Mitochondrial intermembrane space import and assembly protein 40

Overview
NameMitochondrial intermembrane space import and assembly protein 40
Smed IDSMED30022636
Length (bp)509
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 intermembrane space import and assembly protein 40 (SMED30022636) t-SNE clustered cells

Violin plots show distribution of expression levels for Mitochondrial intermembrane space import and assembly protein 40 (SMED30022636) 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 intermembrane space import and assembly protein 40 (SMED30022636) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Mitochondrial intermembrane space import and assembly protein 40 (SMED30022636) 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



SMED30022636

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30022636h1SMcG0010733 SmedASXL_004071SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30022636h1SMcG0010733 dd_Smed_v4_5194_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30022636h1SMcG0010733 dd_Smed_v4_5194_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30022636h1SMcG0010733 dd_Smed_v4_5194_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30022636h1SMcG0010733 dd_Smed_v4_5194_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30022636h1SMcG0010733 dd_Smed_v4_5194_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 Mitochondrial intermembrane space import and assembly protein 40 vs. TrEMBL
Match: A0A0R3T3W1 (Uncharacterized protein OS=Rodentolepis nana OX=102285 GN=HNAJ_LOCUS1716 PE=4 SV=1)

HSP 1 Score: 90.1225 bits (222), Expect = 5.722e-20
Identity = 44/120 (36.67%), Postives = 73/120 (60.83%), Query Frame = 1 
Query:  121 EIYFLSKKEATPSLSFQDYFDIDKAYDKPGLKVRNENNVLKYNFNCPCVIKYISSPCGYFFRNFISGISELSSLEKFA--IEDKKRFDKIRYELDDCMNFFGAYYQSMKDYFHEEI*DVL 474
            ++ ++++ EA+  L  ++Y+DIDK + KPG K RN     ++N++C CV  YI+SPCG++FR F+S +    + E     +E K+ FDK   EL +CM  +  YY+ + + F E + DV 
Sbjct:    8 KVLYITRDEASSPLGLEEYYDIDKIFAKPGFKTRNG----QFNWSCSCVASYITSPCGFYFRKFLSNMDRFMNTEDSINDVEAKRVFDKCYSELGNCMQKYPKYYRPILEQFEESLSDVF 123
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BLAST of Mitochondrial intermembrane space import and assembly protein 40 vs. TrEMBL
Match: A0A0R3S7J2 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS7 PE=4 SV=1)

HSP 1 Score: 88.9669 bits (219), Expect = 1.370e-19
Identity = 47/120 (39.17%), Postives = 74/120 (61.67%), Query Frame = 1 
Query:  124 IYFLSKKEATPSLSFQDYFDIDKAYDKPGLKVRNENNVLKYNFNCPCVIKYISSPCGYFFRNFISGISELSSLEKFAIEDKKR---FDKIRYELDDCMNFFGAYYQSMKDYFHEEI*DVL 474
            I  L+++EA+  L  +DY+D+DK + KPG K R+     ++N++C CV  YI+SPCG++FR F+S +    + E  +I DK+    F+K   EL DCM  +  YY+ + + F E + DVL
Sbjct:    9 ILNLTREEASSPLGLEDYYDMDKKFAKPGFKTRDG----QFNWSCSCVASYITSPCGFYFRKFLSNMDRFMNTED-SINDKEAKQVFEKCYSELGDCMRKYPKYYRPILEQFEESLSDVL 123
[Close]
BLAST of Mitochondrial intermembrane space import and assembly protein 40 vs. TrEMBL
Match: A0A4S2M8J2 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_001873 PE=4 SV=1)

HSP 1 Score: 90.1225 bits (222), Expect = 1.613e-19
Identity = 47/115 (40.87%), Postives = 67/115 (58.26%), Query Frame = 1 
Query:  106 MDSNPEIYFLSKKEATPSLSFQDYFDIDKAYDKPGLKVRNENNVLKYNFNCPCVIKYISSPCGYFFRNFISGISE-LSSLEKFAIEDKKR-FDKIRYELDDCMNFFGAYYQSMKD 444
            M +   + FLS++EA PSL+ +DY+DID+ Y KPG K  +       N++C CV  Y++ PCGYFFRNF+  I   L +   F  E+ +  F +I YEL  C+     YY+S  D
Sbjct:   49 MTTRHTVTFLSREEARPSLNLEDYYDIDRQYAKPGFKTPSG----ALNWHCSCVSAYVTGPCGYFFRNFMKNIDRFLKNDNAFESEENRSLFKRIHYELMGCLKAHPVYYKSFID 159
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BLAST of Mitochondrial intermembrane space import and assembly protein 40 vs. TrEMBL
Match: A0A1S8X0J3 (Methyltransferase TRM13 (Fragment) OS=Opisthorchis viverrini OX=6198 GN=X801_04088 PE=4 SV=1)

HSP 1 Score: 94.7449 bits (234), Expect = 2.056e-19
Identity = 47/125 (37.60%), Postives = 72/125 (57.60%), Query Frame = 1 
Query:  106 MDSNPEIYFLSKKEATPSLSFQDYFDIDKAYDKPGLKVRNENNVLKYNFNCPCVIKYISSPCGYFFRNFISGISE-LSSLEKFAIEDKKR-FDKIRYELDDCMNFFGAYYQSMKDYFHEEI*DVL 474
            M S   + FLS++EA P L+ +DY+DID+ Y KPG K  +       N++C CV  Y++ PCGYFFRNF+  I   L + + F  E+ +  F +I YEL  C+     YY+S  D +   + +++
Sbjct:    1 MTSRHTVTFLSREEAQPRLNLEDYYDIDRQYAKPGFKTPSG----ALNWHCSCVSAYVTGPCGYFFRNFMKNIDRFLKNDDAFESEENRSLFRRIHYELMGCLKAHPVYYKSFIDEYSSPLENIM 121
[Close]
BLAST of Mitochondrial intermembrane space import and assembly protein 40 vs. TrEMBL
Match: A0A0R3U4B3 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS1478 PE=4 SV=1)

HSP 1 Score: 88.1965 bits (217), Expect = 2.603e-19
Identity = 45/128 (35.16%), Postives = 77/128 (60.16%), Query Frame = 1 
Query:  112 SNPEI-----YFLSKKEATPSLSFQDYFDIDKAYDKPGLKVRNENNVLKYNFNCPCVIKYISSPCGYFFRNFISGISELSSLEKFAIEDKKR--FDKIRYELDDCMNFFGAYYQSMKDYFHEEI*DVL 474
            +NP+I      ++S++E+   L+ +DYFD+DK   KPG K  +     K+N++C CV  Y++SPCG +FRNF++ + +        ++DK +  F++   EL  CM  + +YY+S+ D + E + DVL
Sbjct:    2 NNPDIEQHKTLYISREESRSPLNIEDYFDVDKKIAKPGFKTLDG----KFNWHCSCVASYVTSPCGVYFRNFLANMDKFMGTNDSTLDDKAKYTFEQCYAELTTCMKKYPSYYKSILDQYSESLQDVL 125
[Close]
BLAST of Mitochondrial intermembrane space import and assembly protein 40 vs. Planmine SMEST
Match: SMESG000039945.1 (SMESG000039945.1)

HSP 1 Score: 242.662 bits (618), Expect = 1.021e-83
Identity = 119/119 (100.00%), Postives = 119/119 (100.00%), Query Frame = 1 
Query:  106 MDSNPEIYFLSKKEATPSLSFQDYFDIDKAYDKPGLKVRNENNVLKYNFNCPCVIKYISSPCGYFFRNFISGISELSSLEKFAIEDKKRFDKIRYELDDCMNFFGAYYQSMKDYFHEEI 462
            MDSNPEIYFLSKKEATPSLSFQDYFDIDKAYDKPGLKVRNENNVLKYNFNCPCVIKYISSPCGYFFRNFISGISELSSLEKFAIEDKKRFDKIRYELDDCMNFFGAYYQSMKDYFHEEI
Sbjct:    1 MDSNPEIYFLSKKEATPSLSFQDYFDIDKAYDKPGLKVRNENNVLKYNFNCPCVIKYISSPCGYFFRNFISGISELSSLEKFAIEDKKRFDKIRYELDDCMNFFGAYYQSMKDYFHEEI 119
The following BLAST results are available for this feature:
BLAST of Mitochondrial intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0R3T3W15.722e-2036.67Uncharacterized protein OS=Rodentolepis nana OX=10... [more]
A0A0R3S7J21.370e-1939.17Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
A0A4S2M8J21.613e-1940.87Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A1S8X0J32.056e-1937.60Methyltransferase TRM13 (Fragment) OS=Opisthorchis... [more]
A0A0R3U4B32.603e-1935.16Uncharacterized protein OS=Mesocestoides corti OX=... [more]
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BLAST of Mitochondrial intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 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 intermembrane space import and assembly protein 40 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000039945.11.021e-83100.00SMESG000039945.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022636 ID=SMED30022636|Name=Mitochondrial intermembrane space import and assembly protein 40|organism=Schmidtea mediterranea sexual|type=transcript|length=509bp
ATTTTAATTGCTTATTAATTTCTTGACTAACTAAAATTTTGTACGTGATT
TCTAATTATTAAATCTTAAATAGTTTAAACATTTGTTTATATATTGGCAA
TTTAAATGGATTCGAATCCCGAAATCTATTTTTTGTCCAAAAAAGAAGCT
ACTCCTAGTCTTTCTTTCCAAGATTATTTTGATATTGACAAAGCATACGA
TAAACCGGGATTGAAAGTTAGAAATGAAAATAATGTATTGAAATATAATT
TTAATTGTCCATGTGTTATCAAATATATATCATCTCCTTGTGGTTATTTC
TTTAGAAACTTCATTTCAGGAATTAGTGAGTTGTCTTCCCTAGAAAAATT
TGCAATTGAAGATAAAAAACGGTTTGATAAAATACGGTACGAATTGGATG
ATTGCATGAATTTTTTCGGTGCATATTATCAATCTATGAAGGATTATTTT
CACGAAGAAATTTAGGATGTGTTAGTTAAAAAATATATTGATTTAATGTT
AAAAAAAAA
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protein sequence of SMED30022636-orf-1

>SMED30022636-orf-1 ID=SMED30022636-orf-1|Name=SMED30022636-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=120bp
MDSNPEIYFLSKKEATPSLSFQDYFDIDKAYDKPGLKVRNENNVLKYNFN
CPCVIKYISSPCGYFFRNFISGISELSSLEKFAIEDKKRFDKIRYELDDC
MNFFGAYYQSMKDYFHEEI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002109X1 cell