Human Gene RPL4 (uc002apv.3)
  Description: Homo sapiens ribosomal protein L4 (RPL4), mRNA.
RefSeq Summary (NM_000968): Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L4E family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr15:66,791,653-66,797,193 Size: 5,541 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr15:66,791,745-66,797,128 Size: 5,384 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:66,791,653-66,797,193)mRNA (may differ from genome)Protein (427 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RL4_HUMAN
DESCRIPTION: RecName: Full=60S ribosomal protein L4; AltName: Full=60S ribosomal protein L1;
SUBUNIT: May bind IPO9 with low affinity. Interacts with RBM3 (By similarity).
SIMILARITY: Belongs to the ribosomal protein L4P family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1017.05 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 19870.86 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -21.5065-0.331 Picture PostScript Text
3' UTR -13.0092-0.141 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR025755 - Ribos_L4_C_dom
IPR002136 - Ribosomal_L4/L1e
IPR013000 - Ribosomal_L4/L1e_euk/arc_CS
IPR023574 - Ribosomal_L4_dom

Pfam Domains:
PF00573 - Ribosomal protein L4/L1 family
PF14374 - 60S ribosomal protein L4 C-terminal domain

SCOP Domains:
52166 - Ribosomal protein L4

ModBase Predicted Comparative 3D Structure on P36578
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding

Biological Process:
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0006413 translational initiation
GO:0006614 SRP-dependent cotranslational protein targeting to membrane

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005791 rough endoplasmic reticulum
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0022625 cytosolic large ribosomal subunit
GO:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  BC009888 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone MGC:16528 IMAGE:4025800), complete cds.
BC010151 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone MGC:19674 IMAGE:3353592), complete cds.
BC001365 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone MGC:2201 IMAGE:3051487), complete cds.
BC018840 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone IMAGE:3051153).
AK291117 - Homo sapiens cDNA FLJ78445 complete cds, highly similar to Homo sapiens ribosomal protein L4 (RPL4), mRNA.
BC014653 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone MGC:20247 IMAGE:4636179), complete cds.
BC095427 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone MGC:110964 IMAGE:30711782), complete cds.
BC066925 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone MGC:87190 IMAGE:5259747), complete cds.
AK298224 - Homo sapiens cDNA FLJ51018 complete cds, highly similar to 60S ribosomal protein L4.
L20868 - Homo sapiens ribosomal protein L4 (RPL4) mRNA, complete cds.
BC007996 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone MGC:15373 IMAGE:3546003), complete cds.
BC007259 - Homo sapiens cDNA clone IMAGE:3050317, **** WARNING: chimeric clone ****.
AK297490 - Homo sapiens cDNA FLJ50996 complete cds, highly similar to 60S ribosomal protein L4.
AK125772 - Homo sapiens cDNA FLJ43784 fis, clone TESTI2051867, highly similar to 60S ribosomal protein L4.
BC030000 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone IMAGE:5110884).
AK223057 - Homo sapiens mRNA for ribosomal protein L4 variant, clone: KAT00378.
BC005817 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone MGC:11073 IMAGE:3688641), complete cds.
BC001010 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone IMAGE:2961234).
BC040610 - Homo sapiens ribosomal protein L4, mRNA (cDNA clone IMAGE:3897039).
BC002450 - Homo sapiens cDNA clone IMAGE:3344612, **** WARNING: chimeric clone ****.
AK297484 - Homo sapiens cDNA FLJ50994 complete cds, moderately similar to 60S ribosomal protein L4.
AB208977 - Homo sapiens mRNA for ribosomal protein L4 variant protein.
AK130784 - Homo sapiens cDNA FLJ27274 fis, clone TMS00767, highly similar to 60S ribosomal protein L4.
AK291859 - Homo sapiens cDNA FLJ78454 complete cds, highly similar to Homo sapiens ribosomal protein L4 (RPL4), mRNA.
D23660 - Homo sapiens mRNA for ribosomal protein, complete cds.
DQ892189 - Synthetic construct clone IMAGE:100004819; FLH183868.01X; RZPDo839H06142D ribosomal protein L4 (RPL4) gene, encodes complete protein.
KJ892022 - Synthetic construct Homo sapiens clone ccsbBroadEn_01416 RPL4 gene, encodes complete protein.
DQ895383 - Synthetic construct Homo sapiens clone IMAGE:100009843; FLH183864.01L; RZPDo839H06141D ribosomal protein L4 (RPL4) gene, encodes complete protein.
AB463231 - Synthetic construct DNA, clone: pF1KB3433, Homo sapiens RPL4 gene for ribosomal protein L4, without stop codon, in Flexi system.
DQ570914 - Homo sapiens piRNA piR-31026, complete sequence.
AK294113 - Homo sapiens cDNA FLJ56689 complete cds, highly similar to 60S ribosomal protein L4.
DQ578787 - Homo sapiens piRNA piR-46899, complete sequence.
CU675891 - Synthetic construct Homo sapiens gateway clone IMAGE:100019347 5' read RPL4 mRNA.
JD544472 - Sequence 525496 from Patent EP1572962.
JD180811 - Sequence 161835 from Patent EP1572962.
JD420874 - Sequence 401898 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03010 - Ribosome

Reactome (by CSHL, EBI, and GO)

Protein P36578 (Reactome details) participates in the following event(s):

R-HSA-72672 The 60S subunit joins the translation initiation complex
R-HSA-156826 Dissociation of L13a from the 60s ribosomal subunit
R-HSA-72673 Release of 40S and 60S subunits from the 80S ribosome
R-HSA-72671 eIF5B:GTP is hydrolyzed and released
R-HSA-156907 Aminoacyl-tRNA binds to the ribosome at the A-site
R-HSA-2408529 Sec-tRNA(Sec):EEFSEC:GTP binds to 80S Ribosome
R-HSA-141691 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex
R-HSA-156915 Translocation of ribosome by 3 bases in the 3' direction
R-HSA-141671 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex
R-HSA-156912 Peptide transfer from P-site tRNA to the A-site tRNA
R-HSA-927832 UPF1 binds an mRNP with a termination codon preceding an Exon Junction Complex
R-HSA-927789 Formation of UPF1:eRF3 complex on mRNA with a premature termination codon and no Exon Junction Complex
R-HSA-1799332 Nascent polypeptide:mRNA:ribosome complex binds signal recognition particle (SRP)
R-HSA-156923 Hydrolysis of eEF1A:GTP
R-HSA-5333615 80S:Met-tRNAi:mRNA:SECISBP2:Sec-tRNA(Sec):EEFSEC:GTP is hydrolysed to 80S:Met-tRNAi:mRNA:SECISBP2:Sec and EEFSEC:GDP by EEFSEC
R-HSA-141673 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex
R-HSA-927889 SMG1 phosphorylates UPF1 (enhanced by Exon Junction Complex)
R-HSA-1799329 Signal peptidase hydrolyzes signal peptide from ribosome-associated nascent protein
R-HSA-1799330 The SRP receptor binds the SRP:nascent peptide:ribosome complex
R-HSA-1799326 Signal-containing nascent peptide translocates to endoplasmic reticulum
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit
R-HSA-156827 L13a-mediated translation
R-HSA-72689 Formation of a pool of free 40S subunits
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-72737 Cap-dependent Translation Initiation
R-HSA-72613 Eukaryotic Translation Initiation
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-156902 Peptide chain elongation
R-HSA-2408557 Selenocysteine synthesis
R-HSA-72764 Eukaryotic Translation Termination
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
R-HSA-72766 Translation
R-HSA-376176 Signaling by ROBO receptors
R-HSA-192823 Viral mRNA Translation
R-HSA-72312 rRNA processing
R-HSA-156842 Eukaryotic Translation Elongation
R-HSA-2408522 Selenoamino acid metabolism
R-HSA-927802 Nonsense-Mediated Decay (NMD)
R-HSA-392499 Metabolism of proteins
R-HSA-422475 Axon guidance
R-HSA-168273 Influenza Viral RNA Transcription and Replication
R-HSA-8953854 Metabolism of RNA
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-1266738 Developmental Biology
R-HSA-168255 Influenza Life Cycle
R-HSA-1430728 Metabolism
R-HSA-168254 Influenza Infection
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: A8K502, NM_000968, NP_000959, P36578, P39029, Q4VBR0, Q969Z9, RL4_HUMAN, RPL1
UCSC ID: uc002apv.3
RefSeq Accession: NM_000968
Protein: P36578 (aka RL4_HUMAN)
CCDS: CCDS10218.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000968.3
exon count: 10CDS single in 3' UTR: no RNA size: 1458
ORF size: 1284CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2768.00frame shift in genome: no % Coverage: 98.83
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.