COX assembly mitochondrial protein

Overview
NameCOX assembly mitochondrial protein
Smed IDSMED30015031
Length (bp)438
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 COX assembly mitochondrial protein (SMED30015031) t-SNE clustered cells

Violin plots show distribution of expression levels for COX assembly mitochondrial protein (SMED30015031) 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 COX assembly mitochondrial protein (SMED30015031) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for COX assembly mitochondrial protein (SMED30015031) 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



SMED30015031

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
muscle cellSMED30015031SMESG000036571.1 dd_Smed_v4_6296_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
[Close]
BLAST of COX assembly mitochondrial protein vs. Ensembl Fly
Match: CG17996 (gene:FBgn0032595 transcript:FBtr0080937)

HSP 1 Score: 56.9954 bits (136), Expect = 4.183e-11
Identity = 35/107 (32.71%), Postives = 51/107 (47.66%), Query Frame = 2 
Query:   71 MPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCKTEMRDLNECALRSGIFTKLNCSSVQKAAXXXXXXXXXXXXXXXXMRKMYLDIRSEYRRTGVDSK 391
             PA D   P  LGDP+D  L +VE +VLIP +       + C  E+ D  EC   S I     C     A   C+  W  ++ +    +++YL  R++YR TG+  K
Sbjct:    6 QPAVDPHNPHGLGDPNDTRLRKVEREVLIPKIMRDRAKTEFCSKEVADFQECCKASSILMVATCRKQNSALKECLTQWYQNEAFKEECKQIYLQERADYRSTGIPKK 112
[Close]
BLAST of COX assembly mitochondrial protein vs. TrEMBL
Match: A0A2T7PFE2 (COX assembly mitochondrial protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_07571 PE=3 SV=1)

HSP 1 Score: 72.0182 bits (175), Expect = 2.386e-13
Identity = 38/106 (35.85%), Postives = 55/106 (51.89%), Query Frame = 2 
Query:   65 ITMPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCKTEMRDLNECALRSGIFTKLNCSSVQKAAXXXXXXXXXXXXXXXXMRKMYLDIRSEYRRTGV 382
            + +P   G GP  LGDPDD SL  VE ++LIP         ++C  E++D  +CA   G+     C +V K    C+     D  +    ++ YL+ RSEYRRTG+
Sbjct:    9 VVLPGTMGGGPHGLGDPDDKSLRHVETEILIPQKMKEKAKKERCAKEVKDFGDCAKDQGVLLPFMCRAVAKHLEQCLTASYKDPAFKEKCKEEYLEERSEYRRTGI 114
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BLAST of COX assembly mitochondrial protein vs. TrEMBL
Match: A0A151XD99 (COX assembly mitochondrial protein OS=Trachymyrmex zeteki OX=64791 GN=ALC60_02755 PE=3 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 4.629e-13
Identity = 40/114 (35.09%), Postives = 62/114 (54.39%), Query Frame = 2 
Query:   62 FITMPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCKTEMRDLNECALRSGIFTKLNCSSVQKAAXXXXXXXXXXXXXXXXMRKMYLDIRSEYRRTGVDSKLPTV 403
            +  +P   G GPK LGDP D SL +VE  VL+P L    I ++KC  E+++ ++C L SG+   + C         C+  W  + D+     + YL+ RSE+RRTG+  K  ++
Sbjct:    5 YSVLPQKFGGGPKGLGDPSDKSLRKVEKNVLVPKLMRERIKSEKCVNEVKEFHDCCLNSGLLNVIKCRKENDKMIACMKEWFFNQDFIKECTEQYLEERSEFRRTGIPKKQRSI 118
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BLAST of COX assembly mitochondrial protein vs. TrEMBL
Match: A0A443S6Z3 (COX assembly mitochondrial protein OS=Leptotrombidium deliense OX=299467 GN=B4U80_07648 PE=3 SV=1)

HSP 1 Score: 70.0922 bits (170), Expect = 1.444e-12
Identity = 42/104 (40.38%), Postives = 58/104 (55.77%), Query Frame = 2 
Query:   92 GPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCKTEMRDLNECALRSGIFTKLNCSSVQKAAXXXXXXXXXXXXXXXXMRKMYLDIRSEYRRTGVDSKLPTV 403
            GPK LGDPDD SL +VE +VLIP L         C     + ++CA  +G F   NC  V     +C+  W +++++     K YL++RSEYRRTG+  K P V
Sbjct:    9 GPKGLGDPDDLSLRKVEREVLIPKLMREKTRWINCVDVANEFDQCAKENGFFMIFNCRKVNNRMQDCMKSWYENEEFRAECTKEYLEMRSEYRRTGIGQKSPYV 112
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BLAST of COX assembly mitochondrial protein vs. TrEMBL
Match: A0A4Y2EVX7 (COX assembly mitochondrial protein OS=Araneus ventricosus OX=182803 GN=CMC1_0 PE=3 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 1.915e-11
Identity = 43/107 (40.19%), Postives = 58/107 (54.21%), Query Frame = 2 
Query:   71 MPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCKTEMRDLNECALRSGIFTKLNCSSVQKAAXXXXXXXXXXXXXXXXMRKMYLDIRSEYRRTGVDSK 391
            +P     GPK LGDPDD SL +VE +VLIP+        +KC  E +   EC   SG +  L C     A N C++ W +D++      + YL  RSEYRRTG+ +K
Sbjct:    2 LPPSQSGGPKGLGDPDDKSLRKVELEVLIPMKIRDKTKKEKCLEEGQAFTECCKASGFWMFLKCRPQTNALNKCLEKWYNDEEMGKQCTEEYLQERSEYRRTGITAK 108
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BLAST of COX assembly mitochondrial protein vs. TrEMBL
Match: A0A1B0D8E1 (COX assembly mitochondrial protein OS=Phlebotomus papatasi OX=29031 PE=3 SV=1)

HSP 1 Score: 66.6254 bits (161), Expect = 3.460e-11
Identity = 39/97 (40.21%), Postives = 57/97 (58.76%), Query Frame = 2 
Query:   92 GPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCKTEMRDLNECALRSGIFTKLNCSSVQKAAXXXXXXXXXXXXXXXXMRKMYLDIRSEYRRTGV 382
            GPK+LGDPDD SL +VE +VLIP +       +KC  E+ D  +C    G+    +C    +   NC+  W  D+ + +  R++YLD R+E+RRTGV
Sbjct:   16 GPKQLGDPDDKSLRKVELEVLIPKVMRDRAKTEKCVPEVSDFEQCCKDKGLLMVFSCRKENEKLKNCLTKWYQDETFKSECRQIYLDERTEFRRTGV 112
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BLAST of COX assembly mitochondrial protein vs. Planmine SMEST
Match: SMESG000036571.1 (SMESG000036571.1)

HSP 1 Score: 204.912 bits (520), Expect = 2.986e-69
Identity = 117/119 (98.32%), Postives = 118/119 (99.16%), Query Frame = 2 
Query:   47 INRYPFITMPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCKTEMRDLNECALRSGIFTKLNCSSVQKAAXXXXXXXXXXXXXXXXMRKMYLDIRSEYRRTGVDSKLPTV 403
            INRYPFITMPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCK EMRDLNECALRSGIFTKLNCSSVQKAANNCIDYWN+DDDYSNNMRKMYLDIRSEYRRTGVDSKLPTV
Sbjct:    4 INRYPFITMPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCKIEMRDLNECALRSGIFTKLNCSSVQKAANNCIDYWNNDDDYSNNMRKMYLDIRSEYRRTGVDSKLPTV 122
[Close]
BLAST of COX assembly mitochondrial protein vs. Planmine SMEST
Match: SMESG000036571.1 (SMESG000036571.1)

HSP 1 Score: 187.963 bits (476), Expect = 1.237e-62
Identity = 109/111 (98.20%), Postives = 110/111 (99.10%), Query Frame = 2 
Query:   71 MPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCKTEMRDLNECALRSGIFTKLNCSSVQKAAXXXXXXXXXXXXXXXXMRKMYLDIRSEYRRTGVDSKLPTV 403
            MPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCK EMRDLNECALRSGIFTKLNCSSVQKAANNCIDYWN+DDDYSNNMRKMYLDIRSEYRRTGVDSKLPTV
Sbjct:    1 MPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCKIEMRDLNECALRSGIFTKLNCSSVQKAANNCIDYWNNDDDYSNNMRKMYLDIRSEYRRTGVDSKLPTV 111
[Close]
BLAST of COX assembly mitochondrial protein vs. Planmine SMEST
Match: SMESG000044355.1 (SMESG000044355.1)

HSP 1 Score: 62.003 bits (149), Expect = 7.216e-13
Identity = 38/106 (35.85%), Postives = 56/106 (52.83%), Query Frame = 2 
Query:   62 FITMPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIINDKCKTEMRDLNECALRSGIFTKLNCSSVQKAAXXXXXXXXXXXXXXXXMRKMYLDIRSEYRRTG 379
            +  +P + G GPK LGDP+   L + E  +LIP L   II  + CK +  +  +CA  +G  T   C    K   +C   W  DD+++  + + YLD RS YR+TG
Sbjct:   17 YTVLPKESGGGPKGLGDPNSRKLRKAEMDILIPELKRSIIKTENCKPQWLEFGKCAKVNGRKTPTKCQPELKLVEDCHKKWFYDDEFTKQVIEQYLDKRSHYRKTG 122
The following BLAST results are available for this feature:
BLAST of COX assembly mitochondrial 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 COX assembly mitochondrial 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 COX assembly mitochondrial protein vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CG179964.183e-1132.71gene:FBgn0032595 transcript:FBtr0080937[more]
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BLAST of COX assembly mitochondrial 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 COX assembly mitochondrial 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 COX assembly mitochondrial 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 COX assembly mitochondrial 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 COX assembly mitochondrial protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2T7PFE22.386e-1335.85COX assembly mitochondrial protein OS=Pomacea cana... [more]
A0A151XD994.629e-1335.09COX assembly mitochondrial protein OS=Trachymyrmex... [more]
A0A443S6Z31.444e-1240.38COX assembly mitochondrial protein OS=Leptotrombid... [more]
A0A4Y2EVX71.915e-1140.19COX assembly mitochondrial protein OS=Araneus vent... [more]
A0A1B0D8E13.460e-1140.21COX assembly mitochondrial protein OS=Phlebotomus ... [more]
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BLAST of COX assembly mitochondrial 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 COX assembly mitochondrial 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 COX assembly mitochondrial 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 COX assembly mitochondrial 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 COX assembly mitochondrial 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 COX assembly mitochondrial protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000036571.12.986e-6998.32SMESG000036571.1[more]
SMESG000036571.11.237e-6298.20SMESG000036571.1[more]
SMESG000044355.17.216e-1335.85SMESG000044355.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015031 ID=SMED30015031|Name=COX assembly mitochondrial protein|organism=Schmidtea mediterranea sexual|type=transcript|length=438bp
ATTTACTAATAATTTATTTTGAAAATTAAATTTTTTTATGGGCAATATAA
ATCGATATCCTTTCATTACTATGCCTGCAGATGATGGGAAAGGCCCTAAA
AAATTGGGAGATCCTGATGATAATTCGTTATCTGAAGTGGAAAATAAAGT
TTTAATTCCACTTTTACATCATTATATCATTATAAATGATAAATGTAAGA
CCGAGATGCGAGATTTAAATGAATGTGCGCTACGCAGTGGTATTTTTACT
AAATTAAATTGTAGTTCGGTGCAAAAAGCAGCAAATAATTGTATTGATTA
TTGGAACGATGATGACGATTATTCAAACAATATGAGGAAAATGTATTTAG
ATATAAGGTCAGAATACAGGCGGACTGGGGTTGATTCTAAATTGCCGACT
GTTTAATTGTTATATCAAAGTTTTTTAATTTCATACTG
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protein sequence of SMED30015031-orf-1

>SMED30015031-orf-1 ID=SMED30015031-orf-1|Name=SMED30015031-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
MGNINRYPFITMPADDGKGPKKLGDPDDNSLSEVENKVLIPLLHHYIIIN
DKCKTEMRDLNECALRSGIFTKLNCSSVQKAANNCIDYWNDDDDYSNNMR
KMYLDIRSEYRRTGVDSKLPTV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0005739mitochondrion
Vocabulary: INTERPRO
TermDefinition
IPR013892Cyt_c_biogenesis_Cmc1-like
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013892Cytochrome c oxidase biogenesis protein Cmc1-likePFAMPF08583Cmc1coord: 50..107
e-value: 1.7E-6
score: 28.0