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RPGRIP1L RPGRIP1-like [ Homo sapiens (human) ]

Gene ID: 23322, updated on 23-May-2015
Official Symbol
RPGRIP1Lprovided by HGNC
Official Full Name
RPGRIP1-likeprovided by HGNC
Primary source
HGNC:HGNC:29168
See related
Ensembl:ENSG00000103494; HPRD:17204; MIM:610937; Vega:OTTHUMG00000173125
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FTM; MKS5; CORS3; JBTS7; NPHP8; PPP1R134
Summary
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]
Orthologs
See RPGRIP1L in MapViewer
Location:
16q12.2
Exon count:
35
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 16 NC_000016.10 (53599906..53703859, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (53633818..53737771, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371269 Neighboring gene uncharacterized LOC105371270 Neighboring gene fat mass and obesity associated Neighboring gene uncharacterized LOC105371271 Neighboring gene FTO intronic transcript 1

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
COACH syndrome
MedGen: C1857662 OMIM: 216360 GeneReviews: Not available
Compare labs
Familial aplasia of the vermis Compare labs
Joubert syndrome 7 Compare labs
Meckel syndrome type 5
MedGen: C1969052 OMIM: 611561 GeneReviews: Not available
Compare labs
Nephronophthisis 8
MedGen: CN119610 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Propensity score-based nonparametric test revealing genetic variants underlying bipolar disorder.
NHGRI GWA Catalog
Three new single nucleotide polymorphisms identified by a genome-wide association study in Korean patients with vitiligo.
NHGRI GWA Catalog
  • Anchoring of the basal body to the plasma membrane, organism-specific biosystem (from REACTOME)
    Anchoring of the basal body to the plasma membrane, organism-specific biosystemThe primary cilium is a microtubule-based organelle that is present on differentiated cells of nearly all eukaryotes. Cilium biogenesis is initiated by the docking of basal bodies, a centriole-derive...
  • Assembly of the primary cilium, organism-specific biosystem (from REACTOME)
    Assembly of the primary cilium, organism-specific biosystemThe primary cilium is one of two main types of cilia present on the surface of many eukaryotic cells (reviewed in Flieghauf et al, 2007). Unlike the motile cilia, which are generally present in large...
  • Hedgehog 'off' state, organism-specific biosystem (from REACTOME)
    Hedgehog 'off' state, organism-specific biosystemHedgehog is a secreted morphogen that has evolutionarily conserved roles in body organization by regulating the activity of the Ci/Gli transcription factor family. In Drosophila in the absence of Hh ...
  • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
    Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Hedgehog, organism-specific biosystem (from REACTOME)
    Signaling by Hedgehog, organism-specific biosystemHedgehog (Hh) is a secreted morphogen that regulates developmental processes in vertebrates including limb bud formation, neural tube patterning, cell growth and differentiation (reviewed in Hui and ...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • KIAA1005, DKFZp686C0668

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
thromboxane A2 receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
camera-type eye development IEA
Inferred from Electronic Annotation
more info
 
cerebellum development IEA
Inferred from Electronic Annotation
more info
 
cilium assembly IEA
Inferred from Electronic Annotation
more info
 
cochlea development IEA
Inferred from Electronic Annotation
more info
 
corpus callosum development IEA
Inferred from Electronic Annotation
more info
 
determination of left/right symmetry IEA
Inferred from Electronic Annotation
more info
 
embryonic forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic hindlimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
establishment of planar polarity IEA
Inferred from Electronic Annotation
more info
 
establishment or maintenance of cell polarity IEA
Inferred from Electronic Annotation
more info
 
in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
kidney development IEA
Inferred from Electronic Annotation
more info
 
lateral ventricle development IEA
Inferred from Electronic Annotation
more info
 
liver development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of G-protein coupled receptor protein signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
neural tube patterning IEA
Inferred from Electronic Annotation
more info
 
nose development IEA
Inferred from Electronic Annotation
more info
 
olfactory bulb development IEA
Inferred from Electronic Annotation
more info
 
organelle organization TAS
Traceable Author Statement
more info
 
pericardium development IEA
Inferred from Electronic Annotation
more info
 
regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
axoneme IDA
Inferred from Direct Assay
more info
PubMed 
bicellular tight junction IEA
Inferred from Electronic Annotation
more info
 
cell-cell junction IDA
Inferred from Direct Assay
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
ciliary basal body IDA
Inferred from Direct Assay
more info
PubMed 
ciliary transition zone IEA
Inferred from Electronic Annotation
more info
 
cilium IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
Preferred Names
protein fantom
Names
protein fantom
RPGR-interacting protein 1-like protein
fantom homolog
nephrocystin-8
protein phosphatase 1, regulatory subunit 134

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008991.2 RefSeqGene

    Range
    4926..109621
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001127897.2NP_001121369.1  protein fantom isoform b

    See identical proteins and their annotated locations for NP_001121369.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AB023222, AC007497, AC007909, CR749645, DC423209
    Consensus CDS
    CCDS45486.1
    UniProtKB/Swiss-Prot
    Q68CZ1
    Conserved Domains (3) summary
    cd00030
    Location:792891
    C2; C2 domain
    pfam06818
    Location:238447
    Fez1; Fez1
    pfam11618
    Location:631737
    DUF3250; Protein of unknown function (DUF3250)
  2. NM_001308334.1NP_001295263.1  protein fantom isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the central coding region compared to variant 1. The encoded isoform (c) is shorter than isoform a.
    Source sequence(s)
    AC007497, BC136433, BX340768, R45454
    Consensus CDS
    CCDS76868.1
  3. NM_015272.3NP_056087.2  protein fantom isoform a

    See identical proteins and their annotated locations for NP_056087.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC007497, AC007909, CR749645
    Consensus CDS
    CCDS32447.1
    UniProtKB/Swiss-Prot
    Q68CZ1
    Related
    ENSP00000369257, OTTHUMP00000250116, ENST00000379925, OTTHUMT00000422187
    Conserved Domains (3) summary
    cd00030
    Location:792891
    C2; C2 domain
    pfam06818
    Location:238447
    Fez1; Fez1
    pfam11618
    Location:631737
    DUF3250; Protein of unknown function (DUF3250)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p2 Primary Assembly

    Range
    53599906..53703859
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005255867.1XP_005255924.1  

    UniProtKB/TrEMBL
    H3BV03
    Conserved Domains (3) summary
    cd00030
    Location:792891
    C2; C2 domain
    pfam06818
    Location:238447
    Fez1; Fez1
    pfam11618
    Location:631737
    DUF3250; Protein of unknown function (DUF3250)
  2. XM_005255869.1XP_005255926.1  

    UniProtKB/TrEMBL
    A0A087WX34
    Related
    ENSP00000480698, ENST00000621565
    Conserved Domains (3) summary
    cd00030
    Location:792891
    C2; C2 domain
    pfam06818
    Location:238447
    Fez1; Fez1
    pfam11618
    Location:631737
    DUF3250; Protein of unknown function (DUF3250)
  3. XM_005255868.1XP_005255925.1  

    Conserved Domains (3) summary
    cd00030
    Location:796895
    C2; C2 domain
    pfam06818
    Location:238451
    Fez1; Fez1
    pfam11618
    Location:635741
    DUF3250; Protein of unknown function (DUF3250)
  4. XM_011522968.1XP_011521270.1  

    See identical proteins and their annotated locations for XP_011521270.1

    Conserved Domains (3) summary
    cd00030
    Location:792891
    C2; C2 domain
    pfam06818
    Location:238447
    Fez1; Fez1
    pfam11618
    Location:631737
    DUF3250; Protein of unknown function (DUF3250)
  5. XM_011522974.1XP_011521276.1  

    See identical proteins and their annotated locations for XP_011521276.1

    Conserved Domains (2) summary
    cd00030
    Location:207306
    C2; C2 domain
    pfam11618
    Location:46152
    DUF3250; Protein of unknown function (DUF3250)
  6. XM_005255871.2XP_005255928.1  

    See identical proteins and their annotated locations for XP_005255928.1

    Conserved Domains (2) summary
    cd00030
    Location:207306
    C2; C2 domain
    pfam11618
    Location:46152
    DUF3250; Protein of unknown function (DUF3250)
  7. XM_011522969.1XP_011521271.1  

    Related
    ENSP00000456534, OTTHUMP00000250118, ENST00000564374, OTTHUMT00000422189
    Conserved Domains (3) summary
    cd00030
    Location:796895
    C2; C2 domain
    pfam06818
    Location:238451
    Fez1; Fez1
    pfam11618
    Location:635741
    DUF3250; Protein of unknown function (DUF3250)
  8. XM_011522972.1XP_011521274.1  

    Conserved Domains (3) summary
    cd00030
    Location:796895
    C2; C2 domain
    pfam06818
    Location:238451
    Fez1; Fez1
    pfam11618
    Location:635741
    DUF3250; Protein of unknown function (DUF3250)
  9. XM_011522971.1XP_011521273.1  

    Conserved Domains (3) summary
    cd00030
    Location:796895
    C2; C2 domain
    pfam06818
    Location:238451
    Fez1; Fez1
    pfam11618
    Location:635741
    DUF3250; Protein of unknown function (DUF3250)
  10. XM_011522970.1XP_011521272.1  

    Conserved Domains (3) summary
    cd00030
    Location:796895
    C2; C2 domain
    pfam06818
    Location:238451
    Fez1; Fez1
    pfam11618
    Location:635741
    DUF3250; Protein of unknown function (DUF3250)
  11. XM_011522973.1XP_011521275.1  

    Conserved Domains (3) summary
    cd00030
    Location:796895
    C2; C2 domain
    pfam06818
    Location:238451
    Fez1; Fez1
    pfam11618
    Location:635741
    DUF3250; Protein of unknown function (DUF3250)

RNA

  1. XR_933260.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018927.2 Alternate CHM1_1.1

    Range
    55040948..55144907
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)