Small integral membrane protein 15

Overview
NameSmall integral membrane protein 15
Smed IDSMED30007798
Length (bp)499
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 Small integral membrane protein 15 (SMED30007798) t-SNE clustered cells

Violin plots show distribution of expression levels for Small integral membrane protein 15 (SMED30007798) 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 Small integral membrane protein 15 (SMED30007798) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Small integral membrane protein 15 (SMED30007798) 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




SMED30007798

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
neoblastSMED30007798 dd_Smed_v4_2870_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30007798 dd_Smed_v4_2870_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 Small integral membrane protein 15 vs. TrEMBL
Match: A0A504YWC9 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_00975 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 4.562e-10
Identity = 39/93 (41.94%), Postives = 61/93 (65.59%), Query Frame = 1
Query:   67 MSDETKNKITLDHFNMTEAKDWKSWFFQKGLQIVIYAANDPWNFLITVLVFLAPFCMISAYCAWKLVXXXXXXXXXXXXXXXXXXNVSKARRH 345
            +SD  K+ +++D  +     +W  WF   GL++VIY A DPW F  TVL+ L P   +SA+CA+KL KE+  +E++KK +AKR A ++K ++H
Sbjct:    4 LSDSEKDPLSVDLGD--PPAEWSKWFAYIGLKLVIYVAKDPWGFFATVLIILTPLLGLSAFCAFKLAKEVQRQEEEKKLRAKRSAAIAKRQKH 94          
BLAST of Small integral membrane protein 15 vs. TrEMBL
Match: G7YT92 (Small integral membrane protein 15 OS=Clonorchis sinensis OX=79923 GN=SMIM15 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 1.962e-9
Identity = 37/93 (39.78%), Postives = 58/93 (62.37%), Query Frame = 1
Query:   70 SDETKNKITLDHFNMTEA-KDWKSWFFQKGLQIVIYAANDPWNFLITVLVFLAPFCMISAYCAWKLVXXXXXXXXXXXXXXXXXXNVSKARRH 345
            ++  K   +LD  ++ +  +DWK WF    L+  +Y A DPW F  TVL+ L P  M+ A+CA+KL +E+  +E +KK KAKR A ++K+R+ 
Sbjct:    6 AENVKQTPSLDSLDLGDPPEDWKGWFAYMALKFTVYVAKDPWGFFGTVLMILTPLFMLGAFCAYKLAQELKKQEVEKKLKAKRSAAIAKSRKQ 98          
BLAST of Small integral membrane protein 15 vs. TrEMBL
Match: A0A4S2LY99 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_004197 PE=4 SV=1)

HSP 1 Score: 61.6178 bits (148), Expect = 2.277e-9
Identity = 36/93 (38.71%), Postives = 59/93 (63.44%), Query Frame = 1
Query:   70 SDETKNKITLDHFNMTEA-KDWKSWFFQKGLQIVIYAANDPWNFLITVLVFLAPFCMISAYCAWKLVXXXXXXXXXXXXXXXXXXNVSKARRH 345
            ++  K   +LD  ++ +  +DW+ WF    L+  +Y A DPW FL TVL+ + P  M+ A+CA+KL +E+  +E +KK KAKR A ++K+R+ 
Sbjct:    6 AENVKQTPSLDSLDLGDPPEDWRGWFAYMALKFTVYVAKDPWGFLGTVLMIVTPLFMLGAFCAYKLAQELKKQEMEKKLKAKRSAAIAKSRKQ 98          
BLAST of Small integral membrane protein 15 vs. TrEMBL
Match: A0A0X3Q5N5 (Small integral membrane protein 15 OS=Schistocephalus solidus OX=70667 GN=SIM15 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 7.278e-9
Identity = 34/93 (36.56%), Postives = 57/93 (61.29%), Query Frame = 1
Query:   67 MSDETKNKITLDHFNMTEAKDWKSWFFQKGLQIVIYAANDPWNFLITVLVFLAPFCMISAYCAWKLVXXXXXXXXXXXXXXXXXXNVSKARRH 345
            + D    K++LD  N+   +DW  W     L+  ++AA DPW F+  V++ + P  ++SA C+WKL   ++ +  +KK+K +R+AN+SK RRH
Sbjct:   20 LGDVLSKKLSLD--NIPVPQDWVGWLSYTCLKWAVFAAEDPWGFVGHVMMVVGPLFLVSAICSWKLANLLEKEAAEKKQKVRREANISKTRRH 110          
BLAST of Small integral membrane protein 15 vs. TrEMBL
Match: A0A4E0RMW4 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_006438 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 9.641e-9
Identity = 35/73 (47.95%), Postives = 51/73 (69.86%), Query Frame = 1
Query:  127 DWKSWFFQKGLQIVIYAANDPWNFLITVLVFLAPFCMISAYCAWKLVXXXXXXXXXXXXXXXXXXNVSKARRH 345
            +W  WF   GL++VIY A DPW F  TVL+ L P   +SA+CA+KL KE+  +E++KK +AKR A ++K ++H
Sbjct:   22 EWSKWFAYIGLKLVIYVAKDPWGFFATVLIILTPLLGLSAFCAFKLAKEVQRQEEEKKLRAKRSAAIAKRQKH 94          
BLAST of Small integral membrane protein 15 vs. Ensembl Cavefish
Match: smim15 (small integral membrane protein 15 [Source:NCBI gene;Acc:103033273])

HSP 1 Score: 42.743 bits (99), Expect = 6.680e-6
Identity = 29/72 (40.28%), Postives = 48/72 (66.67%), Query Frame = 1
Query:  127 DWKSWFFQKGLQIVIYAANDPWNFLITVLVFLAPFCMISAYCAWKLVXXXXXXXXXXXXXXXXXXNVSKARR 342
            D+K+W       +V +AA DP+ FL TV++ L P  + SA  +WKL K I+ +++++K+K KR  N++KA+R
Sbjct:    3 DFKAW----AEYVVEWAAKDPYGFLTTVILALTPLFIASALLSWKLAKMIEARDREQKKKQKRQENIAKAKR 70          
BLAST of Small integral membrane protein 15 vs. Planmine SMEST
Match: SMESG000017644.1 (SMESG000017644.1)

HSP 1 Score: 163.31 bits (412), Expect = 9.285e-53
Identity = 99/99 (100.00%), Postives = 99/99 (100.00%), Query Frame = 1
Query:   67 MSDETKNKITLDHFNMTEAKDWKSWFFQKGLQIVIYAANDPWNFLITVLVFLAPFCMISAYCAWKLVXXXXXXXXXXXXXXXXXXNVSKARRHSNKKND 363
            MSDETKNKITLDHFNMTEAKDWKSWFFQKGLQIVIYAANDPWNFLITVLVFLAPFCMISAYCAWKLVKEIDHKEKDKKRKAKRDANVSKARRHSNKKND
Sbjct:    1 MSDETKNKITLDHFNMTEAKDWKSWFFQKGLQIVIYAANDPWNFLITVLVFLAPFCMISAYCAWKLVKEIDHKEKDKKRKAKRDANVSKARRHSNKKND 99          
The following BLAST results are available for this feature:
BLAST of Small integral membrane protein 15 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 Small integral membrane protein 15 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 Small integral membrane protein 15 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 Small integral membrane protein 15 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 Small integral membrane protein 15 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 Small integral membrane protein 15 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 Small integral membrane protein 15 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 Small integral membrane protein 15 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A504YWC94.562e-1041.94Uncharacterized protein OS=Fasciola gigantica OX=4... [more]
G7YT921.962e-939.78Small integral membrane protein 15 OS=Clonorchis s... [more]
A0A4S2LY992.277e-938.71Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A0X3Q5N57.278e-936.56Small integral membrane protein 15 OS=Schistocepha... [more]
A0A4E0RMW49.641e-947.95Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
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BLAST of Small integral membrane protein 15 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
smim156.680e-640.28small integral membrane protein 15 [Source:NCBI ge... [more]
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BLAST of Small integral membrane protein 15 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 Small integral membrane protein 15 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 Small integral membrane protein 15 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 Small integral membrane protein 15 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 Small integral membrane protein 15 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000017644.19.285e-53100.00SMESG000017644.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007798 ID=SMED30007798|Name=Small integral membrane protein 15|organism=Schmidtea mediterranea sexual|type=transcript|length=499bp
TTTCTACATTAAACTTCAGCTAGACAAATTGTTATTATAATATTTTAAAT
AATTAAAATTTTTAAAATGAGTGATGAGACTAAGAACAAAATTACTTTAG
ATCATTTTAATATGACAGAAGCTAAAGATTGGAAATCATGGTTTTTTCAA
AAAGGTCTTCAAATAGTAATTTATGCCGCAAATGATCCATGGAATTTTTT
AATTACAGTTCTTGTATTTCTTGCACCATTTTGCATGATAAGTGCATATT
GTGCCTGGAAGTTAGTTAAAGAAATTGATCACAAAGAAAAAGATAAGAAA
CGAAAAGCTAAACGAGATGCCAATGTCTCGAAGGCAAGAAGACACTCTAA
TAAGAAAAATGATTAATTGTGATTGATTTTCTTTTGTGTCTCACTTATTA
ATACTGAAATTCTTTCGGAAATATTTTAAATAATTGTCCAGGAATTTCTG
CAAGCTTATATTTTTTGAATAAAATAAAATTCTTCTTCTGAAATAAAAA
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protein sequence of SMED30007798-orf-1

>SMED30007798-orf-1 ID=SMED30007798-orf-1|Name=SMED30007798-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp
MSDETKNKITLDHFNMTEAKDWKSWFFQKGLQIVIYAANDPWNFLITVLV
FLAPFCMISAYCAWKLVKEIDHKEKDKKRKAKRDANVSKARRHSNKKND*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR027877Smim15
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane