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RFPL3S Gene

protein-coding   GIFtS: 30
GCID: GC22M032755

RFPL3 Antisense

(Previous name: RFPL3 antisense RNA 1)
(Previous symbol: RFPL3-AS1)
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(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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
RFPL3 Antisense1 2     RFPL3-AS2
RFPL3-AS11 2 3     RFPL3ANT2
RFPL3 Antisense RNA 11 3     RFPL3AS2
Non-Protein Coding RNA 51     Ret Finger Protein-Like 3 Antisense Gene Protein3
NCRNA000052     RFPL3 Antisense Gene Protein 13

External Ids:    HGNC: 99811   Entrez Gene: 107372   Ensembl: ENSG000002058537   OMIM: 6059715   UniProtKB: P0C7P23   
ORGUL members:    fRNAdb10:FR374742      

Export aliases for RFPL3S gene to outside databases

Previous GC identifers: GC22M029451 GC22P029280 GC22M031080 GC22M015717


(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 RFPL3S Gene:
RFPL3S (RFPL3 antisense) is a protein-coding gene.


(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 RFPL3S gene promoter:
         HOXA9B   Meis-1a   Meis-1   Meis-1b   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RFPL3S


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

RFPL3S Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RFPL3S gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M032755:  view genomic region     (about GC identifiers)

Start:
32,755,893 bp from pter      End:
32,778,039 bp from pter
Size:
22,147 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for RFPL3S

(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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: RFL3S_HUMAN, P0C7P2 (See protein sequence)
Recommended Name: Putative protein RFPL3S  
Size: 107 amino acids; 11739 Da
Miscellaneous: The gene encoding RFPL3S is located on the opposite strand of the gene encoding RFPL3. Its
transcription may play a role in RFPL3 transcription regulation
Sequence caution: Sequence=CAB38257.1; Type=Erroneous translation; Note=Wrong choice of CDS; Sequence=CAI19584.1;
Type=Erroneous translation; Note=Wrong choice of CDS;
Secondary accessions: Q5TI83 Q5TI84

Explore the universe of human proteins at neXtProt for RFPL3S: NX_P0C7P2

Explore proteomics data for RFPL3S at MOPED


See RFPL3S Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


ENSEMBL proteins: 
 ENSP00000371516   ENSP00000383093   ENSP00000371518   ENSP00000463921  

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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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ProtoNet protein and cluster: P0C7P2


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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 RFPL3S:
ret finger protein-like 3,antisense transcript,overlapping RFRL3

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for RFPL3S

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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
mitochondrion2
nucleus2
cytosol1
extracellular1

(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 RFPL3S
Interactions:

    Search GeneGlobe Interaction Network for RFPL3S

(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
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Browse Tocris compounds for RFPL3S (RFL3S)



(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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Unigene Cluster for RFPL3S:

RFPL3 antisense
Hs.274285  [show with all ESTs]
Unigene Representative Sequence: BC031635
5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000382084 ENST00000400234(uc003amk.3 uc003aml.3) ENST00000461833
ENST00000382086 ENST00000577714
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Additional mRNA sequence: 

AJ010233.1 BC031635.1 BC042824.1 BC066983.1 BC090926.1 CR456565.1 

4 DOTS entries:

DT.308564  DT.87015602  DT.40272940  DT.92001702 

Selected AceView cDNA sequences (see all 39):

BC042824 BM663956 H55552 BU584586 H55681 AI283597 NR_001450 BC066983 
BU584154 BM693961 AA864540 CR456565 AJ010233 BC031635 BU584156 AI914420 
AI149839 AI015976 AL704057 AA868889 BG198113 BG720986 BG723497 AI123305 

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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RFPL3S expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
RFPL3S Expression
About this image

RFPL3S Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

RFPL3S Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.274285

UniProtKB/Swiss-Prot: RFL3S_HUMAN, P0C7P2
Tissue specificity: Strongly expressed in the testis and weakly in brain, placenta and pancreas

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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 human and chimp.

Orthologs for RFPL3S gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia RFPL3S6
RFPL3 antisense
94(a)
1 ↔ 1
22(31029052-31039365)


ENSEMBL Gene Tree for RFPL3S (if available)
TreeFam Gene Tree for RFPL3S (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for RFPL3S gene

Find genes that share paralogs with RFPL3S           About GenesLikeMe


1 Pseudogenes.org Pseudogene for RFPL3S
PGOHUM00000246568


(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 RFPL3S (see all 250)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 22 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs347579281,2
C--32757792(+) AAATCC/TACCAA 2 -- int14Minor allele frequency- T:0.07WA NA EA 360
rs790387581,2
C,F--32757806(+) CTTACG/AAATCC 2 -- int12Minor allele frequency- A:0.04NA EA 240
rs1380570531,2
--32757871(+) TGAGAC/TGAAAA 2 -- int10--------
rs1927793051,2
--32757931(+) ATAACC/TACCCA 2 -- int10--------
rs1847302151,2
--32758069(+) GACTGG/TGGGGG 2 -- int10--------
rs57540161,2
C,A--32758071(+) CTGTGG/AGGGCA 2 -- int16Minor allele frequency- A:0.34WA CSA NA EA 363
rs57540171,2
C,F--32758076(+) GGGGCA/TTGCAT 2 -- int12Minor allele frequency- T:0.24NA EA 240
rs1505492171,2
--32758314(+) ACCAAC/TAGTTG 2 -- int10--------
rs1171551481,2
C,F--32758334(+) CTGGAG/AAAAGA 2 -- int11Minor allele frequency- A:0.01NA 120
rs1876119961,2
--32758405(+) AGATCA/GAAATG 2 -- int10--------

HapMap Linkage Disequilibrium report for RFPL3S (32755893 - 32778039 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for RFPL3S: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing RFPL3S
DNA2.0 Custom Variant and Variant Library Synthesis for RFPL3S

(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: 605971    OMIM disorders: --


Find genes that share disorders with RFPL3S           About GenesLikeMe

Genetic Association Database (GAD): RFPL3S

Export disorders for RFPL3S 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 RFPL3S gene integrated from 10 sources:
(articles sorted by number of sources associating them with RFPL3S)
    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. Genome-wide association with bone mass and geometry in the Framingham Heart Study. (PubMed id 17903296)4 Kiel D.P....Karasik D. (BMC Med. Genet. 2007)
  4. 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)
  5. The DNA sequence of human chromosome 22. (PubMed id 10591208)2 Dunham I.... Wright H. (Nature 1999)

(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: 10737 HGNC: 9981 AceView: RFPL3S Ensembl:ENSG00000205853 euGenes: HUgn10737
ECgene: RFPL3S H-InvDB: RFPL3S

(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 RFPL3S 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 RFPL3S gene:
Search GeneIP for patents involving RFPL3S

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, eBioscience, antibodies-online, 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
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The GeneCards human gene database gene index: 1 3 5 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 


Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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