RP1 RP1 axonemal microtubule associated [Homo sapiens (human)] - Gene

Summary

Official Symbol: RP1provided by HGNC
Official Full Name: RP1 axonemal microtubule associatedprovided by HGNC
Primary source: HGNC:HGNC:10263
See related: Ensembl:ENSG00000104237 MIM:603937; AllianceGenome:HGNC:10263
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: ORP1; DCDC4A
Summary: This gene encodes a member of the doublecortin family. The protein encoded by this gene contains two doublecortin domains, which bind microtubules and regulate microtubule polymerization. The encoded protein is a photoreceptor microtubule-associated protein and is required for correct stacking of outer segment disc. This protein and the RP1L1 protein, another retinal-specific protein, play essential and synergistic roles in affecting photosensitivity and outer segment morphogenesis of rod photoreceptors. Because of its response to in vivo retinal oxygen levels, this protein was initially named ORP1 (oxygen-regulated protein-1). This protein was subsequently designated RP1 (retinitis pigmentosa 1) when it was found that mutations in this gene cause autosomal dominant retinitis pigmentosa. Mutations in this gene also cause autosomal recessive retinitis pigmentosa. Transcript variants resulted from an alternative promoter and alternative splicings have been found, which overlap the current reference sequence and has several exons upstream and downstream of the current reference sequence. However, the biological validity and full-length nature of some variants cannot be determined at this time.[provided by RefSeq, Sep 2010]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 8q11.23-q12.1

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (54559185..54871234)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (54886748..55248781)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (55471745..55783794)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RP1 Dominant p.Ser740* Pathogenic Variant in 20 Knowingly Unrelated Families Affected by Rod-Cone Dystrophy: Potential Founder Effect in Western Sicily.
Title: RP1 Dominant p.Ser740* Pathogenic Variant in 20 Knowingly Unrelated Families Affected by Rod-Cone Dystrophy: Potential Founder Effect in Western Sicily.
LncRNA RP1-276N6.2 Expression and RP1-276N6.2 Gene Polymorphisms Contribute to the Risk of Coronary Artery Disease in Chinese Han Population.
Title: LncRNA RP1-276N6.2 Expression and RP1-276N6.2 Gene Polymorphisms Contribute to the Risk of Coronary Artery Disease in Chinese Han Population.
Identification of RP1 as the genetic cause of retinitis pigmentosa in a multi-generational pedigree using Extremely Low-Coverage Whole Genome Sequencing (XLC-WGS).
Title: Identification of RP1 as the genetic cause of retinitis pigmentosa in a multi-generational pedigree using Extremely Low-Coverage Whole Genome Sequencing (XLC-WGS).
In Silico identification of a common mobile element insertion in exon 4 of RP1.
Title: In Silico identification of a common mobile element insertion in exon 4 of RP1.
Clinical characteristics and high resolution retinal imaging of retinitis pigmentosa caused by RP1 gene variants.
Title: Clinical characteristics and high resolution retinal imaging of retinitis pigmentosa caused by RP1 gene variants.
A founder Alu insertion in RP1 gene in Japanese patients with retinitis pigmentosa.
Title: A founder Alu insertion in RP1 gene in Japanese patients with retinitis pigmentosa.
Clinical heterogeneity in retinitis pigmentosa caused by variants in RP1 and RLBP1 in five extended consanguineous pedigrees.
Title: Clinical heterogeneity in retinitis pigmentosa caused by variants in RP1 and RLBP1 in five extended consanguineous pedigrees.
Retinitis Pigmentosa Due to Rp1 Biallelic Variants.
Title: Retinitis Pigmentosa Due to Rp1 Biallelic Variants.
Homozygous loss-of-function mutations in RP1 gene is associated with retinitis pigmentosa.
Title: Novel homozygous loss-of-function mutations in RP1 and RP1L1 genes in retinitis pigmentosa patients.
Since mutations at various points along exon 4 have divergent consequences, genetic testing alone may be insufficient for counseling, but recessive inheritance should be considered likely in severe early-onset cases.
Title: The Location of Exon 4 Mutations in RP1 Raises Challenges for Genetic Counseling and Gene Therapy.

Submit: New GeneRIF Correction See all GeneRIFs (44)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Retinitis pigmentosa 1 MedGen: C0220701 OMIM: 180100 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH123325 (e-PCR)
- UniSTS:135702

STS-AA018812 (e-PCR)
- UniSTS:72478

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables microtubule binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in axoneme assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in axoneme assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to light stimulus	IEA Inferred from Electronic Annotation more info
involved_in intracellular signal transduction	IEA Inferred from Electronic Annotation more info
involved_in photoreceptor cell development	IBA Inferred from Biological aspect of Ancestor more info
involved_in photoreceptor cell development	ISS Inferred from Sequence or Structural Similarity more info
involved_in photoreceptor cell maintenance	ISS Inferred from Sequence or Structural Similarity more info
involved_in photoreceptor cell outer segment organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in phototransduction, visible light	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of non-motile cilium assembly	IEA Inferred from Electronic Annotation more info
involved_in retina development in camera-type eye	IBA Inferred from Biological aspect of Ancestor more info
involved_in retinal cone cell development	ISS Inferred from Sequence or Structural Similarity more info
involved_in retinal rod cell development	ISS Inferred from Sequence or Structural Similarity more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in axoneme	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary tip	IEA Inferred from Electronic Annotation more info
located_in microtubule	IEA Inferred from Electronic Annotation more info
part_of microtubule associated complex	ISS Inferred from Sequence or Structural Similarity more info
located_in photoreceptor connecting cilium	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor inner segment	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor outer segment	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: oxygen-regulated protein 1

Names: doublecortin domain containing 4A; retinitis pigmentosa 1 (autosomal dominant); retinitis pigmentosa 1 protein; retinitis pigmentosa RP1 protein

NCBI Reference Sequences (RefSeq)

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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

NG_009840.3 RefSeqGene

Range

61913..76651

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001375654.1 → NP_001362583.1 oxygen-regulated protein 1 isoform 2

Status: REVIEWED

Source sequence(s)

AC090137, AC090151, AC091076, AF128525

UniProtKB/TrEMBL

A0A1B0GUH0

Conserved Domains (5) summary

cd01756
Location:392 → 510

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cd17145
Location:36 → 114

DCX1_RP1; Doublecortin-like domain 1 found in retinitis pigmentosa 1 (RP1)-like protein

cd17147
Location:154 → 229

DCX2_RP1; Dublecortin-like domain 2 found in retinitis pigmentosa 1 (RP1)-like protein

cl00011
Location:265 → 381

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...

cl00060
Location:544 → 578

FGF; Acidic and basic fibroblast growth factor family; FGFs are mitogens, which stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family plays essential roles in patterning and differentiation during vertebrate ...
NM_006269.2 → NP_006260.1 oxygen-regulated protein 1 isoform 1

See identical proteins and their annotated locations for NP_006260.1

Status: REVIEWED

Source sequence(s)

AF141021

Consensus CDS

CCDS6160.1

UniProtKB/Swiss-Prot

P56715

Related

ENSP00000220676.1, ENST00000220676.2

Conserved Domains (2) summary

cd17145
Location:36 → 114

DCX1_RP1; Doublecortin-like domain 1 found in retinitis pigmentosa 1 (RP1)-like protein

cd17147
Location:154 → 229

DCX2_RP1; Dublecortin-like domain 2 found in retinitis pigmentosa 1 (RP1)-like protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

54559185..54871234

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047422069.1 → XP_047278025.1 oxygen-regulated protein 1 isoform X1

Related

ENSP00000490104.1, ENST00000637698.1
XM_047422070.1 → XP_047278026.1 oxygen-regulated protein 1 isoform X2
XM_047422071.1 → XP_047278027.1 oxygen-regulated protein 1 isoform X3
XM_047422072.1 → XP_047278028.1 oxygen-regulated protein 1 isoform X4
XM_047422073.1 → XP_047278029.1 oxygen-regulated protein 1 isoform X5

Related

ENSP00000489857.1, ENST00000636932.1
XM_047422074.1 → XP_047278030.1 oxygen-regulated protein 1 isoform X6
XM_017014158.2 → XP_016869647.1 oxygen-regulated protein 1 isoform X7

Conserved Domains (2) summary

cd01756
Location:707 → 829

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:581 → 695

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...