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Aliases for RPGRIP1L Gene

Aliases for RPGRIP1L Gene

  • RPGRIP1-Like 2 3 5
  • RPGR-Interacting Protein 1-Like Protein 3 4
  • Fantom Homolog 2 3
  • Nephrocystin-8 3 4
  • NPHP8 3 4
  • FTM 3 4
  • Protein Phosphatase 1, Regulatory Subunit 134 3
  • Regulatory Subunit 134 2
  • Protein Phosphatase 1 2
  • RPGRIP1-Like Protein 4
  • Meckel Syndrome 2
  • PPP1R134 3
  • KIAA1005 4
  • Type 5 2
  • CORS3 3
  • JBTS7 3
  • MKS5 3

External Ids for RPGRIP1L Gene

Previous GeneCards Identifiers for RPGRIP1L Gene

  • GC16M052193
  • GC16M053633
  • GC16M039520

Summaries for RPGRIP1L Gene

Entrez Gene Summary for RPGRIP1L Gene

  • The protein encoded by this gene can localize to the basal body-centrosome complex or to primary cilia and centrosomes in ciliated cells. The encoded protein has been found to interact with nephrocystin-4. Defects in this gene are a cause of Joubert syndrome type 7 (JBTS7) and Meckel syndrome type 5 (MKS5). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for RPGRIP1L Gene

RPGRIP1L (RPGRIP1-Like) is a Protein Coding gene. Diseases associated with RPGRIP1L include joubert syndrome 7 and meckel syndrome 5. Among its related pathways are Signaling by GPCR and Organelle biogenesis and maintenance. GO annotations related to this gene include thromboxane A2 receptor binding. An important paralog of this gene is RPGRIP1.

UniProtKB/Swiss-Prot for RPGRIP1L Gene

  • Negatively regulates signaling through the G-protein coupled thromboxane A2 receptor (TBXA2R). May be involved in mechanisms like programmed cell death, craniofacial development, patterning of the limbs, and formation of the left-right axis (By similarity). Involved in the organization of apical junctions in kidney cells together with NPHP1 and NPHP4 (By similarity). Does not seem to be strictly required for ciliogenesis (By similarity).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPGRIP1L Gene

Genomics for RPGRIP1L Gene

Regulatory Elements for RPGRIP1L Gene

Promoters for RPGRIP1L Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around RPGRIP1L on UCSC Golden Path with GeneCards custom track

Genomic Location for RPGRIP1L Gene

Chromosome:
16
Start:
53,597,683 bp from pter
End:
53,703,938 bp from pter
Size:
106,256 bases
Orientation:
Minus strand

Genomic View for RPGRIP1L Gene

Genes around RPGRIP1L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPGRIP1L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPGRIP1L Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPGRIP1L Gene

Proteins for RPGRIP1L Gene

  • Protein details for RPGRIP1L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q68CZ1-FTM_HUMAN
    Recommended name:
    Protein fantom
    Protein Accession:
    Q68CZ1
    Secondary Accessions:
    • A0PJ88
    • Q9Y2K8

    Protein attributes for RPGRIP1L Gene

    Size:
    1315 amino acids
    Molecular mass:
    151201 Da
    Quaternary structure:
    • Interacts with NPHP4 in a complex containing NPHP1, NPHP4 and RPGRIP1L/NPHP8. Interacts with TBXA2R (via C-terminus). Interacts with IQCB1; the interaction likely requires additional interactors. Interacts with RPGR. Interacts with NEK4.

    Three dimensional structures from OCA and Proteopedia for RPGRIP1L Gene

    Alternative splice isoforms for RPGRIP1L Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RPGRIP1L Gene

Proteomics data for RPGRIP1L Gene at MOPED

Post-translational modifications for RPGRIP1L Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

No data available for DME Specific Peptides for RPGRIP1L Gene

Domains & Families for RPGRIP1L Gene

Protein Domains for RPGRIP1L Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for RPGRIP1L Gene

Graphical View of Domain Structure for InterPro Entry

Q68CZ1

UniProtKB/Swiss-Prot:

FTM_HUMAN :
  • Contains 2 C2 domains.
  • Belongs to the RPGRIP1 family.
Domain:
  • Contains 2 C2 domains.
Family:
  • Belongs to the RPGRIP1 family.
genes like me logo Genes that share domains with RPGRIP1L: view

Function for RPGRIP1L Gene

Molecular function for RPGRIP1L Gene

UniProtKB/Swiss-Prot Function:
Negatively regulates signaling through the G-protein coupled thromboxane A2 receptor (TBXA2R). May be involved in mechanisms like programmed cell death, craniofacial development, patterning of the limbs, and formation of the left-right axis (By similarity). Involved in the organization of apical junctions in kidney cells together with NPHP1 and NPHP4 (By similarity). Does not seem to be strictly required for ciliogenesis (By similarity).
genes like me logo Genes that share phenotypes with RPGRIP1L: view

Human Phenotype Ontology for RPGRIP1L Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RPGRIP1L Gene

MGI Knock Outs for RPGRIP1L:

Animal Model Products

CRISPR Products

miRNA for RPGRIP1L Gene

miRTarBase miRNAs that target RPGRIP1L

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for RPGRIP1L Gene

Localization for RPGRIP1L Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPGRIP1L Gene

Cytoplasm. Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, cilium axoneme. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Cell junction, tight junction. Note=In cultured renal cells, it localizes diffusely in the cytoplasm but, as cells approach confluence, it accumulates to basolateral tight junctions.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RPGRIP1L Gene COMPARTMENTS Subcellular localization image for RPGRIP1L gene
Compartment Confidence
cytoskeleton 5
cytosol 5
nucleus 3
plasma membrane 2

Gene Ontology (GO) - Cellular Components for RPGRIP1L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0005930 axoneme IDA 17558409
genes like me logo Genes that share ontologies with RPGRIP1L: view

Pathways & Interactions for RPGRIP1L Gene

genes like me logo Genes that share pathways with RPGRIP1L: view

Interacting Proteins for RPGRIP1L Gene

Gene Ontology (GO) - Biological Process for RPGRIP1L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001736 establishment of planar polarity IEA --
GO:0001822 kidney development IEA --
GO:0001889 liver development IEA --
GO:0006996 organelle organization TAS --
GO:0007368 determination of left/right symmetry IEA --
genes like me logo Genes that share ontologies with RPGRIP1L: view

No data available for SIGNOR curated interactions for RPGRIP1L Gene

Drugs & Compounds for RPGRIP1L Gene

No Compound Related Data Available

Transcripts for RPGRIP1L Gene

Unigene Clusters for RPGRIP1L Gene

RPGRIP1-like:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for RPGRIP1L Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24a ·
SP1: - - - -
SP2: - -
SP3:
SP4:

ExUns: 24b · 24c
SP1:
SP2:
SP3:
SP4:

Relevant External Links for RPGRIP1L Gene

GeneLoc Exon Structure for
RPGRIP1L
ECgene alternative splicing isoforms for
RPGRIP1L

Expression for RPGRIP1L Gene

mRNA expression in normal human tissues for RPGRIP1L Gene

Protein differential expression in normal tissues from HIPED for RPGRIP1L Gene

This gene is overexpressed in Plasma (35.6), Peripheral blood mononuclear cells (18.5), and Platelet (11.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for RPGRIP1L Gene



SOURCE GeneReport for Unigene cluster for RPGRIP1L Gene Hs.298382

mRNA Expression by UniProt/SwissProt for RPGRIP1L Gene

Q68CZ1-FTM_HUMAN
Tissue specificity: Ubiquitously expressed with relatively high level of expression in hypothalamus and islet. During early development, expressed in multiple organs including brain, eye, forelimb and kidney.
genes like me logo Genes that share expression patterns with RPGRIP1L: view

Protein tissue co-expression partners for RPGRIP1L Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for RPGRIP1L Gene

Orthologs for RPGRIP1L Gene

This gene was present in the common ancestor of animals.

Orthologs for RPGRIP1L Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RPGRIP1L 35
  • 99.49 (n)
  • 99.35 (a)
RPGRIP1L 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RPGRIP1L 36
  • 91 (a)
OneToOne
RPGRIP1L 35
  • 91.17 (n)
  • 90.85 (a)
dog
(Canis familiaris)
Mammalia RPGRIP1L 35
  • 91.57 (n)
  • 90.84 (a)
RPGRIP1L 36
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rpgrip1l 36
  • 85 (a)
OneToOne
Rpgrip1l 16
Rpgrip1l 35
  • 85.43 (n)
  • 85.43 (a)
oppossum
(Monodelphis domestica)
Mammalia RPGRIP1L 36
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RPGRIP1L 36
  • 72 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rpgrip1l 35
  • 85.04 (n)
  • 84.88 (a)
chicken
(Gallus gallus)
Aves RPGRIP1L 36
  • 57 (a)
OneToOne
RPGRIP1L 35
  • 69.22 (n)
  • 60.14 (a)
lizard
(Anolis carolinensis)
Reptilia RPGRIP1L 36
  • 64 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.31171 35
tropical clawed frog
(Silurana tropicalis)
Amphibia rpgrip1l 35
  • 64.42 (n)
  • 58.69 (a)
zebrafish
(Danio rerio)
Actinopterygii rpgrip1l 36
  • 49 (a)
OneToOne
rpgrip1l 35
  • 58.03 (n)
  • 53.43 (a)
worm
(Caenorhabditis elegans)
Secernentea mks-5 36
  • 16 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6207 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 38 (a)
OneToMany
Species with no ortholog for RPGRIP1L:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for RPGRIP1L Gene

ENSEMBL:
Gene Tree for RPGRIP1L (if available)
TreeFam:
Gene Tree for RPGRIP1L (if available)

Paralogs for RPGRIP1L Gene

Paralogs for RPGRIP1L Gene

genes like me logo Genes that share paralogs with RPGRIP1L: view

Variants for RPGRIP1L Gene

Sequence variations from dbSNP and Humsavar for RPGRIP1L Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs121918198 Joubert syndrome 7 (JBTS7) 53,652,844(-) AAGTA(A/C)CCTTT nc-transcript-variant, reference, missense
VAR_039394 Joubert syndrome 7 (JBTS7)
rs121918200 Joubert syndrome 7 (JBTS7) 53,652,604(-) TTGCA(A/C/G)CATGT nc-transcript-variant, reference, missense
rs2302677 - 53,649,037(+) AAAGT(C/T)GAATT nc-transcript-variant, reference, missense
rs2111119 - 53,637,842(+) ACTGC(C/T)TTCTT nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for RPGRIP1L Gene

Variant ID Type Subtype PubMed ID
nsv906668 CNV Loss 21882294
esv268190 CNV Insertion 20981092
esv2651638 CNV Deletion 19546169
nsv525463 CNV Loss 19592680
esv2714498 CNV Deletion 23290073
esv2714499 CNV Deletion 23290073
esv2714500 CNV Deletion 23290073
esv2660513 CNV Deletion 23128226

Variation tolerance for RPGRIP1L Gene

Residual Variation Intolerance Score: 87.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.76; 89.44% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RPGRIP1L Gene

HapMap Linkage Disequilibrium report
RPGRIP1L
Human Gene Mutation Database (HGMD)
RPGRIP1L

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPGRIP1L Gene

Disorders for RPGRIP1L Gene

MalaCards: The human disease database

(30) MalaCards diseases for RPGRIP1L Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
joubert syndrome 7
  • cerebello-oculo-renal syndrome 3
meckel syndrome 5
  • mks5
coach syndrome
  • cerebellar vermis hypo/aplasia, oligophrenia, ataxia congenital, coloboma, and hepatic fibrosis
joubert syndrome with renal anomalies
  • joubert syndrome 4
meckel syndrome 1
  • meckel syndrome
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

FTM_HUMAN
  • Note=Ciliary dysfunction leads to a broad spectrum of disorders, collectively termed ciliopathies. Overlapping clinical features include retinal degeneration, renal cystic disease, skeletal abnormalities, fibrosis of various organ, and a complex range of anatomical and functional defects of the central and peripheral nervous system. The ciliopathy range of diseases includes Meckel-Gruber syndrome, Bardet-Biedl syndrome, Joubert syndrome, nephronophtisis, Senior-Loken syndrome, and Jeune asphyxiating thoracic dystrophy among others. Single-locus allelism is insufficient to explain the variable penetrance and expressivity of such disorders, leading to the suggestion that variations across multiple sites of the ciliary proteome, including RPGRIP1L, influence the clinical outcome. {ECO:0000269 PubMed:19430481, ECO:0000269 PubMed:21258341}.
  • Joubert syndrome 7 (JBTS7) [MIM:611560]: A disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease. {ECO:0000269 PubMed:17558407, ECO:0000269 PubMed:17558409, ECO:0000269 PubMed:22693042}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Meckel syndrome 5 (MKS5) [MIM:611561]: A disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. {ECO:0000269 PubMed:17558409, ECO:0000269 PubMed:19430481}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • COACH syndrome (COACHS) [MIM:216360]: A disorder characterized by mental retardation, ataxia due to cerebellar hypoplasia, and hepatic fibrosis. Patients present the molar tooth sign, a midbrain-hindbrain malformation pathognomonic for Joubert syndrome and related disorders. Other features, such as coloboma and renal cysts, may be variable. {ECO:0000269 PubMed:19574260}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for RPGRIP1L

Genetic Association Database (GAD)
RPGRIP1L
Human Genome Epidemiology (HuGE) Navigator
RPGRIP1L
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RPGRIP1L
genes like me logo Genes that share disorders with RPGRIP1L: view

No data available for Genatlas for RPGRIP1L Gene

Publications for RPGRIP1L Gene

  1. Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10231032) Nagase T. … Ohara O. (DNA Res. 1999) 2 3 4 67
  2. Three new single nucleotide polymorphisms identified by a genome-wide association study in Korean patients with vitiligo. (PMID: 23678272) Cheong K.A. … Lee A.Y. (J. Korean Med. Sci. 2013) 3
  3. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. (PMID: 22658674) Castello A. … Hentze M.W. (Cell 2012) 3
  4. Molecular approach in the study of AlstrAPm syndrome: analysis of ten Spanish families. (PMID: 22876109) PiA+eiro-Gallego T. … Valverde D. (Mol. Vis. 2012) 3
  5. Genetic association of the gene encoding RPGRIP1L with susceptibility to vascular dementia. (PMID: 22425971) Woo J. … Lee C. (Gene 2012) 3

Products for RPGRIP1L Gene

Sources for RPGRIP1L Gene

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