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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RPL3L |
Basic gene info. | Gene symbol | RPL3L |
Gene name | ribosomal protein L3-like | |
Synonyms | - | |
Cytomap | UCSC genome browser: 16p13.3 | |
Genomic location | chr16 :1994579-2004679 | |
Type of gene | protein-coding | |
RefGenes | NM_005061.2, | |
Ensembl id | ENSG00000140986 | |
Description | 60S ribosomal protein L3-like | |
Modification date | 20141207 | |
dbXrefs | HGNC : HGNC | |
HPRD : 17998 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RPL3L | |
BioGPS: 6123 | ||
Gene Expression Atlas: ENSG00000140986 | ||
The Human Protein Atlas: ENSG00000140986 | ||
Pathway | NCI Pathway Interaction Database: RPL3L | |
KEGG: RPL3L | ||
REACTOME: RPL3L | ||
ConsensusPathDB | ||
Pathway Commons: RPL3L | ||
Metabolism | MetaCyc: RPL3L | |
HUMANCyc: RPL3L | ||
Regulation | Ensembl's Regulation: ENSG00000140986 | |
miRBase: chr16 :1,994,579-2,004,679 | ||
TargetScan: NM_005061 | ||
cisRED: ENSG00000140986 | ||
Context | iHOP: RPL3L | |
cancer metabolism search in PubMed: RPL3L | ||
UCL Cancer Institute: RPL3L | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for RPL3L(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: RPL3L |
Familial Cancer Database: RPL3L |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
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REACTOME_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: RPL3L |
MedGen: RPL3L (Human Medical Genetics with Condition) | |
ClinVar: RPL3L | |
Phenotype | MGI: RPL3L (International Mouse Phenotyping Consortium) |
PhenomicDB: RPL3L |
Mutations for RPL3L |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPL3L related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
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Stat. for Non-Synonymous SNVs (# total SNVs=41) | (# total SNVs=18) |
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(# total SNVs=0) | (# total SNVs=0) |
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* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr16:1997368-1997368 | p.P172L | 2 |
chr16:1997244-1997244 | p.Q213Q | 2 |
chr16:1996721-1996721 | p.R286C | 2 |
chr16:2004105-2004105 | p.F16F | 2 |
chr16:1995845-1995845 | p.T346T | 2 |
chr16:1997070-1997070 | p.L240M | 2 |
chr16:1994852-1994852 | p.S404A | 2 |
chr16:1997089-1997089 | p.S233R | 2 |
chr16:1995929-1995929 | p.G318G | 1 |
chr16:1996982-1996982 | p.A269V | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 1 |   | 8 | 1 |   | 2 |   | 2 |   |   | 6 | 1 |   |   |   | 4 | 3 |   | 7 |
# mutation | 1 | 1 |   | 8 | 1 |   | 2 |   | 2 |   |   | 7 | 1 |   |   |   | 4 | 3 |   | 7 |
nonsynonymous SNV | 1 | 1 |   | 6 | 1 |   | 1 |   | 2 |   |   | 4 | 1 |   |   |   | 3 | 1 |   | 3 |
synonymous SNV |   |   |   | 2 |   |   | 1 |   |   |   |   | 3 |   |   |   |   | 1 | 2 |   | 4 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr16:1996721 | p.R286C | 2 |
chr16:1997325 | p.R268W | 1 |
chr16:2004054 | p.R24R | 1 |
chr16:1994859 | p.T400T | 1 |
chr16:1996644 | p.H258Q | 1 |
chr16:1997346 | p.H19Y | 1 |
chr16:2004081 | p.Q383R | 1 |
chr16:1994862 | p.K250N | 1 |
chr16:1996698 | p.V353A | 1 |
chr16:1997365 | p.G187D | 1 |
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* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
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cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for RPL3L |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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C1QTNF9B,CT45A1,CT45A3,DHRS2,FRG2B,GABPB1,HGC6.3, LOC643008,MAGEA8,MAGEB18,MAGEB2,RGS5,RPL3L,SPPL2A, SUMO2,TYRP1,UGT2B10,UGT2B15,USP29,USP8,ZIM3 | ACTA1,ATP2A1,MIR1-1HG,CKM,CSRP3,LMOD2,LOC151300, MYBPC2,MYH2,MYH6,MYH7,MYL1,MYL2,MYLPF, NEB,NRAP,OR5H15,P2RX6P,PPP1R3A,RPL3L,XIRP2 |
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PPP1R17,LINC00588,CACNG7,CER1,CHRNA4,CPLX3,FAM27L, LHX3,PAQR9,RBMY1A3P,RPL3L,SHISA7,SLC1A6,SLC6A5, TFAP2D,TSPY1,TSPY4,UNCX | ACTBL2,LINC00596,SCP2D1,DUOX1,FAM74A1,FAM92A1P2,FLJ25758, GAL,HELT,KRTAP13-1,LY6D,MCHR1,OR1J2,PFN3, PRAMEF12,RBMXL3,RPL3L,SNORA64,SNORA74A,tAKR,TM4SF19, TRIM42,USP26,VWCE,X |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Pharmacological Information for RPL3L |
There's no related Drug. |
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Cross referenced IDs for RPL3L |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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