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RPL39L Gene

protein-coding   GIFtS: 46
GCID: GC03M186839

Ribosomal Protein L39-Like

(Previous name: ribosomal protein L39-like 1)
(Previous symbol: RPL39L1)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Ribosomal Protein L39-Like1 2     60S Ribosomal Protein L39-Like2
RPL39L11 2 3     L39-22
Ribosomal Protein L39-Like 11 2     Ribosomal Protein L39-Like Protein2
60S Ribosomal Protein L39-22 3     

External Ids:    HGNC: 170941   Entrez Gene: 1168322   Ensembl: ENSG000001639237   OMIM: 6075475   UniProtKB: Q96EH53   

Export aliases for RPL39L gene to outside databases

Previous GC identifers: GC03M183636 GC03M188095 GC03M188240 GC03M188159 GC03M188321 GC03M184243


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RPL39L Gene:
This gene encodes a protein sharing high sequence similarity with ribosomal protein L39. Although the name of this
gene has been referred to as 'ribosomal protein L39' in the public databases, its official name is 'ribosomal
protein L39-like'. It is not currently known whether the encoded protein is a functional ribosomal protein or
whether it has evolved a function that is independent of the ribosome. (provided by RefSeq, Jul 2008)

GeneCards Summary for RPL39L Gene:
RPL39L (ribosomal protein L39-like) is a protein-coding gene. Diseases associated with RPL39L include cervical squamous cell carcinoma, and cervicitis. GO annotations related to this gene include structural constituent of ribosome. An important paralog of this gene is RPL39.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000003.12  NC_018914.2  NT_005612.17  
Regulatory elements:
   Search for regulatory transcription factor binding sites for RPL39L
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRPL39L promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RPL39L


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q27   Ensembl cytogenetic band:  3q27.3   HGNC cytogenetic band: 3q27.3

RPL39L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPL39L gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M186839:  view genomic region     (about GC identifiers)

Start:
186,838,736 bp from pter      End:
186,898,696 bp from pter
Size:
59,961 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: RL39L_HUMAN, Q96EH5 (See protein sequence)
Recommended Name: 60S ribosomal protein L39-like  
Size: 51 amino acids; 6293 Da
Secondary accessions: Q8IUD0

Explore the universe of human proteins at neXtProt for RPL39L: NX_Q96EH5

REFSEQ proteins: NP_443201.1  
ENSEMBL proteins: 
 ENSP00000397240   ENSP00000296277   ENSP00000389356  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
RPL: L ribosomal proteins

3 InterPro protein domains:
 IPR020083 Ribosomal_L39_CS
 IPR000077 Ribosomal_L39
 IPR023626 Ribosomal_L39e_dom

Graphical View of Domain Structure for InterPro Entry Q96EH5

ProtoNet protein and cluster: Q96EH5

1 Blocks protein domain: IPB000077 Ribosomal protein L39e

UniProtKB/Swiss-Prot: RL39L_HUMAN, Q96EH5
Similarity: Belongs to the ribosomal protein L39e family


RPL39L for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003735structural constituent of ribosome IEA--
     
RPL39L for ontologies           About GeneDecksing


Phenotypes:
     1 GenomeRNAi human phenotype for RPL39L:
 Decreased viability of wild-ty 

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hsa-mir-100-5p (MIRT048437)

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol5
mitochondrion1
nucleus1

Gene Ontology (GO): 3 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005622intracellular ----
GO:0005840ribosome ----
GO:0022625cytosolic large ribosomal subunit NAS12490704

RPL39L for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RPL39L
Interactions:

    Search GeneGlobe Interaction Network for RPL39L

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for RPL39L (ENSP000002962774) via UniProtKB, MINT, STRING, and/or I2D (see all 136)
InteractantInteraction Details
GeneCardExternal ID(s)
RPL5ENSP000003593454STRING: ENSP00000359345
RPL18ENSP000000847954STRING: ENSP00000084795
RPL30ENSP000002870384STRING: ENSP00000287038
RPL35ENSP000002594694STRING: ENSP00000259469
RPL11ENSP000003636764STRING: ENSP00000363676
About this table

Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006412translation IEA--
GO:0007283spermatogenesis IEP12490704

RPL39L for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for RPL39L (RL39L)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for RPL39L gene: 
NM_052969.1  

Unigene Cluster for RPL39L:

Ribosomal protein L39-like
Hs.647900  [show with all ESTs]
Unigene Representative Sequence: BQ216858
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000455270 ENST00000296277(uc003fre.1) ENST00000433055
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Additional mRNA sequence: 

AB063610.1 AF548529.1 BC012328.1 L05096.1 

6 DOTS entries:

DT.91667170  DT.120840364  DT.100750125  DT.100807522  DT.99984622  DT.100741480 

Selected AceView cDNA sequences (see all 49):

BX281758 BQ430980 BI850392 AF548529 CR603001 AA603655 BQ219675 AA460213 
AB063610 AW571519 BU543807 L05096 CD248852 BI462659 BF972493 CD048049 
BE895146 BQ014271 BF037216 AL558328 BM769958 BE875914 BG339821 BG030062 

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for RPL39L    About this scheme

ExUns: 1a · 1b ^ 2 ^ 3a · 3b
SP1:                              
SP2:              -               


ECgene alternative splicing isoforms for RPL39L

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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RPL39L expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
RPL39L Expression
About this image


RPL39L expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 5) fully expand
 
 Testis (Reproductive System)    fully expand to see all 4 entries
         XY Germ Cells Testis Cord
         Testis Interstitium
 
 Dermis (Integumentary System)    fully expand to see all 2 entries
         Zigzag Dermal Papilla Cells Dermal Papilla
 
 Gonad
         XY Germ Cells Testis Cord
 
 Ovary (Reproductive System)
         XX Germ Cells Ovigerous Cord
 
 Adipose (Muscoskeletal System)
         Interscapular Brown Adipose Depot
RPL39L Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.647900

UniProtKB/Swiss-Prot: RL39L_HUMAN, Q96EH5
Tissue specificity: Testis specific

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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for RPL39L gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Rpl39l5 ribosomal protein L39-like   --   16 (5.49 cM) 10170226 
chicken
(Gallus gallus)
Aves RPL396
Gallus gallus ribosomal protein L39 (RPL39), mRNA....
92(a)
1 → many
4(16462841-16465105)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
90(a)
1 → many
GL343950.1(105208-107407)
zebrafish
(Danio rerio)
Actinopterygii rpl396
ribosomal protein L39
90(a)
1 → many
14(34306764-34309051) ENSDARG00000036316
fruit fly
(Drosophila melanogaster)
Insecta RpL396
Ribosomal protein L39
65(a)
1 → many
2R(19949376-19949952)
worm
(Caenorhabditis elegans)
Secernentea rpl-396
Protein RPL-39 (rpl-39) mRNA, complete cds
69(a)
1 → many
V(7775738-7776086) WBGene00004453
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPL396
Protein component of the large (60S) ribosomal sub...
55(a)
1 → many
X(75933-76474) YJL189W


ENSEMBL Gene Tree for RPL39L (if available)
TreeFam Gene Tree for RPL39L (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for RPL39L gene
RPL392  
2 SIMAP similar genes for RPL39L using alignment to 1 protein entry:     RL39L_HUMAN:
RPL39    RPL39P5

RPL39L for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for RPL39L (see all 396)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 3 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1444931771,2
--186838289(+) GCTTTA/CTACGC 1 -- int10--------
rs1466742071,2
--186838292(+) TTCTAC/TGCTCT 1 -- int10--------
rs1166251751,2
C,F--186838305(+) CCAGCT/CCCTTT 1 -- int11Minor allele frequency- C:0.01NA 120
rs1390929351,2
--186838309(+) CTCCTG/TTCTAT 1 -- int10--------
rs738883561,2
C,F--186838311(+) CCTTTC/TTATGC 1 -- int12Minor allele frequency- T:0.11WA 120
rs1861923601,2
--186838432(+) TGACTC/TGTGCC 1 -- int10--------
rs1914342971,2
--186838494(+) AGTGGG/TTCTCC 1 -- int10--------
rs1832195321,2
--186838576(+) TTATAC/TATCTG 1 -- int10--------
rs1440663541,2
--186838601(+) CATCTA/CTCCCT 1 -- int10--------
rs68015531,2
C,F,A,H--186838657(+) CATTAC/TCCAGG 1 -- int117Minor allele frequency- T:0.25NA EA NS WA CSA 1685

HapMap Linkage Disequilibrium report for RPL39L (186838736 - 186898696 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for RPL39L:    About this table    
Variant IDTypeSubtypePubMed ID
nsv4157CNV Insertion18451855
nsv878073CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing RPL39L
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 607547    OMIM disorders: --

3 diseases for RPL39L:    
About MalaCards
cervical squamous cell carcinoma    cervicitis    squamous cell carcinoma


RPL39L for disorders           About GeneDecksing


Export disorders for RPL39L gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for RPL39L gene integrated from 10 sources:
(articles sorted by number of sources associating them with RPL39L)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  2. Functional second genes generated by retrotransposition of the X- linked ribosomal protein genes. (PubMed id 12490704)1, 2 Uechi T.... Kenmochi N. (Nucleic Acids Res. 2002)
  3. A human gene encoding a protein homologous to ribosomal protein L39 is normally expressed in the testis and derepressed in multiple cancer cells. (PubMed id 12359333)1, 2 Nadano D.... Sato T.-A. (Biochim. Biophys. Acta 2002)
  4. The protein interaction landscape of the human CMGC kinase group. (PubMed id 23602568)1 Varjosalo M....Gstaiger M. (Cell Rep 2013)
  5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
  6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  7. (PubMed id )2 

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 116832 HGNC: 17094 AceView: RPL39L Ensembl:ENSG00000163923 euGenes: HUgn116832
ECgene: RPL39L H-InvDB: RPL39L

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for RPL39L Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for RPL39L gene:
Search GeneIP for patents involving RPL39L

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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