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	Gene Summary
	Translation studies in PubMed
	Exon Skipping Events
	Expression
	Expression Regulation
	Associated Genes
	Protein 3D Structure
	Protein-Protein Interaction
	Mutations
	Prognostic Analysis
	Gender Association
	Age Association
	Related Drugs
	Related Diseases

Translation Factor: RPL39 (NCBI Gene ID:6170)

Gene Summary

Gene Summary

Gene Information	Gene Name: RPL39
	Gene ID: 6170
	Gene Symbol	RPL39
	Gene ID	6170
	Gene Name	ribosomal protein L39
	Synonyms	L39\|RPL39P42\|RPL39_23_1806
	Cytomap	Xq24
	Type of Gene	protein-coding
	Description	60S ribosomal protein L39large ribosomal subunit protein eL39
	Modification date	20200313
	UniProtAcc	P62891

Child GO biological process term(s) under GO:0006412

GO ID	GO term
GO:0005840	Ribosome
GO:0002181	Cytoplasmic translation
GO:0006412	Translation

Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	RPL39	GO:0002181	cytoplasmic translation	25957688
Hgene	RPL39	GO:0002227	innate immune response in mucosa	12860195
Hgene	RPL39	GO:0019731	antibacterial humoral response	12860195
Hgene	RPL39	GO:0050830	defense response to Gram-positive bacterium	12860195
Hgene	RPL39	GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide	12860195

Inferred gene age of translation factor.

Gene	Inferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
RPL39	>1119.25

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Translation Studies in PubMed

We searched PubMed using 'RPL39[title] AND translation [title] AND human.'

Gene	Title	PMID
RPL39	.	.

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Exon Skipping Events

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
For more annotations, please visit our ExonSkipDB.

Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	ORF
ENST00000361575	118923870	118923974	Frame-shift

Exon skipping position in the amino acid sequence.

ENST

Exon skip start (DNA)

Exon Skip end (DNA)

Len(transcript seq)

Exon skip start (mRNA)

Exon Skip end (mRNA)

Len(amino acid seq)

Exon skip start (AA)

Exon Skip end (AA)

Potentially (partially) lost protein functional features of UniProt.

UniProtAcc

Exon skip start (AA)

Exon Skip end (AA)

Function feature start (AA)

Function feature end (AA)

Functional feature type

Functional feature desc.

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Expression

Gene expression level across TCGA pancancer

Gene expression level across GTEx pantissue

Expression level of gene isoforms across TCGA pancancer

Expression level of gene isoforms across GTEx pantissue

Cancer(tissue) type-specific expression level of Translation factor using z-score distriution

Differential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)

Cancer type	Translation factor	FC	adj.pval
BRCA	RPL39	-1.41219628848121	0.00163371967664225
LUSC	RPL39	-2.23543914303094	0.00457577784727754
PRAD	RPL39	-2.63448396305036	0.0291755363147523
THCA	RPL39	-1.21516043459116	0.0375744128896741

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Expression Regulation

Translation factor expression regulation through miRNA binding

Cancer type

Gene

miRNA

TargetScan binding score (Context++ score percentile)

Coefficient

Pvalue

Translation factor expression regulation through methylation in the promoter of Translation factor

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through copy number variation of Translation factor

Cancer type	Gene	Coefficient	Pvalue
ESCA	RPL39	-0.019790999	0.011398417

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with RPL39 (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)

Cancer type	Gene group	Translation factor	Correlated gene	Coefficient	Pvalue
DLBC	Cell metabolism gene	RPL39	TBCA	0.805396971	5.12E-12
DLBC	Cell metabolism gene	RPL39	POLD4	0.807423631	4.12E-12
DLBC	Cell metabolism gene	RPL39	B3GAT3	0.815584695	1.67E-12
DLBC	Cell metabolism gene	RPL39	PSMB3	0.818534194	1.19E-12
DLBC	Cell metabolism gene	RPL39	PHKG2	0.822820956	7.23E-13
DLBC	Cell metabolism gene	RPL39	GEMIN7	0.830707968	2.78E-13
DLBC	Cell metabolism gene	RPL39	PGLS	0.854686227	1.09E-14
DLBC	Cell metabolism gene	RPL39	FAU	0.881385076	1.38E-16
DLBC	Cell metabolism gene	RPL39	PFDN5	0.886360129	5.43E-17
DLBC	CGC	RPL39	SDHAF2	0.809871391	3.16E-12
DLBC	Epifactor	RPL39	TAF10	0.80714357	4.24E-12
DLBC	Epifactor	RPL39	DMAP1	0.807868133	3.92E-12
DLBC	Epifactor	RPL39	ZNHIT1	0.811190293	2.73E-12
DLBC	Epifactor	RPL39	PPP4C	0.813204488	2.18E-12
DLBC	IUPHAR	RPL39	ATG4B	0.80308193	6.54E-12
DLBC	IUPHAR	RPL39	SIRT3	0.804277912	5.76E-12
DLBC	IUPHAR	RPL39	PHKG2	0.822820956	7.23E-13
DLBC	Kinase	RPL39	PHKG2	0.822820956	7.23E-13
DLBC	TF	RPL39	THAP7	0.809368248	3.33E-12
DLBC	TF	RPL39	THAP3	0.821577739	8.37E-13
DLBC	TSG	RPL39	TSSC4	0.801377859	7.82E-12
DLBC	TSG	RPL39	SIRT3	0.804277912	5.76E-12
DLBC	TSG	RPL39	GADD45GIP1	0.832627616	2.18E-13
DLBC	TSG	RPL39	GNB2L1	0.840660806	7.72E-14
GBM	Cell metabolism gene	RPL39	NME2	0.801569687	8.09E-40
GBM	Cell metabolism gene	RPL39	PFDN5	0.809221438	4.06E-41
GBM	Cell metabolism gene	RPL39	SEC61B	0.817359782	1.45E-42
GBM	Cell metabolism gene	RPL39	PIGC	0.819837809	5.07E-43
GBM	Cell metabolism gene	RPL39	PSMB4	0.829965914	5.88E-45
GBM	Cell metabolism gene	RPL39	LSM1	0.832571336	1.78E-45
GBM	Cell metabolism gene	RPL39	PSMA5	0.841745248	2.24E-47
GBM	Cell metabolism gene	RPL39	SSR2	0.843456093	9.59E-48
GBM	Cell metabolism gene	RPL39	SNRPG	0.844178222	6.69E-48
GBM	Cell metabolism gene	RPL39	SSR4	0.872175081	1.14E-54
GBM	TF	RPL39	NME2	0.801569687	8.09E-40
GBM	TSG	RPL39	GAS5	0.803000037	4.67E-40
KIRP	Cell metabolism gene	RPL39	PFDN5	0.800327376	2.69E-73
KIRP	Cell metabolism gene	RPL39	FAU	0.827411371	1.97E-82
KIRP	Cell metabolism gene	RPL39	SNRPD2	0.841882976	5.41E-88
MESO	Cell metabolism gene	RPL39	FAU	0.814138203	9.05E-22
PCPG	Cell metabolism gene	RPL39	PFDN5	0.837157519	2.32E-50
PRAD	Cell metabolism gene	RPL39	FAU	0.800149963	9.47E-124
PRAD	Cell metabolism gene	RPL39	SNRPD2	0.829581815	8.57E-141
PRAD	Epifactor	RPL39	FBL	0.814879198	6.73E-132
PRAD	TSG	RPL39	GNB2L1	0.812031547	2.88E-130
THYM	Cell metabolism gene	RPL39	TIMM9	0.801503628	1.44E-28
THYM	Cell metabolism gene	RPL39	TIMM50	0.801650816	1.39E-28
THYM	Cell metabolism gene	RPL39	SSR2	0.802159383	1.21E-28
THYM	Cell metabolism gene	RPL39	TOMM7	0.803228028	9.03E-29
THYM	Cell metabolism gene	RPL39	POLR2J	0.805428015	4.93E-29
THYM	Cell metabolism gene	RPL39	PFDN5	0.807173149	3.04E-29
THYM	Cell metabolism gene	RPL39	ITPA	0.807815107	2.54E-29
THYM	Cell metabolism gene	RPL39	POLR2F	0.808826063	1.91E-29
THYM	Cell metabolism gene	RPL39	PSMB7	0.810393713	1.23E-29
THYM	Cell metabolism gene	RPL39	ACOT8	0.810891269	1.06E-29
THYM	Cell metabolism gene	RPL39	SNRPD2	0.81259113	6.53E-30
THYM	Cell metabolism gene	RPL39	EBP	0.815196829	3.06E-30
THYM	Cell metabolism gene	RPL39	POLR2I	0.818024874	1.33E-30
THYM	Cell metabolism gene	RPL39	WBSCR22	0.81821588	1.26E-30
THYM	Cell metabolism gene	RPL39	SLC27A5	0.822270841	3.69E-31
THYM	Cell metabolism gene	RPL39	GEMIN6	0.826594961	9.66E-32
THYM	Cell metabolism gene	RPL39	FAU	0.831292045	2.16E-32
THYM	Cell metabolism gene	RPL39	PSMC1	0.838964868	1.68E-33
THYM	Cell metabolism gene	RPL39	POLR2H	0.839023544	1.65E-33
THYM	Cell metabolism gene	RPL39	DPM3	0.840790176	8.99E-34
THYM	Cell metabolism gene	RPL39	TIMM8B	0.864304518	1.28E-37
THYM	CGC	RPL39	COX6C	0.814026158	4.31E-30
THYM	Epifactor	RPL39	SIRT6	0.802694232	1.04E-28
THYM	Epifactor	RPL39	BRMS1	0.807365339	2.88E-29
THYM	Epifactor	RPL39	ZNHIT1	0.814148677	4.16E-30
THYM	IUPHAR	RPL39	SIRT6	0.802694232	1.04E-28
THYM	IUPHAR	RPL39	SLC27A5	0.822270841	3.69E-31
THYM	TSG	RPL39	SIRT6	0.802694232	1.04E-28
THYM	TSG	RPL39	BRMS1	0.807365339	2.88E-29
THYM	TSG	RPL39	ST20	0.818055382	1.32E-30
THYM	TSG	RPL39	NPRL2	0.822149036	3.83E-31
THYM	TSG	RPL39	GADD45GIP1	0.826033739	1.15E-31
UCEC	Cell metabolism gene	RPL39	PFDN5	0.828299155	5.84E-52
UCS	Cell metabolism gene	RPL39	TIMM9	0.801503628	1.44E-28
UCS	Cell metabolism gene	RPL39	TIMM50	0.801650816	1.39E-28
UCS	Cell metabolism gene	RPL39	SSR2	0.802159383	1.21E-28
UCS	Cell metabolism gene	RPL39	TOMM7	0.803228028	9.03E-29
UCS	Cell metabolism gene	RPL39	POLR2J	0.805428015	4.93E-29
UCS	Cell metabolism gene	RPL39	PFDN5	0.807173149	3.04E-29
UCS	Cell metabolism gene	RPL39	ITPA	0.807815107	2.54E-29
UCS	Cell metabolism gene	RPL39	POLR2F	0.808826063	1.91E-29
UCS	Cell metabolism gene	RPL39	PSMB7	0.810393713	1.23E-29
UCS	Cell metabolism gene	RPL39	ACOT8	0.810891269	1.06E-29
UCS	Cell metabolism gene	RPL39	SNRPD2	0.81259113	6.53E-30
UCS	Cell metabolism gene	RPL39	EBP	0.815196829	3.06E-30
UCS	Cell metabolism gene	RPL39	POLR2I	0.818024874	1.33E-30
UCS	Cell metabolism gene	RPL39	WBSCR22	0.81821588	1.26E-30
UCS	Cell metabolism gene	RPL39	SLC27A5	0.822270841	3.69E-31
UCS	Cell metabolism gene	RPL39	GEMIN6	0.826594961	9.66E-32
UCS	Cell metabolism gene	RPL39	FAU	0.831292045	2.16E-32
UCS	Cell metabolism gene	RPL39	PSMC1	0.838964868	1.68E-33
UCS	Cell metabolism gene	RPL39	POLR2H	0.839023544	1.65E-33
UCS	Cell metabolism gene	RPL39	DPM3	0.840790176	8.99E-34
UCS	Cell metabolism gene	RPL39	TIMM8B	0.864304518	1.28E-37
UCS	CGC	RPL39	COX6C	0.814026158	4.31E-30
UCS	Epifactor	RPL39	SIRT6	0.802694232	1.04E-28
UCS	Epifactor	RPL39	BRMS1	0.807365339	2.88E-29
UCS	Epifactor	RPL39	ZNHIT1	0.814148677	4.16E-30
UCS	IUPHAR	RPL39	SIRT6	0.802694232	1.04E-28
UCS	IUPHAR	RPL39	SLC27A5	0.822270841	3.69E-31
UCS	TSG	RPL39	SIRT6	0.802694232	1.04E-28
UCS	TSG	RPL39	BRMS1	0.807365339	2.88E-29
UCS	TSG	RPL39	ST20	0.818055382	1.32E-30
UCS	TSG	RPL39	NPRL2	0.822149036	3.83E-31
UCS	TSG	RPL39	GADD45GIP1	0.826033739	1.15E-31
UVM	Cell metabolism gene	RPL39	FAU	0.803736535	2.87E-19
UVM	TSG	RPL39	GLTSCR2	0.817270155	2.33E-20

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Protein structure

Protein 3D structure
Visit iCn3D.

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Protein-Protein Interaction

Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

Overlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

* Edge colors based on TCGA cancer types.

* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))

Cancer type	Translation factor	Interacting protein coding gene	FC	adj.pval
KIRP	RPL39	RPL18A	-1.51651392808885	0.00016188295558095
KICH	RPL39	RPS27A	1.75396693785956	0.000187873840332031
KIRP	RPL39	RPS16	-1.35957043617517	0.00019507110118866
COAD	RPL39	RPS3	1.48730375143014	0.000411599874496461
KIRP	RPL39	RPS11	-1.01861570565103	0.00105937570333481
LIHC	RPL39	RPL8	-4.84588284974558	0.00110314154326131
PRAD	RPL39	RPL18A	1.40600175748499	0.00205137828390396
KICH	RPL39	RPL19	1.36901182894089	0.00250792503356934
KICH	RPL39	RPS12	1.26997381758431	0.00308787822723389
LUAD	RPL39	RPL19	-1.31398026615725	0.00993159558412698
THCA	RPL39	RPS16	-6.16322798156577	0.0115764821363307
BLCA	RPL39	RPS12	-1.47804673440421	0.0204124450683594
BLCA	RPL39	RPS27A	-1.04747470069188	0.0258216857910156
HNSC	RPL39	RPS3	-4.73505819095135	0.0273726439852453
COAD	RPL39	RPS11	1.35307548998204	0.0312207043170929
LUSC	RPL39	RPL19	-2.14669889516666	0.044366810398747
KIRC	RPL39	RPL19	-2.73485271276676	1.33980982873695e-10
BRCA	RPL39	RPS12	-4.91239327478244	1.85340619742495e-09
KIRP	RPL39	RPL37	-1.17421621947139	2.26888805627823e-05
KIRC	RPL39	RPL35	-1.06475238059392	2.72286325678163e-08
KIRC	RPL39	RPL8	-1.18252459971773	5.64962994208288e-07
KIRP	RPL39	RPL8	-1.53003692350119	6.0301274061203e-05
KIRC	RPL39	RPS16	-1.66149869889384	7.8509870430991e-09
BRCA	RPL39	RPS27A	-4.28512148200424	7.8788217967112e-14
KIRC	RPL39	RPL37	-2.87198822058464	8.03913394748564e-12
KIRP	RPL39	RPL35	-1.52981101975496	9.0546440333128e-05
KIRC	RPL39	RPS3	-1.29560847926387	9.05905681935088e-10
KIRC	RPL39	RPL18A	-4.43079304960843	9.2516163152192e-11

Protein-protein interactors with this translation factor (BIOGRID-3.4.160)

PPI interactors with RPL39

IMPACT, HNRNPA2B1, ARAF, BUB1B, RPL37A, CDC5L, FTSJ3, PABPC1, PABPC4, RPL23, RPL32, RPL35A, RPL3L, RPL9, RPS15, RPS18, RPS3A, RPS4X, RPS9, HIST1H3E, RBM3, AEBP2, ASXL1, LCOR, E2F6, L3MBTL4, SUV39H2, TRIP12, ZNF211, RBBP7, RNF31, TNF, ESR2, MEPCE, LARP7, LAMP1, CDK7, FBL, GSK3B, RPS6, HIST1H3A, CANX, PHB, IRF2, OAS3, P2RY6, VMP1, ITFG1, TEX101, PLEKHA4, E, ZC3H18, AXL, CAMK2A, DUSP6, GRB7, PTPN6, SOCS1, ERCC6, N, Apc2, ATG7, ZBTB2, PER2, KLF12, CPEB1, KLF15, KLF16, KLF5, KLF8, NKX2-5, SOX2, SOX5, TLX2,

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Mutations

Clinically associated variants from ClinVar.

Gene

Chr

Position

RefSeq

VarSeq

RefSeeq

VarType

Pathogenic

Disease

VarInfo

nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.

SNVs and Indels

Gene	Cancer type	Chromosome	Start	End	RefSeeq	MutSeq	Mutation type	AAchange	# samples
RPL39	UCEC	chrX	118923917	118923917	G	A	Missense_Mutation	p.R21C	4
RPL39	UCEC	chrX	118923932	118923932	T	C	Missense_Mutation	p.K16E	3
RPL39	HNSC	chrX	118920696	118920696	C	T	Splice_Site		2
RPL39	UCEC	chrX	118920674	118920674	A	T	Missense_Mutation	p.H43Q	2
RPL39	UCEC	chrX	118923897	118923897	A	G	Silent	p.S75P	2
RPL39	UCEC	chrX	118923906	118923906	G	T	Silent	p.P72T	2
RPL39	COAD	chrX	118923899	118923899	T	C	Missense_Mutation	p.I27V	1
RPL39	GBM	chrX	118923963	118923963	C	A	Missense_Mutation		1
RPL39	SKCM	chrX	118923891	118923891	C	T	Missense_Mutation	p.M29I	1
RPL39	SKCM	chrX	118923942	118923942	G	A	Silent	p.F12F	1
RPL39	ACC	chrX	118923904	118923904	T	A	Missense_Mutation	p.Q25L	1
RPL39	CESC	chrX	118920604	118920604	C	A	RNA	NULL	1
RPL39	CESC	chrX	118921285	118921285	C	T	RNA	NULL	1

Copy number variation (CNV) of RPL39
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across RPL39
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion genes with this translation factor from FusionGDB2.0.

FusionGDB2 ID	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
102363	N/A	BF848943	FKTN	chr9	108401945	-	RPL39	chrX	118920621	-
94976	N/A	BE737974	RPL39	chrX	118920470	-	EP300	chr22	41526529	+
97338	STAD	TCGA-HU-A4GT-01A	RPL39	chrX	118923871	-	UBE2K	chr4	39776454	+
102832	N/A	EC560994	RPL39	chrX	118923906	-	ZNF195	chr11	3362676	-
102363	PCPG	TCGA-QT-A5XO-01A	SEPT6	chrX	118763281	-	RPL39	chrX	118923974	-
102363	UCS	TCGA-N7-A4Y8-01A	SEPT6	chrX	118797445	-	RPL39	chrX	118923974	-
102363	ESCA	TCGA-IG-A3YC	ZNF558	chr19	8941994	-	RPL39	chrX	118923974	-

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Prognostic Analysis

Kaplan-Meier plots with logrank tests of overall survival (OS)

Cancer type	Translation factor	Coefficent	Hazard ratio	Wald test pval	Likelihool ratio pval	Logrank test pval	# samples
LGG	RPL39	1.26787142115798	0.237339448001159	0.000168824592934211	0.000234293743802644	0.000172482840070709	525
PAAD	RPL39	1.26160672928739	0.2323860905835	0.004688720883585	0.00292756296537792	0.00467589017412838	182
PAAD	RPL39	1.26160672928739	0.2323860905835	0.004688720883585	0.00292756296537792	0.00467589017412838	182
THCA	RPL39	0.641058184198087	-0.444635055201048	0.0177843331704986	0.0259855759321053	0.01764622324964	571
THCA	RPL39	0.641058184198087	-0.444635055201048	0.0177843331704986	0.0259855759321053	0.01764622324964	571
BRCA	RPL39	0.889763340364418	-0.116799761319106	0.0332665041460413	0.038377885873054	0.0335052777137057	1200
DLBC	RPL39	0.440465935765211	-0.819922167435563	0.0411611939955509	0.0316412042018833	0.0378538198002674	47
DLBC	RPL39	0.440465935765211	-0.819922167435563	0.0411611939955509	0.0316412042018833	0.0378538198002674	47
GBM	RPL39	1.2538120787838	0.226188573551797	4.0077478923352e-05	3.62230118353673e-05	3.5186178626529e-05	165

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Translation factor and Gender

Differential gene expression between female and male. (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
KIRC	RPL39	0.00122456349811706	0.034
MESO	RPL39	0.00869009974501628	0.23
ACC	RPL39	0.0113106635748959	0.29
SARC	RPL39	0.0200234036484706	0.5
LIHC	RPL39	0.039780119853517	0.95

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Translation factor and Age

Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
LUSC	RPL39	0.0184363286320384	0.59
LAML	RPL39	0.0209316393192472	0.65
BRCA	RPL39	0.00814431886987825	0.27

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Related Drugs

Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases

Diseases associated with this translation factor.
(DisGeNet 4.0)

Disease ID

Disease Name

# PubMeds

Disease source