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Aliases for RP1L1 Gene

Aliases for RP1L1 Gene

  • RP1 Like 1 2 3 5
  • Doublecortin Domain Containing 4B 2 3
  • Retinitis Pigmentosa 1 Like 1 2 3
  • Retinitis Pigmentosa 1-Like 1 Protein 3
  • Retinitis Pigmentosa 1-Like 1 2
  • DCDC4B 3

External Ids for RP1L1 Gene

Previous GeneCards Identifiers for RP1L1 Gene

  • GC00U991063
  • GC08U900030
  • GC08M010335
  • GC08M010501
  • GC08M009394

Summaries for RP1L1 Gene

Entrez Gene Summary for RP1L1 Gene

  • 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]

GeneCards Summary for RP1L1 Gene

RP1L1 (RP1 Like 1) is a Protein Coding gene. Diseases associated with RP1L1 include Occult Macular Dystrophy and Retinitis Pigmentosa 1. An important paralog of this gene is RP1.

UniProtKB/Swiss-Prot for RP1L1 Gene

  • Required for the differentiation of photoreceptor cells. Plays a role in the organization of outer segment of rod and cone photoreceptors (By similarity).

Additional gene information for RP1L1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RP1L1 Gene

Genomics for RP1L1 Gene

GeneHancer (GH) Regulatory Elements for RP1L1 Gene

Promoters and enhancers for RP1L1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08I010652 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 561.3 +58.3 58298 3.8 HDGF PKNOX1 FEZF1 ZNF2 GLIS2 FOS ZNF263 TSHZ1 ZNF488 SMARCA4 RP1L1 LOC101929290 PINX1 LOC105379241 PRSS51 MIR4286 LOC105379237
GH08I010709 Enhancer 1.2 Ensembl ENCODE dbSUPER 550.8 +0.5 477 3.5 ATF1 BRCA1 RCOR1 ATF7 CREM SMARCC1 CEBPB ELF1 ZNF623 ZNF592 RP1L1 ENSG00000269918 SOX7 RNA5SP252
GH08I010713 Enhancer 0.7 ENCODE dbSUPER 550.8 -1.8 -1839 0.2 MAZ SREBF2 CEBPB HNF4A RP1L1 C8orf74 ENSG00000269918 SOX7 LOC102723313
GH08I010775 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 20 -65.1 -65056 3.3 PKNOX1 SMAD1 ARNT ZNF766 CBX5 REST ZNF592 SMARCA4 NBN HMBOX1 RP1L1 LOC101929290 PINX1 SOX7 ENSG00000255310 ENSG00000269918 GC08M010757 GC08M010803 LOC102723313 ENSG00000258724
GH08I010798 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 17.5 -88.3 -88259 4 PKNOX1 ATF1 ARNT ARID4B FEZF1 ETS1 YY1 TCF12 ATF7 FOS RP1L1 C8orf74 LOC102723313 ENSG00000269918 SOX7 ENSG00000255310 GC08M010803 GC08M010757 ENSG00000258724 PINX1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RP1L1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RP1L1 gene promoter:

Genomic Locations for RP1L1 Gene

Genomic Locations for RP1L1 Gene
105,839 bases
Minus strand

Genomic View for RP1L1 Gene

Genes around RP1L1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RP1L1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RP1L1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RP1L1 Gene

Proteins for RP1L1 Gene

  • Protein details for RP1L1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Retinitis pigmentosa 1-like 1 protein
    Protein Accession:
    Secondary Accessions:
    • Q86SQ1
    • Q8IWN8
    • Q8IWN9
    • Q8IWP0
    • Q8IWP1
    • Q8IWP2

    Protein attributes for RP1L1 Gene

    2480 amino acids
    Molecular mass:
    261207 Da
    Quaternary structure:
    • Interacts with RP1; has a synergistic effect with RP1 in photoreceptor differentiation.

    Alternative splice isoforms for RP1L1 Gene


neXtProt entry for RP1L1 Gene

Post-translational modifications for RP1L1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RP1L1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RP1L1 Gene

Domains & Families for RP1L1 Gene

Gene Families for RP1L1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RP1L1 Gene

Suggested Antigen Peptide Sequences for RP1L1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The C-terminal part contains a large repetitive region which contains an unusually high percentage of glutamine, glycine and above all glutamic acid residues.
  • The C-terminal part contains a large repetitive region which contains an unusually high percentage of glutamine, glycine and above all glutamic acid residues.
genes like me logo Genes that share domains with RP1L1: view

Function for RP1L1 Gene

Molecular function for RP1L1 Gene

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

Phenotypes From GWAS Catalog for RP1L1 Gene

Phenotypes for RP1L1 Gene

genes like me logo Genes that share phenotypes with RP1L1: view

Human Phenotype Ontology for RP1L1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RP1L1 Gene

MGI Knock Outs for RP1L1:

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for RP1L1 Gene

Localization for RP1L1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RP1L1 Gene

Cytoplasm, cytoskeleton, cilium axoneme. Cell projection, cilium, photoreceptor outer segment. Note=Localized to the axoneme of outer segments and connecting cilia in rod photoreceptors. {ECO:0000250}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RP1L1 gene
Compartment Confidence
extracellular 5
cytoskeleton 4
mitochondrion 2
nucleus 2
cytosol 2

Gene Ontology (GO) - Cellular Components for RP1L1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001750 photoreceptor outer segment ISS --
GO:0005874 microtubule IEA --
GO:0005930 axoneme ISS --
GO:0032391 photoreceptor connecting cilium ISS --
GO:0070062 extracellular exosome HDA 23376485
genes like me logo Genes that share ontologies with RP1L1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RP1L1 Gene

Pathways & Interactions for RP1L1 Gene

SuperPathways for RP1L1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RP1L1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007601 visual perception IEA --
GO:0035082 axoneme assembly IBA --
GO:0035556 intracellular signal transduction IEA --
GO:0042461 photoreceptor cell development ISS --
GO:0045494 photoreceptor cell maintenance ISS --
genes like me logo Genes that share ontologies with RP1L1: view

No data available for Pathways by source and SIGNOR curated interactions for RP1L1 Gene

Drugs & Compounds for RP1L1 Gene

No Compound Related Data Available

Transcripts for RP1L1 Gene

mRNA/cDNA for RP1L1 Gene

Unigene Clusters for RP1L1 Gene

Retinitis pigmentosa 1-like 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RP1L1 Gene

No ASD Table

Relevant External Links for RP1L1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RP1L1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RP1L1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RP1L1 Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x5.5) and Skin - Not Sun Exposed (Suprapubic) (x4.2).

Protein differential expression in normal tissues from HIPED for RP1L1 Gene

This gene is overexpressed in CD4 Tcells (21.4), Retina (16.3), Fetal Brain (14.2), and Heart (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RP1L1 Gene

Protein tissue co-expression partners for RP1L1 Gene

NURSA nuclear receptor signaling pathways regulating expression of RP1L1 Gene:


SOURCE GeneReport for Unigene cluster for RP1L1 Gene:


mRNA Expression by UniProt/SwissProt for RP1L1 Gene:

Tissue specificity: Retinal-specific; expressed in photoreceptor.

Evidence on tissue expression from TISSUES for RP1L1 Gene

  • Eye(4.5)
  • Intestine(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RP1L1 Gene

Germ Layers:
  • ectoderm
  • nervous
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
  • peripheral nervous system
genes like me logo Genes that share expression patterns with RP1L1: view

Primer Products

Orthologs for RP1L1 Gene

This gene was present in the common ancestor of animals.

Orthologs for RP1L1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RP1L1 33 34
  • 95.06 (n)
(Canis familiaris)
Mammalia RP1L1 33 34
  • 70.13 (n)
(Bos Taurus)
Mammalia RP1L1 33 34
  • 68.84 (n)
(Rattus norvegicus)
Mammalia LOC683404 33
  • 64.24 (n)
(Mus musculus)
Mammalia Rp1l1 33 16 34
  • 64.05 (n)
(Monodelphis domestica)
Mammalia RP1L1 34
  • 40 (a)
(Gallus gallus)
Aves RP1L1 34
  • 27 (a)
(Anolis carolinensis)
Reptilia RP1L1 34
  • 25 (a)
(Danio rerio)
Actinopterygii rp1l1 34
  • 15 (a)
RP1L1 (1 of 2) 34
  • 10 (a)
(Caenorhabditis elegans)
Secernentea F27C1.13 34
  • 28 (a)
Species where no ortholog for RP1L1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for RP1L1 Gene

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

Paralogs for RP1L1 Gene

Paralogs for RP1L1 Gene

genes like me logo Genes that share paralogs with RP1L1: view

Variants for RP1L1 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for RP1L1 Gene

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.

Sequence variations from dbSNP and Humsavar for RP1L1 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1024256263 uncertain-significance, Occult macular dystrophy 10,616,522(-) G/A coding_sequence_variant, synonymous_variant
rs111646478 benign, Occult macular dystrophy 10,608,452(-) C/A coding_sequence_variant, missense_variant
rs112534810 benign, Occult macular dystrophy 10,608,455(-) T/C coding_sequence_variant, synonymous_variant
rs112609335 likely-benign, Occult macular dystrophy 10,622,758(-) A/C/G coding_sequence_variant, synonymous_variant
rs115126172 likely-benign, Occult macular dystrophy 10,622,655(-) C/A/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for RP1L1 Gene

Variant ID Type Subtype PubMed ID
dgv7010n100 CNV loss 25217958
esv1658461 CNV insertion 17803354
esv2669109 CNV deletion 23128226
esv997256 CNV insertion 20482838
nsv1025557 CNV gain 25217958
nsv1030934 CNV gain 25217958
nsv1129295 CNV insertion 24896259
nsv523113 CNV loss 19592680
nsv527445 CNV loss 19592680
nsv610267 CNV gain 21841781
nsv610268 CNV loss 21841781
nsv824532 CNV gain 20364138

Variation tolerance for RP1L1 Gene

Residual Variation Intolerance Score: 99.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 29.90; 99.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RP1L1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

Disorders for RP1L1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for RP1L1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search RP1L1 in MalaCards View complete list of genes associated with diseases


  • 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. {ECO:0000269 PubMed:20826268, ECO:0000269 PubMed:22605915}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for RP1L1

genes like me logo Genes that share disorders with RP1L1: view

No data available for Genatlas for RP1L1 Gene

Publications for RP1L1 Gene

  1. Identification and characterisation of the retinitis pigmentosa 1-like1 gene (RP1L1): a novel candidate for retinal degenerations. (PMID: 12634863) Conte I … Banfi S (European journal of human genetics : EJHG 2003) 2 3 4 22 58
  2. Characterization of RP1L1, a highly polymorphic paralog of the retinitis pigmentosa 1 (RP1) gene. (PMID: 12724644) Bowne SJ … Sullivan LS (Molecular vision 2003) 3 4 22 58
  3. Dominant mutations in RP1L1 are responsible for occult macular dystrophy. (PMID: 20826268) Akahori M … Iwata T (American journal of human genetics 2010) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. Putative digenic inheritance of heterozygous RP1L1 and C2orf71 null mutations in syndromic retinal dystrophy. (PMID: 27029556) Liu YP … Cremers FP (Ophthalmic genetics 2017) 3 58

Products for RP1L1 Gene

Sources for RP1L1 Gene

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