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RFPL3 Gene

protein-coding   GIFtS: 42
GCID: GC22P032750

Ret Finger Protein-Like 3

  Search for RFPL3
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
Ret Finger Protein-Like 31 2

External Ids:    HGNC: 99801   Entrez Gene: 107382   Ensembl: ENSG000001282767   OMIM: 6059705   UniProtKB: O756793   

Export aliases for RFPL3 gene to outside databases

Previous GC identifers: GC22P029449 GC22P031075 GC22P031078 GC22P015708


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for RFPL3 Gene:
RFPL3 (ret finger protein-like 3) is a protein-coding gene. An important paralog of this gene is TRIML2.


(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 at NCBI GenBank:
NC_000022.10  NC_018933.2  NT_011520.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the RFPL3 gene promoter:
         POU2F1   POU2F1b   POU2F1a   POU2F1c   LyF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRFPL3 promoter sequence
   Search Chromatin IP Primers for RFPL3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RFPL3


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

Entrez Gene cytogenetic band: 22q12.3   Ensembl cytogenetic band:  22q12.3   HGNC cytogenetic band: 22q12

RFPL3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RFPL3 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P032750:  view genomic region     (about GC identifiers)

Start:
32,750,872 bp from pter      End:
32,757,148 bp from pter
Size:
6,277 bases      Orientation:
plus 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: RFPL3_HUMAN, O75679 (See protein sequence)
Recommended Name: Ret finger protein-like 3  
Size: 317 amino acids; 35386 Da
Sequence caution: Sequence=CAA09046.1; Type=Erroneous initiation;
Secondary accessions: A2A279 Q6IC03 Q6IC04 Q6NSX3 Q8N5R4
Alternative splicing: 2 isoforms:  O75679-1   O75679-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RFPL3: NX_O75679

Explore proteomics data for RFPL3 at MOPED


See RFPL3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001092005.1  NP_006595.1  

ENSEMBL proteins: 
 ENSP00000380609   ENSP00000249007   ENSP00000371520  

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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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Selected InterPro protein domains (see all 9):
 IPR001841 Znf_RING
 IPR001870 B30.2/SPRY
 IPR013083 Znf_RING/FYVE/PHD
 IPR003879 Butyrophylin
 IPR006574 PRY

Graphical View of Domain Structure for InterPro Entry O75679

ProtoNet protein and cluster: O75679

3 Blocks protein domains:
IPB001841 Zn-finger
IPB003879 Butyrophylin C-terminal DUF signature
IPB006574 SPRY-associated domain


UniProtKB/Swiss-Prot: RFPL3_HUMAN, O75679
Similarity: Contains 1 B30.2/SPRY domain
Similarity: Contains 1 RING-type zinc finger


Find genes that share domains with RFPL3           About GenesLikeMe


(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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:
     Genatlas biochemistry entry for RFPL3:
ret finger protein-like 3,B box family

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
GO:0008270zinc ion binding IEA--
     
Find genes that share ontologies with RFPL3           About GenesLikeMe


Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RFPL3
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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
extracellular2
cytosol1
mitochondrion1
nucleus1

(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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    Pathway & Disease-focused RT2 Profiler PCR Array including RFPL3: 
          Ubiquitin Ligases in human mouse rat

Interactions:

    Search GeneGlobe Interaction Network for RFPL3

(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 Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for RFPL3



(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,
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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for RFPL3 gene (2 alternative transcripts): 
NM_001098535.1  NM_006604.2  

Unigene Cluster for RFPL3:

Ret finger protein-like 3
Hs.558455  [show with all ESTs]
Unigene Representative Sequence: AK097738
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000397468(uc010gwn.3) ENST00000249007(uc003amj.3) ENST00000382088

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Additional mRNA sequence: 

AJ010232.1 AK097738.1 BC031689.1 BC069753.1 CR456564.1 

1 DOTS entry:

DT.91754466 

10 AceView cDNA sequences:

CR456564 NM_006604 AJ010232 BX280855 BC069753 BC031689 AK097738 BI826818 
BI827007 BG207403 

GeneLoc Exon Structure


(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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RFPL3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
RFPL3 Expression
About this image

RFPL3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

RFPL3 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.558455
    Pathway & Disease-focused RT2 Profiler PCR Array including RFPL3: 
          Ubiquitin Ligases in human mouse rat

Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RFPL3

(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 chordates.

Orthologs for RFPL3 gene from Selected species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
13(a)
many ↔ many
2(193493147-193519599)
        Species with no ortholog for RFPL3

ENSEMBL Gene Tree for RFPL3 (if available)
TreeFam Gene Tree for RFPL3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for RFPL3 gene
RFPL11 2  TRIML22  MEFV2  RFPL4AL12  RFPL4A2  RFPL22  RFPL4B2  
14 SIMAP similar genes for RFPL3 using alignment to 1 protein entry:     RFPL3_HUMAN:
RFPL1    RFPL2    RFPL4A    RFPL4AL1    MEFV    TRIM27
TRIM39    RFPL4B    TRIM11    BT3.3    BTN3A3    TRIM21
BTN1A1    BTNL9

Find genes that share paralogs with RFPL3           About GenesLikeMe


1 Pseudogenes.org Pseudogene for RFPL3
PGOHUM00000241019


(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 RFPL3 (see all 241)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 22 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs121589831,2
C,F--32748873(+) ccagcG/Actgag 1 -- us2k17Minor allele frequency- A:0.08WA CSA NA EA 365
rs1443804341,2
--32749029(+) GTAGCA/GTTAGA 1 -- us2k10--------
rs1152288401,2
F--32749037(+) AGAGCC/TTCACC 1 -- us2k11Minor allele frequency- T:0.08WA 118
rs1166720011,2
F--32749114(+) GTCCAG/TCCTCT 1 -- us2k11Minor allele frequency- T:0.15WA 118
rs1841487721,2
--32749155(+) GCCTGC/GAGTGG 1 -- us2k10--------
rs726173021,2
C,F--32749169(+) CTGGAG/AACACC 1 -- us2k12Minor allele frequency- A:0.25NA EA 240
rs1169624731,2
C,F--32749184(+) TGCCCG/AGGCTT 1 -- us2k11Minor allele frequency- A:0.03EA 120
rs726204031,2
C,F--32749197(+) TACTCT/CACTAG 1 -- us2k13Minor allele frequency- C:0.22WA NA EA 358
rs1886430921,2
--32749206(+) AGAACC/TGCTGG 1 -- us2k10--------
rs1154510091,2
F--32749389(+) TAGAGG/AGCGCG 1 -- us2k11Minor allele frequency- A:0.15WA 118

HapMap Linkage Disequilibrium report for RFPL3 (32750872 - 32757148 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for RFPL3:    About this table    
Variant IDTypeSubtypePubMed ID
esv2422247CNV Duplication17116639
nsv459874CNV Gain19166990

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 605970    OMIM disorders: --


Find genes that share disorders with RFPL3           About GenesLikeMe


Export disorders for RFPL3 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 RFPL3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with RFPL3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Duplications on human chromosome 22 reveal a novel Ret finger protein-like gene family with sense and endogenous antisense transcripts. (PubMed id 10508838)1, 2, 3, 9 Seroussi E.... Dumanski J.P. (Genome Res. 1999)
  2. A genome annotation-driven approach to cloning the human ORFeome. (PubMed id 15461802)1, 2 Collins J.E.... Dunham I. (Genome Biol. 2004)
  3. The DNA sequence of human chromosome 22. (PubMed id 10591208)1, 2 Dunham I.... Wright H. (Nature 1999)
  4. Evolutionary forces shape the human RFPL1,2,3 genes toward a role in neocortex development. (PubMed id 18656177)1 Bonnefont J....Krause K.H. (Am. J. Hum. Genet. 2008)
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  7. 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)

(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: 10738 HGNC: 9980 AceView: RFPL3 Ensembl:ENSG00000128276 euGenes: HUgn10738
ECgene: RFPL3 H-InvDB: RFPL3

(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 RFPL3 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 RFPL3 gene:
Search GeneIP for patents involving RFPL3

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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RFPL3
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RFPL3
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for RFPL3
 LSBio Antibodies in human, mouse, rat for RFPL3
Customized transgenic rodents for:
 Humanization
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 Tissue-specific gene expresssion
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 Browse compounds at ApexBio
 Search Addgene for plasmids for RFPL3
  Search eBioscience for proteins for RFPL3
  Search eBioscience for elisas for RFPL3
  eBioscience FlowRNA Probe Sets
       
GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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