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    RPGRIP1L RPGRIP1 like [ Homo sapiens (human) ]

    Gene ID: 23322, updated on 8-Jul-2021

    Summary

    Official Symbol
    RPGRIP1Lprovided by HGNC
    Official Full Name
    RPGRIP1 likeprovided by HGNC
    Primary source
    HGNC:HGNC:29168
    See related
    Ensembl:ENSG00000103494 MIM:610937
    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; COACH3; 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]
    Expression
    Broad expression in testis (RPKM 3.8), brain (RPKM 1.3) and 19 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RPGRIP1L in Genome Data Viewer
    Location:
    16q12.2
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (53598153..53703859, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (53632065..53737771, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371268 Neighboring gene uncharacterized LOC105371269 Neighboring gene VISTA enhancer hs59 Neighboring gene FTO alpha-ketoglutarate dependent dioxygenase Neighboring gene Sharpr-MPRA regulatory region 10092 Neighboring gene VISTA enhancer hs155

    Genomic regions, transcripts, and products

    Expression

    • 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    COACH syndrome 3
    MedGen: C5436841 OMIM: 619113 GeneReviews: Not available
    not available
    Joubert syndrome
    MedGen: C0431399 GeneReviews: Joubert Syndrome
    Compare labs
    Joubert syndrome 7
    MedGen: C1969053 OMIM: 611560 GeneReviews: Joubert Syndrome
    Compare labs
    Meckel syndrome, type 5
    MedGen: C1969052 OMIM: 611561 GeneReviews: Not available
    Compare labs
    Nephronophthisis 8
    MedGen: CN119610 GeneReviews: Not available
    Compare labs
    Propensity score-based nonparametric test revealing genetic variants underlying bipolar disorder.
    GeneReviews: Not available
    Three new single nucleotide polymorphisms identified by a genome-wide association study in Korean patients with vitiligo.
    GeneReviews: Not available

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA1005, DKFZp686C0668

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables thromboxane A2 receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables thromboxane A2 receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cerebellum development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cochlea development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in corpus callosum development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in determination of left/right symmetry IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic forelimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic hindlimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in establishment of planar polarity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in establishment or maintenance of cell polarity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in kidney development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lateral ventricle development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in liver development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of G protein-coupled receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in neural tube patterning IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in non-motile cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in nose development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in olfactory bulb development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in pericardium development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retinal rod cell development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in axonemal microtubule IEA
    Inferred from Electronic Annotation
    more info
     
    located_in axoneme IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in bicellular tight junction IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cell-cell junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in ciliary rootlet IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in ciliary transition zone IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in ciliary transition zone IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cilium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in photoreceptor connecting cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    protein fantom
    Names
    RPGR-interacting protein 1-like protein
    fantom homolog
    nephrocystin-8
    protein phosphatase 1, regulatory subunit 134

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      5001..110707
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_696

    mRNA and Protein(s)

    1. NM_001127897.4NP_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, CR749645, DC423209
      Consensus CDS
      CCDS45486.1
      UniProtKB/Swiss-Prot
      Q68CZ1
      Related
      ENSP00000262135.4, ENST00000262135.9
      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_001308334.3NP_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
      UniProtKB/TrEMBL
      A0A087WX34, B7ZKJ9
      Related
      ENSP00000480698.1, ENST00000621565.5
      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_001328422.2NP_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
      Consensus CDS
      CCDS86527.1
      UniProtKB/TrEMBL
      H3BPS4
      Related
      ENSP00000455451.3, ENST00000568653.7
    4. NM_001328423.2NP_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
      Consensus CDS
      CCDS86526.1
      UniProtKB/TrEMBL
      I3L1B5
      Related
      ENSP00000458705.1, ENST00000566096.5
    5. NM_001330538.2NP_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, AC084795, AK307929, BX340768, R45454
      Consensus CDS
      CCDS81980.1
      UniProtKB/TrEMBL
      H3BV03
      Related
      ENSP00000457889.1, ENST00000563746.5
      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_015272.5NP_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
      ENSP00000493946.1, ENST00000647211.2
      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 Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

      Range
      53598153..53703859 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017023095.2XP_016878584.1  protein fantom isoform X3

    2. XM_005255868.2XP_005255925.1  protein fantom isoform X2

      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)
    3. XM_017023094.2XP_016878583.1  protein fantom isoform X1

    4. XM_017023099.1XP_016878588.1  protein fantom isoform X9

    5. XM_017023098.1XP_016878587.1  protein fantom isoform X9

    6. XM_017023096.2XP_016878585.1  protein fantom isoform X4

      Related
      ENSP00000456534.1, ENST00000564374.5
    7. XM_011522971.3XP_011521273.1  protein fantom isoform X6

      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
    8. XM_011522970.2XP_011521272.1  protein fantom isoform X5

      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)
    9. XM_011522973.3XP_011521275.1  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
    10. XM_017023097.2XP_016878586.1  protein fantom isoform X8

    11. XM_017023100.2XP_016878589.1  protein fantom isoform X10

    RNA

    1. XR_933260.3 RNA Sequence

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