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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
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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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