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NPHP3-ACAD11 NPHP3-ACAD11 readthrough (NMD candidate) [ Homo sapiens (human) ]

Gene ID: 100532724, updated on 10-Oct-2023

Summary

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Official Symbol
NPHP3-ACAD11provided by HGNC
Official Full Name
NPHP3-ACAD11 readthrough (NMD candidate)provided by HGNC
Primary source
HGNC:HGNC:48351
See related
Ensembl:ENSG00000274810 AllianceGenome:HGNC:48351
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NPHP3
Summary
This locus represents naturally occurring read-through transcription between the neighboring NPHP3 (nephronophthisis 3, adolescent) and ACAD11 (acyl-CoA dehydrogenase family, member 11) genes on chromosome 3. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]
Expression
Ubiquitous expression in kidney (RPKM 14.0), liver (RPKM 13.3) and 25 other tissues See more
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Genomic context

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Location:
3q22.1
Exon count:
45
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (132558138..132722459, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (135302648..135466962, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (132276982..132441303, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14741 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:132136675-132137210 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:132190883-132191410 Neighboring gene DnaJ heat shock protein family (Hsp40) member C13 Neighboring gene uncharacterized LOC124909436 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:132337002-132338201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:132345519-132346020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:132346021-132346520 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:132348758-132349957 Neighboring gene acyl-CoA dehydrogenase family member 11 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:132360104-132360294 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:132378955-132379493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20539 Neighboring gene atypical chemokine receptor 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:132411873-132412374 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:132412375-132412874 Neighboring gene heat shock protein family A (Hsp70) member pseudogene 19 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14743 Neighboring gene NPHP3 antisense RNA 1 Neighboring gene ubiquitin like modifier activating enzyme 5 Neighboring gene nephrocystin 3 Neighboring gene uncharacterized LOC105374115 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64751 Neighboring gene NANOG hESC enhancer GRCh37_chr3:132598533-132599069 Neighboring gene MPRA-validated peak4836 silencer Neighboring gene Sharpr-MPRA regulatory region 13907 Neighboring gene Sharpr-MPRA regulatory region 9074 Neighboring gene transmembrane protein 108 Neighboring gene TMEM108 antisense RNA 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis. Olbrich H, et al. Nat Genet, 2003 Aug. PMID 12872122
  2. Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method. Ohara O, et al. DNA Res, 2002 Apr 30. PMID 12056414
  3. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. Prakash T, et al. PLoS One, 2010 Oct 12. PMID 20967262, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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General gene information

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Markers

Other Names

  • Nephrocystin-3

Clone Names

  • KIAA2000

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.

RNA

  1. NR_037804.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AB082531, AC020632
    Related
    ENST00000471702.2

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

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    132558138..132722459 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    135302648..135466962 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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