P3H4 prolyl 3-hydroxylase family member 4 (inactive) [Homo sapiens (human)] - Gene

Summary

Official Symbol: P3H4provided by HGNC
Official Full Name: prolyl 3-hydroxylase family member 4 (inactive)provided by HGNC
Primary source: HGNC:HGNC:16946
See related: Ensembl:ENSG00000141696 MIM:617419
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NO55; SC65; NOL55; LEPREL4
Summary: This nucleolar protein was first characterized because it was an autoantigen in cases on interstitial cystitis. The protein, with a predicted molecular weight of 50 kDa, appears to be localized in the particulate compartment of the interphase nucleolus, with a distribution distinct from that of nucleolar protein B23. During mitosis it is associated with chromosomes. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in placenta (RPKM 4.3), thyroid (RPKM 4.3) and 24 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 17q21.2

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
109.20200228	current	GRCh38.p13 (GCF_000001405.39)	17	NC_000017.11 (41801952..41812710, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (39958204..39968881, complement)

Chromosome 17 - NC_000017.11 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?

High P3H4 expression is associated with bladder cancer.
Title: P3H4 is correlated with clinicopathological features and prognosis in bladder cancer.
SC65 protein is identified as an autoimmune target in idiopathic membranous nephropathy.
Title: Identification and characterization of a new autoimmune protein in membranous nephropathy by immunoscreening of a renal cDNA library.

Submit: New GeneRIF Correction

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

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

L17709 (e-PCR)
- UniSTS:42599

D1S1425 (e-PCR)
- UniSTS:149621

SHGC-67307 (e-PCR)
- UniSTS:89991

Homology

Homologs of the P3H4 gene: The P3H4 gene is conserved in chimpanzee, Rhesus monkey, dog, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 220 organisms have orthologs with human gene P3H4
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
contributes_to collagen binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Process	Evidence Code	Pubs
bone remodeling	ISS Inferred from Sequence or Structural Similarity more info
collagen biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
collagen fibril organization	IBA Inferred from Biological aspect of Ancestor more info	PubMed
collagen fibril organization	ISS Inferred from Sequence or Structural Similarity more info
peptidyl-lysine hydroxylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
peptidyl-lysine hydroxylation	ISS Inferred from Sequence or Structural Similarity more info
synaptonemal complex assembly	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
catalytic complex	IEA Inferred from Electronic Annotation more info
condensed nuclear chromosome	TAS Traceable Author Statement more info	PubMed
endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info	PubMed
endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
nucleolus	TAS Traceable Author Statement more info	PubMed
synaptonemal complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: endoplasmic reticulum protein SC65

Names: leprecan-like 4; leprecan-like protein 4; nucleolar autoantigen (55kD); nucleolar autoantigen No55; nucleolar autoantigen, 55kDa; prolyl 3-hydroxylase family member 4 (non-enzymatic); synaptonemal complex 65; synaptonemal complex protein SC65

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.

mRNA and Protein(s)

NM_006455.3 → NP_006446.1 endoplasmic reticulum protein SC65 precursor

See identical proteins and their annotated locations for NP_006446.1

Status: VALIDATED

Source sequence(s)

AK056085, BC007942, U47621

Consensus CDS

CCDS11408.1

UniProtKB/Swiss-Prot

Q92791

Related

ENSP00000377505.1, ENST00000393928.6

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p13 Primary Assembly

Range

41801952..41812710 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024450538.1 → XP_024306306.1 endoplasmic reticulum protein SC65 isoform X2

Conserved Domains (1) summary

cl27975
Location:31 → 94

EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)
XM_006721640.4 → XP_006721703.1 endoplasmic reticulum protein SC65 isoform X1

Conserved Domains (1) summary

PHA03378
Location:9 → 101

PHA03378; EBNA-3B; Provisional