Vault protein inter alpha trypsin-1

Overview
NameVault protein inter alpha trypsin-1
Smed IDSMED30030795
Length (bp)1703
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 Vault protein inter alpha trypsin-1 (SMED30030795) t-SNE clustered cells

Violin plots show distribution of expression levels for Vault protein inter alpha trypsin-1 (SMED30030795) 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 Vault protein inter alpha trypsin-1 (SMED30030795) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Vault protein inter alpha trypsin-1 (SMED30030795) 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




SMED30030795

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30030795SMESG000053671.1 SMESG000053669.1 SMESG000053667.1 SMESG000053664.1 SMESG000053657.1 SMESG000053638.1 dd_Smed_v4_1027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30030795SMESG000053671.1 SMESG000053669.1 SMESG000053667.1 SMESG000053664.1 SMESG000053657.1 SMESG000053638.1 dd_Smed_v4_1027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30030795SMESG000053671.1 SMESG000053669.1 SMESG000053667.1 SMESG000053664.1 SMESG000053657.1 SMESG000053638.1 dd_Smed_v4_1027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30030795SMESG000053671.1 SMESG000053669.1 SMESG000053667.1 SMESG000053664.1 SMESG000053657.1 SMESG000053638.1 dd_Smed_v4_1027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30030795SMESG000053671.1 SMESG000053669.1 SMESG000053667.1 SMESG000053664.1 SMESG000053657.1 SMESG000053638.1 dd_Smed_v4_1027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30030795SMESG000053671.1 SMESG000053669.1 SMESG000053667.1 SMESG000053664.1 SMESG000053657.1 SMESG000053638.1 dd_Smed_v4_1027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030795SMESG000010333.1 SMESG000000079.1 SMESG000074134.1 SMESG000072420.1 SMESG000069427.1 SMESG000063486.1 SMESG000059936.1 SMESG000056847.1 SMESG000054630.1 SMESG000054168.1 SMESG000053671.1 SMESG000053669.1 SMESG000053664.1 SMESG000053657.1 SMESG000053638.1 SMESG000052400.1 SMESG000051558.1 SMESG000051017.1 SMESG000043567.1 SMESG000035748.1 SMESG000032351.1 SMESG000030698.1 SMESG000029834.1 SMESG000029267.1 SMESG000023200.1 SMESG000021127.1 SMESG000013659.1 Contig19290newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030795SMESG000010333.1 SMESG000000079.1 SMESG000074134.1 SMESG000072420.1 SMESG000069427.1 SMESG000063486.1 SMESG000059936.1 SMESG000056847.1 SMESG000054630.1 SMESG000054168.1 SMESG000053671.1 SMESG000053669.1 SMESG000053664.1 SMESG000053657.1 SMESG000053638.1 SMESG000052400.1 SMESG000051558.1 SMESG000051017.1 SMESG000043567.1 SMESG000035748.1 SMESG000032351.1 SMESG000030698.1 SMESG000029834.1 SMESG000029267.1 SMESG000023200.1 SMESG000021127.1 SMESG000013659.1 Contig19290uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030795SMESG000053671.1 SMESG000053669.1 SMESG000053667.1 SMESG000053657.1 SMESG000053638.1 Contig27090newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030795SMESG000053671.1 SMESG000053669.1 SMESG000053667.1 SMESG000053657.1 SMESG000053638.1 Contig27090uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30030795SMESG000053671.1 SMESG000053669.1 SMESG000053664.1 SMESG000053657.1 SMESG000053638.1 SMESG000053667.1 dd_Smed_v6_1027_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30030795SMESG000053671.1 SMESG000053669.1 SMESG000053664.1 SMESG000053657.1 SMESG000053638.1 SMESG000053667.1 dd_Smed_v6_1027_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30030795SMESG000053671.1 SMESG000053669.1 SMESG000053667.1 SMESG000053664.1 SMESG000053657.1 SMESG000053638.1 dd_Smed_v4_1027_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
BLAST of Vault protein inter alpha trypsin-1 vs. TrEMBL
Match: I1ZID1 (Vault protein inter alpha trypsin-1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 134.42 bits (337), Expect = 2.078e-29
Identity = 62/69 (89.86%), Postives = 63/69 (91.30%), Query Frame = 2
Query:    2 TKYTTFVAIDQNAPGEPLVTNIEEEFPIEKRRLSYSRRMYFQSDSLMKAGAPQMATAPKMVCNFEMLER 208
            TKYTTFVAIDQNAPGEPLVTNIEEEFPIEKRRLSYSRRMYFQSDSLMK GAPQM TAP MVCNF+   R
Sbjct:  451 TKYTTFVAIDQNAPGEPLVTNIEEEFPIEKRRLSYSRRMYFQSDSLMKTGAPQMETAPNMVCNFQKHAR 519          
BLAST of Vault protein inter alpha trypsin-1 vs. Planmine SMEST
Match: SMESG000053671.1 (SMESG000053671.1)

HSP 1 Score: 89.7373 bits (221), Expect = 2.048e-18
Identity = 57/108 (52.78%), Postives = 66/108 (61.11%), Query Frame = 2
Query:    2 TKYTTFVAIDQNAPGEPLVTNIEEEFPIEKRRLSYSRRMYFQSDSLMKAGAPQMATAPKMVCNFEMLERFVSYPIPPAMKCSAM---ESKRMFLKKKKVIYLFKINKL 316
            TKYTTFVAIDQ+APGEPLVTNIEE    EK   S SRRM FQ   LMKAGAPQ+           + +R+   P PP MKC      +SKR  LKK+ + YL KI  +
Sbjct:  579 TKYTTFVAIDQDAPGEPLVTNIEE----EKTHFSCSRRMNFQCVPLMKAGAPQI-----------VYDRY--EPNPPPMKCPEAKFKKSKRTSLKKEDIGYLDKIKNM 669          
BLAST of Vault protein inter alpha trypsin-1 vs. Planmine SMEST
Match: SMESG000053671.1 (SMESG000053671.1)

HSP 1 Score: 79.337 bits (194), Expect = 3.061e-15
Identity = 47/81 (58.02%), Postives = 52/81 (64.20%), Query Frame = 2
Query:    2 TKYTTFVAIDQNAPGEPLVTNIEEEFPIEKRRLSYSRRMYFQSDSLMKAGAPQMATAPKMVCNFEMLERFVSYPIPPAMKC 244
            TKYTTFVAIDQ+APGEPLVTNIEE    EK   S SRRM FQ   LMKAGAPQ+           + +R+   P PP MKC
Sbjct:  579 TKYTTFVAIDQDAPGEPLVTNIEE----EKTHFSCSRRMNFQCVPLMKAGAPQI-----------VYDRY--EPNPPPMKC 642          
BLAST of Vault protein inter alpha trypsin-1 vs. Planmine SMEST
Match: SMESG000053667.1 (SMESG000053667.1)

HSP 1 Score: 73.559 bits (179), Expect = 3.132e-15
Identity = 34/36 (94.44%), Postives = 34/36 (94.44%), Query Frame = 2
Query:  761 MVGEKLSDTFIFWDHPILTILSLYIPTVYQSFSV*K 868
            MVGEKLSDTFIFWDHPILTILSLYIPTVYQSFS  K
Sbjct:    1 MVGEKLSDTFIFWDHPILTILSLYIPTVYQSFSASK 36          
BLAST of Vault protein inter alpha trypsin-1 vs. Planmine SMEST
Match: SMESG000053657.1 (SMESG000053657.1)

HSP 1 Score: 52.373 bits (124), Expect = 6.613e-7
Identity = 23/24 (95.83%), Postives = 24/24 (100.00%), Query Frame = 2
Query:    2 TKYTTFVAIDQNAPGEPLVTNIEE 73
            TKYTTFVAIDQ+APGEPLVTNIEE
Sbjct:  555 TKYTTFVAIDQDAPGEPLVTNIEE 578          
BLAST of Vault protein inter alpha trypsin-1 vs. Planmine SMEST
Match: SMESG000053657.1 (SMESG000053657.1)

HSP 1 Score: 52.373 bits (124), Expect = 6.919e-7
Identity = 23/24 (95.83%), Postives = 24/24 (100.00%), Query Frame = 2
Query:    2 TKYTTFVAIDQNAPGEPLVTNIEE 73
            TKYTTFVAIDQ+APGEPLVTNIEE
Sbjct:  578 TKYTTFVAIDQDAPGEPLVTNIEE 601          
The following BLAST results are available for this feature:
BLAST of Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZID12.078e-2989.86Vault protein inter alpha trypsin-1 (Fragment) OS=... [more]
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BLAST of Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 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 Vault protein inter alpha trypsin-1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000053671.12.048e-1852.78SMESG000053671.1[more]
SMESG000053671.13.061e-1558.02SMESG000053671.1[more]
SMESG000053667.13.132e-1594.44SMESG000053667.1[more]
SMESG000053657.16.613e-795.83SMESG000053657.1[more]
SMESG000053657.16.919e-795.83SMESG000053657.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030795 ID=SMED30030795|Name=Vault protein inter alpha trypsin-1|organism=Schmidtea mediterranea sexual|type=transcript|length=1703bp
AACAAAATACACGACATTTGTGGCAATAGACCAAAACGCCCCAGGTGAAC
CTTTGGTCACAAACATTGAAGAAGAATTTCCGATAGAAAAACGTCGATTA
TCGTACTCAAGAAGGATGTATTTTCAATCTGATTCATTAATGAAGGCGGG
AGCTCCACAGATGGCGACAGCTCCAAAGATGGTTTGTAATTTTGAAATGC
TCGAAAGGTTTGTGTCGTATCCCATTCCTCCAGCAATGAAATGTTCAGCA
ATGGAATCTAAAAGAATGTTTTTGAAAAAAAAGAAAGTAATTTATTTGTT
CAAAATTAATAAGTTGAATTTTGACACATACTGATAACATTCAAACAATC
CCCAAGACTTAGCAATTACTGATTTGTTGCTAGTGAAAGATAAGGGGAAT
TTCTCTGAACTATTTTTGCTTTTACCAACTATATATTTTGTATAACATAT
GAACTGAATTTGCGGCATGCACCAACAAGCAAACATCATGACATTTAGGT
TTATGGGCATAAAATATAAATTAAAACATTCGCTGTAAATTGTGGAGCAA
TGCAGCATTTTATTTACAATGAGAATATTGCTGATTAAATGTGCAAATAA
ATTCTTTGTTAGCTCTTCATTCTTGTTGACATTTTTTTAAAAATATGTCG
CGGCGCTCAACGCCACTATGGCAAATTAATGCATTGGGCAAGTCCTAAAT
ATTAGTATATCTCGCTCAAATTTTTACCATAACATCAACGCAGTTTGCAT
CATACAACAGATGGTCGGAGAGAAACTTTCTGATACTTTCATATTTTGGG
ACCACCCTATACTAACGATATTATCACTATATATTCCGACCGTTTATCAG
TCTTTTTCAGTATAGAAATAACATTAACAATAACTGAATGAAAATAACAA
TATTTAAACAAATTAACTAATAATAATCGCAATCAAATATTATCAGAAAA
ATATTAAGTTATTTTTATTTTAAGAAAATCAACTTGTAAATTTAGTTTTA
AAAAACGCAAATAATCATTTCTTATATAAGTTTATAAAACAATAAATTTT
AAAATTCCTTTTATATAATAAAATCTTTTCACATACCACAAAATAACACC
AAACATATTATATACACAATTCACATTCTTTTATTTACATACATTGAAAA
TGCCTGTAAACTGAGCATTTTGAACATAATTTATAGGATTTAAAGATGTA
ATCAACAACGCCTTATGGGTTATTTGTTTCCAATAATTCTTATTTCGATA
TTAGTCCCGTTGTTCTGGAATCAAATTAAATAATTAAATAAAATCAATTT
TTTCTAGGGAGAAAATCAAAAGTTAAAGACGAAAAAAATAATTAAAAATT
AATAGAATACAAAAAAAATTTTACTATAATATTTTCATAATTAAATAAAC
ATTTCTCTGGGATAATTTCTTTAATGTAATTTTTTTTAGTTATTCTGCTT
TAGAAAAAAGGTTAATTAATATTTTGTGTATAATCTATGTAATTATTTCG
CATTCCTTTTCATTAATATCCATGAAAAAATTTCAATCAATTAGATTTCA
AATAAATATAATAAATAATTTAACGAAATTGGATATACAGTCAATTTTTT
TATGCGTAGATAAGTTCCTCAGAAAGCCGCATAAAAAGGCACGACTTACA
CTGTTCAATAATTTCGAAAAGCACATAAGATACAAATAAATTAAGAGTTG
GCG
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protein sequence of SMED30030795-orf-1

>SMED30030795-orf-1 ID=SMED30030795-orf-1|Name=SMED30030795-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=111bp
TKYTTFVAIDQNAPGEPLVTNIEEEFPIEKRRLSYSRRMYFQSDSLMKAG
APQMATAPKMVCNFEMLERFVSYPIPPAMKCSAMESKRMFLKKKKVIYLF
KINKLNFDTY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0002032epidermal cell