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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RFPL4A Gene

protein-coding   GIFtS: 42
GCID: GC19P056270

Ret Finger Protein-Like 4A

(Previous name: ret finger protein-like 4)
(Previous symbol: RFPL4)
  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)
About This Section

Aliases
Ret Finger Protein-Like 4A1 2
RFPL41 2 3
RNF2102 3 5
Ret Finger Protein-Like 41 2
RING Finger Protein 2102 3

External Ids:    HGNC: 164491   Entrez Gene: 3429312   Ensembl: ENSG000002236387   OMIM: 6126015   UniProtKB: A6NLU03   

Export aliases for RFPL4A gene to outside databases

Previous GC identifer: GC19P060963


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for RFPL4A Gene: 
RFPL4A (ret finger protein-like 4A) is a protein-coding gene. Diseases associated with RFPL4A include amenorrhea, and premature ovarian failure. GO annotations related to this gene include zinc ion binding. An important paralog of this gene is RFPL1.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NC_018930.2  NT_011109.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RFPL4A gene promoter:
         C/EBPbeta   FOXD1   Nkx2-5   NF-kappaB   Nkx6-1   NF-kappaB2   NF-Y   NF-kappaB1   En-1   CBF(2)   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for RFPL4A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RFPL4A


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

Entrez Gene cytogenetic band: 19q13.42   Ensembl cytogenetic band:  19q13.42   HGNC cytogenetic band: 19q13.42

RFPL4A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RFPL4A gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P056270:  view genomic region     (about GC identifiers)

Start:
56,270,380 bp from pter      End:
56,274,541 bp from pter
Size:
4,162 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RFPLA_HUMAN, A6NLU0 (See protein sequence)
Recommended Name: Ret finger protein-like 4A  
Size: 287 amino acids; 32238 Da
1 PDB 3D structure from and Proteopedia for RFPL4A:
2FBE (3D)    

Explore the universe of human proteins at neXtProt for RFPL4A: NX_A6NLU0

Explore proteomics data for RFPL4A at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_A6NLU0

  • RFPL4A Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RFPL4A Protein Expression
    REFSEQ proteins: NP_001138486.1  
    ENSEMBL proteins: 
     ENSP00000392936  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    RNF: RING-type (C3HC4) zinc fingers

    5/9 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 A6NLU0

    ProtoNet protein and cluster: A6NLU0

    UniProtKB/Swiss-Prot: RFPLA_HUMAN, A6NLU0
    Similarity: Contains 1 B30.2/SPRY domain
    Similarity: Contains 1 RING-type zinc finger


    RFPL4A 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
         
    RFPL4A for ontologies           About GeneDecksing


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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RFPL4A

    3 Interacting proteins for RFPL4A (A6NLU03) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CCNB1P146353I2D: score=1 
    PSMB1P206183I2D: score=1 
    UBE2AP494593I2D: score=1 
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RFPL4A (RFPLA)

    Search CenterWatch for drugs/clinical trials and news about RFPL4A / RFPLA

    (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,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RFPL4A gene: 
    NM_001145014.1  

    Unigene Cluster for RFPL4A:

    Ret finger protein-like 4A
    Hs.631553  [show with all ESTs]
    Unigene Representative Sequence: NM_001145014
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000434937(uc010yge.2)
    miRNA
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    Inhib. RNA
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    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RFPL4A

    1 AceView cDNA sequence:

    CA454993 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RFPL4A expression in normal human tissues (normalized intensities)      RFPL4A embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCTGAGCACT
    RFPL4A Expression
    About this image


    RFPL4A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/1 selected tissues (see all 1) fully expand
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Secondary follicles
             oocyte   

    See RFPL4A Protein Expression from SPIRE MOPED and PaxDB
    SOURCE GeneReport for Unigene cluster: Hs.631553
        SABiosciences Custom PCR Arrays for RFPL4A
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RFPL4A

    (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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for RFPL4A gene from 3/5 species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rfpl45 ret finger protein-like 4   --   7 (2.96 cM) 5109787 
    chicken
    (Gallus gallus)
    Aves ZNF7776
    Uncharacterized protein
    30(a)
    possible ortholog
    2(564030-564628)
    zebrafish
    (Danio rerio)
    Actinopterygii btr306
    bloodthirsty-related gene family, member 30
    13(a)
    possible ortholog
    19(49825613-49832914)


    ENSEMBL Gene Tree for RFPL4A (if available)
    TreeFam Gene Tree for RFPL4A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RFPL4A gene
    LOC729974  RFPL12  MEFV2  RFPL4AL12  RFPL32  RFPL22  RNF392  RFPL4B2  
    11 SIMAP similar genes for RFPL4A using alignment to 1 protein entry:     RFPLA_HUMAN:
    RFPL4AL1    RFPL1    RFPL3    RFPL2    MEFV    TRIM21
    TRIM27    RFPL4B    TRIM11    TRIM39    BT3.3

    RFPL4A for paralogs           About GeneDecksing


    5 Pseudogenes.org Pseudogenes for RFPL4A
    PGOHUM00000258587 PGOHUM00000246557 PGOHUM00000245479 PGOHUM00000232590 PGOHUM00000249702


    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/173 SNPs in RFPL4A are shown (see all 173)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1900279971,2
    --56268513(+) ATGTTA/CTCACT 1 -- us2k10--------
    rs745919641,2
    C--56268552(+) CATGGA/GCACAG 1 -- us2k13Minor allele frequency- G:0.00NA 8
    rs1131568101,2
    C,F--56268574(+) TCACAC/TACTGG 1 -- us2k11Minor allele frequency- T:0.50CSA 2
    rs759203411,2
    F--56268583(+) GGGACC/TTGTCG 1 -- us2k12Minor allele frequency- T:0.50NA 6
    rs1418597211,2
    C--56268595(+) GGGGCG/TGGGGG 1 -- us2k10--------
    rs129779351,2
    C,A--56268615(+) GGATAG/ACATTA 1 -- us2k15Minor allele frequency- A:0.11NA WA CSA 9
    rs1175897421,2
    C--56268631(+) AAATAC/TCTAAT 1 -- us2k10--------
    rs1176402241,2
    C--56268638(+) TAATGC/TAGGTG 1 -- us2k10--------
    rs578117221,2
    C--56268653(+) GTTGAC/TGGGTG 1 -- us2k12Minor allele frequency- T:0.24CSA NA 121
    rs1822576031,2
    C--56268675(+) CATGGC/GACATC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for RFPL4A (56270380 - 56274541 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/23 variations for RFPL4A (see all 23):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv3329CNV Deletion18987735
    esv2664981CNV Deletion23128226
    esv2432344CNV Deletion19546169
    esv2718988CNV Deletion23290073
    nsv435699CNV Deletion17901297
    nsv821063CNV Duplication20802225
    nsv509753CNV Insertion20534489
    nsv2556CNV Insertion18451855
    nsv9772CNV Loss18304495
    esv6309CNV Loss19470904

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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.)
    About This Section
    OMIM gene information: 612601    OMIM disorders: --

    2 diseases for RFPL4A:    About MalaCards
    amenorrhea    premature ovarian failure

    1 disease from the University of Copenhagen DISEASES database for RFPL4A:
    Premature ovarian failure

    RFPL4A for disorders           About GeneDecksing

    Genetic Association Database (GAD): RFPL4A
    Human Genome Epidemiology (HuGE) Navigator: RFPL4A (1 document)

    Export disorders for RFPL4A 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)
    About This Section

    PubMed articles for RFPL4A gene integrated from 9 sources:
    (articles sorted by number of sources associating them with RFPL4A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (2010)
    2. Structure of the PRYSPRY-domain: implications for autoinflammatory diseases. (PubMed id 16364311)1, 2 Gruetter C.... Gruetter M.G. (2006)
    3. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (2004)
    4. The ret finger protein-like 4 gene, Rfpl4, encodes a putative E3 ubiquitin-protein ligase expressed in adult germ cells. (PubMed id 11850190)1, 3 Rajkovic A....Matzuk M.M. (2002)
    5. Common genetic variation and antidepressant efficacy i n major depressive disorder: a meta-analysis of three genome-wide pharmacogeneti c studies. (PubMed id 23377640)1 (2013)
    6. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 342931 HGNC: 16449 AceView: LOC342931 Ensembl:ENSG00000223638 euGenes: HUgn342931
    ECgene: RFPL4A H-InvDB: RFPL4A

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RFPL4A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for RFPL4A gene:
    Search GeneIP for patents involving RFPL4A

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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