C domain-containing protein 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 Sec16_C domain-containing protein 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 Sec16_C domain-containing protein 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 Sec16_C domain-containing protein 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 Sec16_C domain-containing protein 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 Sec16_C domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000023280.14.054e-127100.00SMESG000023280.1[more]
SMESG000023280.16.841e-127100.00SMESG000023280.1[more]
SMESG000023280.11.757e-12495.89SMESG000023280.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000482 ID=SMED30000482|Name=Sec16_C domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=661bp
TATAGATATTTCTATGGATAAGGAATCTGATTCAAATTTAACTGAAGAAG
GTAGTTTTTCAGTTATTTCTAATGAAGAAGTAACAAGAAGACATTACGAT
GTGCCAAATTCACAGTATAGAGATCGACAAGGACAAAATATTTTAAATAA
CCAAATGTTTTTACATGGACATAATAACCAAAATTCGAACGGTCAAAATA
TATCCGATCAACAAATGACGTATTATGTTCAAAATCTTTGTATCTATTTA
CGAGCTCAACATCCAAAAATATTCGAAAACCTAATGCCGTTTATTGCAGC
AAATAATGACGATGATATGGGGCGAAATACTCCGATAAAATTTGCGAATA
ATCATTCAATCTGCAAGCTAGATTTCCCAGGAATTATTTACCAGGTGCTA
TCGAACGGCATCACCCAAGAAGGGGGGACCATAACCATATCAGATGAGAT
CTACAGCCAGCAATTGAGTGAGGAATCACTCAGTGATGAATACCCAGGCC
CATTAACCGTCCATAGGACGACGGAAGAACAAATCTATTCATATCTCAAA
GACCAAATGTCAATGGAATTGCAGGATTCCTCACCGGTCGACTGGGATTC
CGGCCAATTGCTGATTAATTTCCTGGAATTACTCATTAAGGAAAATGGAG
TTCGGTTTTTT
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protein sequence of SMED30000482-orf-1

>SMED30000482-orf-1 ID=SMED30000482-orf-1|Name=SMED30000482-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=220bp
IDISMDKESDSNLTEEGSFSVISNEEVTRRHYDVPNSQYRDRQGQNILNN
QMFLHGHNNQNSNGQNISDQQMTYYVQNLCIYLRAQHPKIFENLMPFIAA
NNDDDMGRNTPIKFANNHSICKLDFPGIIYQVLSNGITQEGGTITISDEI
YSQQLSEESLSDEYPGPLTVHRTTEEQIYSYLKDQMSMELQDSSPVDWDS
GQLLINFLELLIKENGVRFF
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002032epidermal cell
Vocabulary: cellular component
TermDefinition
GO:0000139Golgi membrane
Vocabulary: biological process
TermDefinition
GO:0048208COPII vesicle coating