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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).

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

Regulatory Elements for RP1L1 Gene

Enhancers for RP1L1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08G010775 1.8 FANTOM5 Ensembl ENCODE dbSUPER 20 -65.1 -65056 3.3 PKNOX1 ATF1 CREB3L1 ARNT E2F7 TCF12 ZNF766 CBX5 ELK1 GATA2 RP1L1 SOX7 ENSG00000255310 ENSG00000269918 GC08M010757 GC08M010803
GH08G010798 1.8 FANTOM5 Ensembl ENCODE dbSUPER 17.5 -88.3 -88260 4.0 PKNOX1 ATF1 ARNT SIN3A ARID4B FEZF1 YY1 TCF12 ELK1 GATA2 RP1L1 C8orf74 ENSG00000269918 SOX7 ENSG00000255310 GC08M010803 GC08M010757
GH08G010760 0.9 ENCODE 20.4 -48.9 -48919 1.1 PKNOX1 ATF1 TBL1XR1 TCF12 ZNF766 CREM EGR2 NCOA1 REST POLR2H RP1L1 SOX7 GC08M010757
GH08G010812 1.1 ENCODE dbSUPER 16.2 -101.7 -101717 2.1 ZSCAN4 RAD21 ZNF121 EGR1 GATA2 ETV6 ELF4 USF2 ZEB2 REST SOX7 RP1L1 LOC101929229 PINX1 ENSG00000269918 GC08M010803 MIR1322
GH08G010737 0.9 ENCODE dbSUPER 19.5 -22.2 -22159 0.2 CTCF PKNOX1 NRF1 RBBP5 GATA3 CTBP2 KDM1A ZBTB33 EZH2 RP1L1 SOX7 GC08M010757
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RP1L1 on UCSC Golden Path with GeneCards custom track

Genomic Location for RP1L1 Gene

Chromosome:
8
Start:
10,606,349 bp from pter
End:
10,712,187 bp from pter
Size:
105,839 bases
Orientation:
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:
    Q8IWN7-RP1L1_HUMAN
    Recommended name:
    Retinitis pigmentosa 1-like 1 protein
    Protein Accession:
    Q8IWN7
    Secondary Accessions:
    • Q86SQ1
    • Q8IWN8
    • Q8IWN9
    • Q8IWP0
    • Q8IWP1
    • Q8IWP2

    Protein attributes for RP1L1 Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

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

Protein Domains for RP1L1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for RP1L1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8IWN7

UniProtKB/Swiss-Prot:

RP1L1_HUMAN :
  • The C-terminal part contains a large repetitive region which contains an unusually high percentage of glutamine, glycine and above all glutamic acid residues.
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.
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 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

COMPARTMENTS
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:0005737 cytoplasm IEA --
GO:0005874 microtubule IEA --
GO:0005930 axoneme IEA,ISS --
GO:0032391 photoreceptor connecting cilium IEA,ISS --
genes like me logo Genes that share ontologies with RP1L1: view

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,IEA --
GO:0045494 photoreceptor cell maintenance ISS,IEA --
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
RP1L1
ECgene alternative splicing isoforms for
RP1L1

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:

RP1L1

SOURCE GeneReport for Unigene cluster for RP1L1 Gene:

Hs.33538

mRNA Expression by UniProt/SwissProt for RP1L1 Gene:

Q8IWN7-RP1L1_HUMAN
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
Systems:
  • nervous
Organs:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
General:
  • 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
chimpanzee
(Pan troglodytes)
Mammalia RP1L1 34 35
  • 95.06 (n)
dog
(Canis familiaris)
Mammalia RP1L1 34 35
  • 70.13 (n)
cow
(Bos Taurus)
Mammalia RP1L1 34 35
  • 68.84 (n)
rat
(Rattus norvegicus)
Mammalia LOC683404 34
  • 64.24 (n)
mouse
(Mus musculus)
Mammalia Rp1l1 34 16 35
  • 64.05 (n)
oppossum
(Monodelphis domestica)
Mammalia RP1L1 35
  • 40 (a)
OneToOne
chicken
(Gallus gallus)
Aves RP1L1 35
  • 27 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RP1L1 35
  • 25 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii rp1l1 35
  • 15 (a)
OneToMany
RP1L1 (1 of 2) 35
  • 10 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea F27C1.13 35
  • 28 (a)
OneToMany
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

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

RP1L1_HUMAN-Q8IWN7
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 Sequence Context AA Info Type
VAR_065126 Occult macular dystrophy (OCMD) [MIM:613587]
VAR_065127 Occult macular dystrophy (OCMD) [MIM:613587]
VAR_068350 Occult macular dystrophy (OCMD) [MIM:613587]
rs267607018 Pathogenic 10,611,220(-) GCGAA(C/T)GGCTG reference, missense
rs377269054 Likely pathogenic 10,622,967(+) AGAGC(A/G)CACCC reference, missense

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)

Relevant External Links for RP1L1 Gene

Human Gene Mutation Database (HGMD)
RP1L1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RP1L1

Disorders for RP1L1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for RP1L1 Gene - From: OMIM, ClinVar, GeneTests, 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

UniProtKB/Swiss-Prot

RP1L1_HUMAN
  • 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.

Relevant External Links for RP1L1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 characterization of the retinitis pigmentosa 1- like1 gene (rp1l1): a novel candidate for retinal degenerations. (PMID: 12634863) Conte I. … Banfi S. (Eur. J. Hum. Genet. 2003) 2 3 4 22 64
  2. Characterization of RP1L1, a highly polymorphic paralog of the retinitis pigmentosa 1 (RP1) gene. (PMID: 12724644) Bowne S.J. … Sullivan L.S. (Mol. Vis. 2003) 3 4 22 64
  3. Dominant mutations in RP1L1 are responsible for occult macular dystrophy. (PMID: 20826268) Akahori M. … Iwata T. (Am. J. Hum. Genet. 2010) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. Occult macular dystrophy in an Italian family carrying a mutation in the RP1L1 gene. (PMID: 26782618) Piermarocchi S. … Miotto S. (Mol Med Rep 2016) 3 64

Products for RP1L1 Gene

Sources for RP1L1 Gene

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