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

RP1L1 Gene

protein-coding   GIFtS: 47
GCID: GC08M010501

retinitis pigmentosa 1-like 1

 Explore 6 diseases affiliated with
RP1L1 via our new
 Human Malady Compendium 
Biological research products
for RP1L1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Retinitis Pigmentosa 1-Like 11 2
DCDC4B1 2
Retinitis Pigmentosa 1-Like 1 Protein2

External Ids:    HGNC: 159461   Entrez Gene: 941372   Ensembl: ENSG000001836387   OMIM: 6085815   UniProtKB: Q8IWN73   

Export aliases for RP1L1 gene to outside databases

Previous GC identifers: GC00U991063 GC08U900030 GC08M010335 GC08M009394


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

Entrez Gene summary for RP1L1:
This gene encodes a member of the doublecortin family. The protein encoded by this gene contains two N-terminal
doublecortin domains, which bind microtubules and regulate microtubule polymerization, and two C-terminal large
repetitive regions, both of which contain a high percentage of glutamine and glutamic acid residues. This protein is a
retinal-specific protein. Its exact length varies among individuals due to the presence of a 16aa repeat in the first
C-terminal repetitive region. The 16aa repeat is encoded by the highly polymorphic 48-bp repeat, and 1-6 copies of the
16aa repeat have been identified in normal individuals. The current reference sequence shown here has a single copy of
the 16aa repeat. This protein and the RP1 protein, another retinal-specific protein, play essential and synergistic
roles in affecting photosensitivity and outer segment morphogenesis of rod photoreceptors. Mutations in this gene
cause occult macular dystrophy (OMD). (provided by RefSeq, Sep 2010)

UniProtKB/Swiss-Prot: RP1L1_HUMAN, Q8IWN7
Function: Required for the differentiation of photoreceptor cells. Plays a role in the organization of outer segment of
rod and cone photoreceptors (By similarity)




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000008.10  NC_018919.1  NT_077531.4  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RP1L1 gene promoter:
         Tal-1   POU6F1 (c2)   NF-kappaB   Tal-1beta   Cdc5   E47   Ik-2   NF-kappaB2   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRP1L1 promoter sequence
   Search SABiosciences Chromatin IP Primers for RP1L1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RP1L1


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

Entrez Gene cytogenetic band: 8p23.1   Ensembl cytogenetic band:  8p23.1   HGNC cytogenetic band: 8p23.1

RP1L1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RP1L1 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M010501:  view genomic region     (about GC identifiers)

Start:
10,463,859 bp from pter      End:
10,569,697 bp from pter
Size:
105,839 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: RP1L1_HUMAN, Q8IWN7 (See protein sequence)
Recommended Name: Retinitis pigmentosa 1-like 1 protein  
Size: 2480 amino acids; 261207 Da
Subunit: Interacts with RP1; has a synergistic effect with RP1 in photoreceptor differentiation (By similarity)
Subcellular location: Cytoplasm, cytoskeleton, cilium axoneme. Cell projection, cilium, photoreceptor outer segment (By
similarity). Note=Localized to the axoneme of outer segments and connecting cilia in rod photoreceptors (By
similarity)
Secondary accessions: Q86SQ1 Q8IWN8 Q8IWN9 Q8IWP0 Q8IWP1 Q8IWP2
Alternative splicing: 2 isoforms:  Q8IWN7-1   Q8IWN7-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RP1L1: NX_Q8IWN7

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8IWN7

  • RP1L1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_849188.4  
    ENSEMBL proteins: 
     ENSP00000371923  

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    Uscn Proteins for RP1L1

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001750photoreceptor outer segment ISS--
    GO:0005874microtubule IEA--
    GO:0032391photoreceptor connecting cilium ISS--
    GO:0035085cilium axoneme ISS--


    RP1L1 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    RP1L1 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR003533 Doublecortin_dom

    Graphical View of Domain Structure for InterPro Entry Q8IWN7

    ProtoNet protein and cluster: Q8IWN7

    1 Blocks protein family: IPB003533 Doublecortin

    UniProtKB/Swiss-Prot: RP1L1_HUMAN, Q8IWN7
    Domain: The C-terminal part contains a large repetitive region which contains an unusually high percentage of
    glutamine, glycine and above all glutamic acid residues
    Similarity: Contains 2 doublecortin domains


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: RP1L1_HUMAN, Q8IWN7
    Function: Required for the differentiation of photoreceptor cells. Plays a role in the organization of outer segment of
    rod and cone photoreceptors (By similarity)

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    Animal Models:
         Mouse knock-out Rp1l1tm1Jnz for RP1L1
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Rp1l1):
     nervous system  vision/eye 

    RP1L1 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RP1L1

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for RP1L1 (Q8IWN72, 3 ENSP000003719234) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARL3P364052, 3, ENSP000002607464MINT-6602258 I2D: score=1 STRING: ENSP00000260746
    FYNP062413, ENSP000003576564I2D: score=1 STRING: ENSP00000357656
    GRB2P629933, ENSP000003390074I2D: score=1 STRING: ENSP00000339007
    NCK1P163333, ENSP000002889864I2D: score=1 STRING: ENSP00000288986
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030030cell projection organization IEA--
    GO:0035556intracellular signal transduction IEA--
    GO:0042461photoreceptor cell development ISS--
    GO:0045494photoreceptor cell maintenance ISS--


    RP1L1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 RP1L1
    Search CenterWatch for drugs/clinical trials and news about RP1L1 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RP1L1 gene: 
    NM_178857.5  

    Unigene Cluster for RP1L1:

    Retinitis pigmentosa 1-like 1
    Hs.33538  [show with all ESTs]
    Unigene Representative Sequence: AY168346
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000382483(uc003wtc.3) ENST00000329335

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    Additional cDNA sequence: 

    AJ491324.2 AY168341.1 AY168342.1 AY168343.1 AY168344.1 AY168345.1 AY168346.1 

    4 DOTS entries:

    DT.411175  DT.100020964  DT.100748800  DT.100020963 

    24/29 AceView cDNA sequences (see all 29):

    BX101250 AA019117 AK127545 AY168342 BQ186792 AY168344 AY168341 BQ184755 
    BM719479 CK299909 BG395268 AA059256 BM682803 BM558973 BQ186229 H85580 
    AY168345 R84770 NM_178857 BM930879 AY168343 AJ491324 R85514 AA019118 

    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

    RP1L1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTGTCCTGGG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    RP1L1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    EyeOuter Nuclear LayerMature Rod CellsPhotoreceptors, Retina
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See RP1L1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RP1L1

    SOURCE GeneReport for Unigene cluster: Hs.33538

    UniProtKB/Swiss-Prot: RP1L1_HUMAN, Q8IWN7
    Tissue specificity: Retinal-specific; expressed in photoreceptor

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    In Situ
    Assay Products:
     

     
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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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for RP1L1 gene from 5/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves RP1L16
    Uncharacterized protein
    35(a)
    1 ↔ 1
    3(109565091-109568468)
    lizard
    (Anolis carolinensis)
    Reptilia RP1L16
    --
    25(a)
    1 ↔ 1
    4(41026363-41042736)
    zebrafish
    (Danio rerio)
    Actinopterygii CABZ01072735.16
    CU929322.16
    (see all 3)
    --
    9(a)
    16(a)
    (see all 3)
    possible ortholog
    1 ↔ many
    (see all 3)
    Zv9_NA625(17617-31182)
    17(5562212-5583829)
    honey bee
    (Apis mellifera)
    Insecta --
    --
    6(a)
    1 → many
    Group11.9(48197-48806)
    worm
    (Caenorhabditis elegans)
    Secernentea F27C1.136
    Protein F27C1.13
    23(a)
    1 → many
    I(5443881-5446858)


    ENSEMBL Gene Tree for RP1L1 (if available)
    TreeFam Gene Tree for RP1L1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RP1L1 gene
    RP12  

    RP1L1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    UniProtKB/Swiss-Prot: RP1L1_HUMAN, Q8IWN7
    Polymorphism: The exact length of RP1L1 is variable between individuals due to the presence of several length
    polymorphisms. The sequence shown here is that of allele RP1L1-6 and includes 8 repeats (from aa 1292-1422) with a
    length of 16 amino acids. The number of repeats is highly polymorphic and varies among different alleles, ranging from
    3 to 8


    10/1477 NCBI SNPs in RP1L1 are shown (see all 1477    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2020744321,2
    C,other12575475(+) TACCTC/TCCCCA 2 K E mis10--------
    rs770445291,2
    C,F,--9393954(+) TTAATG/AGCACA 1 -- ds50012Minor allele frequency- A:0.04WA NA 238
    rs119925571,2
    C,F,A,H,--9394006(+) TGATTC/TTGAGA 1 -- ds50017Minor allele frequency- T:0.05NS EA NA WA 658
    rs793531661,2
    F,--9394421(+) CACTTG/CCTAGC 1 -- ut311Minor allele frequency- C:0.09WA 118
    rs48405001,2
    --9398200(+) TTAGTC/TTCCTC 2 E syn10--------
    rs2010746711,2
    C--9400355(-) GGCTGG/TGACAA 2 G V mis10--------
    rs802052681,2
    F,--9401728(+) GTAGTA/GTGCCC 1 -- int11Minor allele frequency- G:0.02EA 120
    rs801959611,2
    F,--9401827(+) CACTGC/AGCTCC 1 -- int11Minor allele frequency- A:0.02WA 118
    rs754138181,2
    C,--9402026(+) GCCTGT/CTTTCT 1 -- int12Minor allele frequency- C:0.13NA 122
    rs119846401,2
    C,F,H,--9402050(+) agcatA/Tataat 1 -- int16Minor allele frequency- T:0.01NS EA NA WA 522

    HapMap Linkage Disequilibrium report for RP1L1 (10463859 - 10569697 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 16 variations for RP1L1
         15/16 Inversions (see all 16): 37318 37316 37307 37317 37311 37319 37320 37315 37312 37321 37304 37313 37314 37305 37306
    Human Gene Mutation Database (HGMD): RP1L1

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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.)
    About This Section

    RP1L1 for disorders           About GeneDecksing

    OMIM gene information: 608581   
    OMIM disorders: 613587  
    UniProtKB/Swiss-Prot: RP1L1_HUMAN, Q8IWN7
  • Defects in RP1L1 are the cause of occult macular dystrophy (OCMD) [MIM:613587]. An inherited macular dystrophy
  • characterized by progressive loss of macular function but normal ophthalmoscopic appearance. It is typically
    characterized by a central cone dysfunction leading to a loss of vision despite normal ophthalmoscopic appearance,
    normal fluorescein angiography, and normal full-field electroretinogram (ERGs), but the amplitudes of the focal
    macular ERGs and multifocal ERGs are significantly reduced at the central retina

    6 diseases for RP1L1:    About MalaCards
    occult macular dystrophy    retinitis    macular dystrophy    retinitis pigmentosa
    retinal degeneration    thyroiditis

    1 disease from the University of Copenhagen DISEASES database for RP1L1:
    Occult macular dystrophy

    Export disorders for RP1L1 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 RP1L1 gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with RP1L1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of the retinitis pigmentosa 1- like1 gene (rp1l1): a novel candidate for retinal degenerations. (PubMed id 12634863)1, 2, 3, 9 Conte I.... Banfi S. (2003)
    2. Characterization of RP1L1, a highly polymorphic paralog of the retinitis pigmentosa 1 (RP1) gene. (PubMed id 12724644)1, 2, 9 Bowne S.J.... Sullivan L.S. (2003)
    3. Dominant mutations in RP1L1 are responsible for occul t macular dystrophy. (PubMed id 20826268)1, 2 Akahori M....Iwata T. (2010)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    5. Autosomal dominant occult macular dystrophy with an RP 1L1 mutation (R45W). (PubMed id 22504327)1 Hayashi T....Tsuneoka H. (2012)
    6. A new mutation in the RP1L1 gene in a patient with occult macular dystrophy associated with a depolarizing pattern of focal macular electroretinograms. (PubMed id 22605915)2 Kabuto T.... Takahashi H. (2012)
    7. Clinical characteristics of occult macular dystrophy i n family with mutation of RP1l1 gene. (PubMed id 22466457)1 Tsunoda K....Miyake Y. (2012)
    8. The doublecortin gene family and disorders of neurona l structure. (PubMed id 20236041)1 Dijkmans T.F....Vreugdenhil E. (2010)
    9. Transmitted duplication of 8p23.1-8p23.2 associated with speech delay, autism and learning difficulties. (PubMed id 18716609)1 Glancy M....Barber J.C. (2009)
    10. Essential and synergistic roles of RP1 and RP1L1 in r od photoreceptor axoneme and retinitis pigmentosa. (PubMed id 19657028)1 Yamashita T....Zuo J. (2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 94137 HGNC: 15946 AceView: RP1L1 Ensembl:ENSG00000183638 euGenes: HUgn94137
    ECgene: RP1L1 H-InvDB: RP1L1

    (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 RP1L1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for RP1L1 gene:
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