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    RPGRIP1L RPGRIP1 like [ Homo sapiens (human) ]

    Gene ID: 23322, updated on 27-May-2017
    Official Symbol
    RPGRIP1Lprovided by HGNC
    Official Full Name
    RPGRIP1 likeprovided by HGNC
    Primary source
    HGNC:HGNC:29168
    See related
    Ensembl:ENSG00000103494 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). [provided by RefSeq, Jun 2016]
    Orthologs
    Location:
    16q12.2
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 16 NC_000016.10 (53599239..53703934, 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 LOC105371268 Neighboring gene uncharacterized LOC105371269 Neighboring gene FTO, alpha-ketoglutarate dependent dioxygenase Neighboring gene uncharacterized LOC105371271 Neighboring gene FTO intronic transcript 1

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    COACH syndrome
    MedGen: C1857662 OMIM: 216360 GeneReviews: Not available
    Compare labs
    Joubert syndrome 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 biosystemCilium biogenesis is initiated by the docking of basal bodies, a centriole-derived organelle, to the plasma membrane (reviewed in Reiter et al, 2012). The centriole consists of a multiprotein core su...
    • Cilium Assembly, organism-specific biosystem (from REACTOME)
      Cilium Assembly, organism-specific biosystemCilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguishe...
    • 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
     
    ciliary basal body docking TAS
    Traceable Author Statement
    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
     
    non-motile cilium assembly 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
     
    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
    axonemal microtubule IEA
    Inferred from Electronic Annotation
    more info
     
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cilium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    photoreceptor connecting cilium IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    Preferred Names
    protein fantom
    Names
    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
      4922..109621
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001127897.3NP_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
      Related
      ENSP00000262135.4, OTTHUMP00000250115, ENST00000262135.8, OTTHUMT00000422186
      Conserved Domains (4) summary
      cd00030
      Location:792891
      C2; C2 domain
      pfam06818
      Location:244445
      Fez1; Fez1
      pfam11618
      Location:598737
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
      cl23720
      Location:214350
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    2. NM_001308334.2NP_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, AC007909, BC136433, BX340768, R45454
      Consensus CDS
      CCDS76868.1
      UniProtKB/TrEMBL
      A0A087WX34, B7ZKJ9
      Related
      ENSP00000480698.1, ENST00000621565.4
      Conserved Domains (4) summary
      cd00030
      Location:792891
      C2; C2 domain
      pfam06818
      Location:244445
      Fez1; Fez1
      pfam11618
      Location:598737
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
      cl23720
      Location:214350
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    3. NM_001328422.1NP_001315351.1  protein fantom isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks several 3' exons, and uses an alternate 3' terminal exon, compared to variant 1. The encoded isoform (d) has a shorter and distinct C-terminus compared to isoform a.
      Source sequence(s)
      AC007909, BX340768, CA313857, EF565106
      UniProtKB/TrEMBL
      H3BPS4
    4. NM_001328423.1NP_001315352.1  protein fantom isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks several 3' exons, and has a 3' end that extends into an intron compared to variant 1. The encoded isoform (e) has a shorter and distinct C-terminus compared to isoform a.
      Source sequence(s)
      AC007909, BX340768, CD674885
      UniProtKB/TrEMBL
      I3L1B5
    5. NM_001330538.1NP_001317467.1  protein fantom isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (f) is shorter than isoform 1.
      Source sequence(s)
      AC007497, AC007909, AC084795, AK307929, BX340768, R45454
      Consensus CDS
      CCDS81980.1
      UniProtKB/TrEMBL
      H3BV03
      Conserved Domains (5) summary
      cd00030
      Location:792891
      C2; C2 domain
      pfam06818
      Location:244445
      Fez1; Fez1
      pfam10482
      Location:338459
      CtIP_N; Tumour-suppressor protein CtIP N-terminal domain
      pfam11618
      Location:598737
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
      cl23720
      Location:214350
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    6. NM_015272.4NP_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 longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC007497, AC007909, CR749645
      Consensus CDS
      CCDS32447.1
      UniProtKB/Swiss-Prot
      Q68CZ1
      Related
      ENSP00000369257.3, OTTHUMP00000250116, ENST00000379925.7, OTTHUMT00000422187
      Conserved Domains (5) summary
      cd00030
      Location:792891
      C2; C2 domain
      pfam06818
      Location:244445
      Fez1; Fez1
      pfam10482
      Location:338459
      CtIP_N; Tumour-suppressor protein CtIP N-terminal domain
      pfam11618
      Location:598737
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
      cl23720
      Location:214350
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p7 Primary Assembly

      Range
      53599239..53703934 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005255867.1XP_005255924.1  protein fantom isoform X2

      Related
      ENSP00000457889.1, OTTHUMP00000250117, ENST00000563746.5, OTTHUMT00000422188
      Conserved Domains (5) summary
      cd00030
      Location:792891
      C2; C2 domain
      pfam06818
      Location:244445
      Fez1; Fez1
      pfam10482
      Location:338459
      CtIP_N; Tumour-suppressor protein CtIP N-terminal domain
      pfam11618
      Location:598737
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
      cl23720
      Location:214350
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    2. XM_017023095.1XP_016878584.1  protein fantom isoform X4

    3. XM_005255868.1XP_005255925.1  protein fantom isoform X3

      Conserved Domains (4) summary
      cd00030
      Location:796895
      C2; C2 domain
      pfam06818
      Location:244449
      Fez1; Fez1
      pfam11618
      Location:602741
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
      cl23720
      Location:214350
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    4. XM_017023094.1XP_016878583.1  protein fantom isoform X1

    5. XM_017023099.1XP_016878588.1  protein fantom isoform X10

    6. XM_017023098.1XP_016878587.1  protein fantom isoform X10

    7. XM_017023096.1XP_016878585.1  protein fantom isoform X5

      Related
      ENSP00000456534.1, OTTHUMP00000250118, ENST00000564374.5, OTTHUMT00000422189
    8. XM_011522971.2XP_011521273.1  protein fantom isoform X7

      Conserved Domains (3) summary
      cd00030
      Location:796895
      C2; C2 domain
      pfam06818
      Location:244449
      Fez1; Fez1
      pfam11618
      Location:602741
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
    9. XM_011522970.1XP_011521272.1  protein fantom isoform X6

      Conserved Domains (4) summary
      cd00030
      Location:796895
      C2; C2 domain
      pfam06818
      Location:244449
      Fez1; Fez1
      pfam11618
      Location:602741
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
      cl23720
      Location:214350
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    10. XM_011522973.2XP_011521275.1  protein fantom isoform X8

      Conserved Domains (3) summary
      cd00030
      Location:796895
      C2; C2 domain
      pfam06818
      Location:244449
      Fez1; Fez1
      pfam11618
      Location:602741
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
    11. XM_017023097.1XP_016878586.1  protein fantom isoform X9

    12. XM_017023100.1XP_016878589.1  protein fantom isoform X11

    RNA

    1. XR_933260.2 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018927.2 Alternate CHM1_1.1

      Range
      55040281..55144982 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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