Mitochondrial ribosome protein 63

Overview
NameMitochondrial ribosome protein 63
Smed IDSMED30020645
Length (bp)566
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 Mitochondrial ribosome protein 63 (SMED30020645) t-SNE clustered cells

Violin plots show distribution of expression levels for Mitochondrial ribosome protein 63 (SMED30020645) 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 Mitochondrial ribosome protein 63 (SMED30020645) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Mitochondrial ribosome protein 63 (SMED30020645) 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




SMED30020645

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30020645 SmedASXL_019301SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30020645 dd_Smed_v4_6347_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020645 dd_Smed_v4_6347_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30020645 dd_Smed_v4_6347_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30020645 dd_Smed_v4_6347_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 Mitochondrial ribosome protein 63 vs. TrEMBL
Match: A0A0R3W8L7 (Uncharacterized protein OS=Taenia asiatica OX=60517 GN=TASK_LOCUS6718 PE=4 SV=1)

HSP 1 Score: 110.538 bits (275), Expect = 7.017e-28
Identity = 54/115 (46.96%), Postives = 75/115 (65.22%), Query Frame = 2
Query:   53 MRISYAVLGRFVPYKQVPGSLWAGKQRKIPLLTNYRKAGMLDRILVEDQNLKILSNPYISKEVESAYLELIEKPRELKRIDDNIIQNYVNSFNERFPNTSLDEFWNCIKKYKNYE 397
            MR++Y +LG F+PYK+VPGSLWAGKQRKIP LT  RKA  +D +L+  QN + LS P+ISKE E+  L   E+ +EL   ++   + Y   F  RFPN  L+ FW+ +   K ++
Sbjct:    1 MRLTYFLLGHFIPYKRVPGSLWAGKQRKIPRLTASRKAAFMDELLMTQQNERYLSKPFISKEAEATTLP-AEQAKELAAENEVFYKIYEEKFRIRFPNRKLENFWSHLNNSKKFD 114          
BLAST of Mitochondrial ribosome protein 63 vs. TrEMBL
Match: A0A0R3XCJ6 (Uncharacterized protein OS=Hydatigena taeniaeformis OX=6205 GN=TTAC_LOCUS11256 PE=4 SV=1)

HSP 1 Score: 110.153 bits (274), Expect = 9.202e-28
Identity = 51/115 (44.35%), Postives = 75/115 (65.22%), Query Frame = 2
Query:   53 MRISYAVLGRFVPYKQVPGSLWAGKQRKIPLLTNYRKAGMLDRILVEDQNLKILSNPYISKEVESAYLELIEKPRELKRIDDNIIQNYVNSFNERFPNTSLDEFWNCIKKYKNYE 397
            MR+++ + GRF+PYK+VPGSLWAGKQRKIP LT  RKA  +D +L+  QN + LS P+I +E E+  L   E+ +EL + ++   + Y   F  RFPN  L+ FW+ +   K ++
Sbjct:    1 MRLTFLLSGRFIPYKRVPGSLWAGKQRKIPRLTASRKAAFMDELLLAQQNERYLSKPFIGQEAEATTLP-AEQAKELAKENETFYRIYEAKFRTRFPNRRLEHFWSHLNVTKKFD 114          
BLAST of Mitochondrial ribosome protein 63 vs. TrEMBL
Match: A0A3P7LNY8 (Uncharacterized protein OS=Dibothriocephalus latus OX=60516 GN=DILT_LOCUS8494 PE=4 SV=1)

HSP 1 Score: 109.768 bits (273), Expect = 1.451e-27
Identity = 50/114 (43.86%), Postives = 75/114 (65.79%), Query Frame = 2
Query:   53 MRISYAVLGRFVPYKQVPGSLWAGKQRKIPLLTNYRKAGMLDRILVEDQNLKILSNPYISKEVESAYLELIEKPRELKRIDDNIIQNYVNSFNERFPNTSLDEFWNCIKKYKNY 394
            MR+S+++LGRF+P++ VPGSLW GK+RKIP LT  RKA  +D +L+  QN + LSNPY+S E E+  L   E+ RE+   D    + Y + F +RFP+  L+ FW+ +   + +
Sbjct:    1 MRLSFSLLGRFIPWRSVPGSLWGGKRRKIPRLTGARKAAFMDELLLTQQNERYLSNPYLSVEAEATTLA-AEQAREIAAEDRVFYKVYEDKFRKRFPDRKLENFWSHLNTTRKF 113          
BLAST of Mitochondrial ribosome protein 63 vs. TrEMBL
Match: A0A4Z2DCF1 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_002417 PE=4 SV=1)

HSP 1 Score: 109.768 bits (273), Expect = 1.515e-27
Identity = 55/115 (47.83%), Postives = 72/115 (62.61%), Query Frame = 2
Query:   53 MRISYAVLGRFVPYKQVPGSLWAGKQRKIPLLTNYRKAGMLDRILVEDQNLKILSNPYISKEVESAYLELIEKPRELKRIDDNIIQNYVNSFNERFPNTSLDEFWNCIKKYKNYE 397
            M ++ A  GRFV +K++PGS+W GKQRKIPLLTN RK   LD +L+  QN   L  PY ++EVESA L   EK REL+  D      Y   FN RFP  +++ FW+ + K K Y+
Sbjct:    1 MILTAACYGRFVRWKRIPGSVWGGKQRKIPLLTNSRKEAFLDELLISHQNHMYLQKPYFTEEVESATLAE-EKARELQMEDRFFYDRYAEQFNRRFPTRNIEAFWDKLYKTKRYD 114          
BLAST of Mitochondrial ribosome protein 63 vs. TrEMBL
Match: W6URX7 (Uncharacterized protein OS=Echinococcus granulosus OX=6210 GN=EGR_01116 PE=4 SV=1)

HSP 1 Score: 110.153 bits (274), Expect = 2.354e-27
Identity = 53/115 (46.09%), Postives = 76/115 (66.09%), Query Frame = 2
Query:   53 MRISYAVLGRFVPYKQVPGSLWAGKQRKIPLLTNYRKAGMLDRILVEDQNLKILSNPYISKEVESAYLELIEKPRELKRIDDNIIQNYVNSFNERFPNTSLDEFWNCIKKYKNYE 397
            MR++  +LG F+PYK+VPGSLWAGKQRKIP LT  RKA  +D +L+  QN + LS P++S+E E+  L   EK +EL R ++   + Y   F  RFPN  L++FW+ +   K ++
Sbjct:   35 MRLTSLLLGHFIPYKRVPGSLWAGKQRKIPRLTASRKAAFMDELLLTQQNERYLSRPFLSQEAEATTLP-AEKAKELARENEVFYKIYEEKFRIRFPNRKLEDFWSHLNNCKKFD 148          
BLAST of Mitochondrial ribosome protein 63 vs. Planmine SMEST
Match: SMESG000077978.1 (SMESG000077978.1)

HSP 1 Score: 237.269 bits (604), Expect = 2.555e-81
Identity = 116/116 (100.00%), Postives = 116/116 (100.00%), Query Frame = 2
Query:   53 MRISYAVLGRFVPYKQVPGSLWAGKQRKIPLLTNYRKAGMLDRILVEDQNLKILSNPYISKEVESAYLELIEKPRELKRIDDNIIQNYVNSFNERFPNTSLDEFWNCIKKYKNYEN 400
            MRISYAVLGRFVPYKQVPGSLWAGKQRKIPLLTNYRKAGMLDRILVEDQNLKILSNPYISKEVESAYLELIEKPRELKRIDDNIIQNYVNSFNERFPNTSLDEFWNCIKKYKNYEN
Sbjct:    1 MRISYAVLGRFVPYKQVPGSLWAGKQRKIPLLTNYRKAGMLDRILVEDQNLKILSNPYISKEVESAYLELIEKPRELKRIDDNIIQNYVNSFNERFPNTSLDEFWNCIKKYKNYEN 116          
The following BLAST results are available for this feature:
BLAST of Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0R3W8L77.017e-2846.96Uncharacterized protein OS=Taenia asiatica OX=6051... [more]
A0A0R3XCJ69.202e-2844.35Uncharacterized protein OS=Hydatigena taeniaeformi... [more]
A0A3P7LNY81.451e-2743.86Uncharacterized protein OS=Dibothriocephalus latus... [more]
A0A4Z2DCF11.515e-2747.83Uncharacterized protein OS=Schistosoma japonicum O... [more]
W6URX72.354e-2746.09Uncharacterized protein OS=Echinococcus granulosus... [more]
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BLAST of Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 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 Mitochondrial ribosome protein 63 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000077978.12.555e-81100.00SMESG000077978.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020645 ID=SMED30020645|Name=Mitochondrial ribosome protein 63|organism=Schmidtea mediterranea sexual|type=transcript|length=566bp
TTTCAATAAAGTAATTTATATGATTTCTTATTTAAATAAAATAAATATAT
AAATGCGTATATCATATGCAGTTTTAGGTCGATTTGTACCTTACAAGCAA
GTACCGGGTTCATTGTGGGCTGGTAAACAAAGAAAAATCCCTTTACTGAC
AAACTATCGAAAAGCTGGAATGTTAGATAGAATTTTGGTAGAGGATCAAA
ATTTAAAAATCTTGTCTAATCCATATATATCAAAAGAAGTTGAATCTGCA
TATTTGGAATTAATAGAAAAACCTAGAGAACTAAAGCGAATTGACGATAA
TATTATTCAAAATTATGTAAATTCTTTCAATGAAAGGTTCCCAAATACTA
GCTTAGATGAATTTTGGAATTGCATTAAAAAGTATAAAAATTATGAAAAT
TAACTCTCAATGTTTGTAATAAAGTTTTGCCAAATTATGATTTTATTCTG
ATTTTTATGCATCTATGTTGGTAAATTAATTATTTAAAATTTATTGAGGT
TTTTATCACGGATAATATATGTAGATAAATTATTGAAATTATATTATCTA
TTTTTTAAAGGCGGCT
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protein sequence of SMED30020645-orf-1

>SMED30020645-orf-1 ID=SMED30020645-orf-1|Name=SMED30020645-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=117bp
MRISYAVLGRFVPYKQVPGSLWAGKQRKIPLLTNYRKAGMLDRILVEDQN
LKILSNPYISKEVESAYLELIEKPRELKRIDDNIIQNYVNSFNERFPNTS
LDEFWNCIKKYKNYEN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002032epidermal cell
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR016576Ribosomal_MRP63_mit
Vocabulary: cellular component
TermDefinition
GO:0005761mitochondrial ribosome
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR016576Ribosomal protein 63, mitochondrialPFAMPF14978MRP-63coord: 18..110
e-value: 1.6E-11
score: 44.7