Human Gene P4HA1 (ENST00000394890.7_6) from GENCODE V47lift37

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Description: prolyl 4-hydroxylase subunit alpha 1, transcript variant 3 (from RefSeq NM_001142595.2)
Gencode Transcript: ENST00000394890.7_6
Gencode Gene: ENSG00000122884.13_11
Transcript (Including UTRs)
Position: hg19 chr10:74,766,975-74,856,624 Size: 89,650 Total Exon Count: 15 Strand: -
Coding Region
Position: hg19 chr10:74,767,980-74,834,641 Size: 66,662 Coding Exon Count: 14

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr10:74,766,975-74,856,624)			mRNA (may differ from genome)		Protein (534 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	MGI	OMIM	PubMed	Reactome	UniProtKB
Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: P4HA1_HUMAN DESCRIPTION: RecName: Full=Prolyl 4-hydroxylase subunit alpha-1; Short=4-PH alpha-1; EC=1.14.11.2; AltName: Full=Procollagen-proline,2-oxoglutarate-4-dioxygenase subunit alpha-1; Flags: Precursor; FUNCTION: Catalyzes the post-translational formation of 4- hydroxyproline in -Xaa-Pro-Gly- sequences in collagens and other proteins. CATALYTIC ACTIVITY: L-proline-[procollagen] + 2-oxoglutarate + O(2) = trans-4-hydroxy-L-proline-[procollagen] + succinate + CO(2). COFACTOR: Binds 1 Fe(2+) ion per subunit. COFACTOR: Ascorbate. SUBUNIT: Heterotetramer of two alpha-1 chains and two beta chains (the beta chain is the multi-functional PDI). SUBCELLULAR LOCATION: Endoplasmic reticulum lumen. SIMILARITY: Belongs to the P4HA family. SIMILARITY: Contains 1 Fe2OG dioxygenase domain. SIMILARITY: Contains 1 TPR repeat.

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D013749 Tetrachlorodibenzodioxin C023514 2,6-dinitrotoluene D010100 Oxygen D010634 Phenobarbital C022838 nickel chloride C049325 1,2-dithiol-3-thione D015655 1-Methyl-4-phenylpyridinium C016403 2,4-dinitrotoluene C547126 AZM551248 D000082 Acetaminophen more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 63.17 RPKM in Cells - EBV-transformed lymphocytes Total median expression: 641.98 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-48.40	133	-0.364	Picture	PostScript	Text
3' UTR	-223.20	1005	-0.222	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR005123 - Oxoglu/Fe-dep_dioxygenase
IPR006620 - Pro_4_hyd_alph
IPR013547 - Pro_4_hyd_alph_N
IPR013026 - TPR-contain_dom
IPR011990 - TPR-like_helical
IPR019734 - TPR_repeat

Pfam Domains:
PF03171 - 2OG-Fe(II) oxygenase superfamily
PF08336 - Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
PF13640 - 2OG-Fe(II) oxygenase superfamily

SCOP Domains:
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1TJC - X-ray MuPIT

2V5F - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P13674


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details		Gene Details
Gene Sorter	Gene Sorter		Gene Sorter
	RGD	Ensembl

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0004656 procollagen-proline 4-dioxygenase activity GO:0005506 iron ion binding GO:0005515 protein binding GO:0016491 oxidoreductase activity GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen GO:0031418 L-ascorbic acid binding GO:0042802 identical protein binding GO:0046872 metal ion binding GO:0051213 dioxygenase activity Biological Process: GO:0018401 peptidyl-proline hydroxylation to 4-hydroxy-L-proline GO:0030199 collagen fibril organization GO:0055114 oxidation-reduction process Cellular Component: GO:0005739 mitochondrion GO:0005783 endoplasmic reticulum GO:0005788 endoplasmic reticulum lumen GO:0016020 membrane GO:0016222 procollagen-proline 4-dioxygenase complex GO:0043231 intracellular membrane-bounded organelle

Descriptions from all associated GenBank mRNAs


	AK222960 - Homo sapiens mRNA for procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I variant, clone: HRT00758. BC034998 - Homo sapiens prolyl 4-hydroxylase, alpha polypeptide I, mRNA (cDNA clone MGC:33137 IMAGE:4797051), complete cds. LF384636 - JP 2014500723-A/192139: Polycomb-Associated Non-Coding RNAs. M24486 - Human prolyl 4-hydroxylase alpha subunit mRNA, complete cds, clone PA-11. M24487 - Human prolyl 4-hydroxylase alpha subunit mRNA, complete cds, clone PA-15. AK312593 - Homo sapiens cDNA, FLJ92969. MA620213 - JP 2018138019-A/192139: Polycomb-Associated Non-Coding RNAs. LF322505 - JP 2014500723-A/130008: Polycomb-Associated Non-Coding RNAs. LF322504 - JP 2014500723-A/130007: Polycomb-Associated Non-Coding RNAs. JD441938 - Sequence 422962 from Patent EP1572962. JD268213 - Sequence 249237 from Patent EP1572962. JD260553 - Sequence 241577 from Patent EP1572962. JD410885 - Sequence 391909 from Patent EP1572962. BX648829 - Homo sapiens mRNA; cDNA DKFZp686N21109 (from clone DKFZp686N21109). LF322503 - JP 2014500723-A/130006: Polycomb-Associated Non-Coding RNAs. JD259995 - Sequence 241019 from Patent EP1572962. LF322502 - JP 2014500723-A/130005: Polycomb-Associated Non-Coding RNAs. JD145542 - Sequence 126566 from Patent EP1572962. LF322501 - JP 2014500723-A/130004: Polycomb-Associated Non-Coding RNAs. JD307264 - Sequence 288288 from Patent EP1572962. LF322500 - JP 2014500723-A/130003: Polycomb-Associated Non-Coding RNAs. LF322499 - JP 2014500723-A/130002: Polycomb-Associated Non-Coding RNAs. LF322498 - JP 2014500723-A/130001: Polycomb-Associated Non-Coding RNAs. DQ891669 - Synthetic construct clone IMAGE:100004299; FLH179137.01X; RZPDo839D03130D procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I (P4HA1) gene, encodes complete protein. DQ894855 - Synthetic construct Homo sapiens clone IMAGE:100009315; FLH179133.01L; RZPDo839D03129D procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I (P4HA1) gene, encodes complete protein. AB529124 - Synthetic construct DNA, clone: pF1KB4957, Homo sapiens P4HA1 gene for prolyl 4-hydroxylase, alpha polypeptide I, without stop codon, in Flexi system. LF322497 - JP 2014500723-A/130000: Polycomb-Associated Non-Coding RNAs. AK123653 - Homo sapiens cDNA FLJ41659 fis, clone FEBRA2026769. LF322496 - JP 2014500723-A/129999: Polycomb-Associated Non-Coding RNAs. LF322495 - JP 2014500723-A/129998: Polycomb-Associated Non-Coding RNAs. LF322490 - JP 2014500723-A/129993: Polycomb-Associated Non-Coding RNAs. LF322488 - JP 2014500723-A/129991: Polycomb-Associated Non-Coding RNAs. LF322487 - JP 2014500723-A/129990: Polycomb-Associated Non-Coding RNAs. LF322486 - JP 2014500723-A/129989: Polycomb-Associated Non-Coding RNAs. LF322485 - JP 2014500723-A/129988: Polycomb-Associated Non-Coding RNAs. LF322482 - JP 2014500723-A/129985: Polycomb-Associated Non-Coding RNAs. LF322478 - JP 2014500723-A/129981: Polycomb-Associated Non-Coding RNAs. LF322477 - JP 2014500723-A/129980: Polycomb-Associated Non-Coding RNAs. LF322476 - JP 2014500723-A/129979: Polycomb-Associated Non-Coding RNAs. LF322474 - JP 2014500723-A/129977: Polycomb-Associated Non-Coding RNAs. LF322473 - JP 2014500723-A/129976: Polycomb-Associated Non-Coding RNAs. MA558082 - JP 2018138019-A/130008: Polycomb-Associated Non-Coding RNAs. MA558081 - JP 2018138019-A/130007: Polycomb-Associated Non-Coding RNAs. MA558080 - JP 2018138019-A/130006: Polycomb-Associated Non-Coding RNAs. MA558079 - JP 2018138019-A/130005: Polycomb-Associated Non-Coding RNAs. MA558078 - JP 2018138019-A/130004: Polycomb-Associated Non-Coding RNAs. MA558077 - JP 2018138019-A/130003: Polycomb-Associated Non-Coding RNAs. MA558076 - JP 2018138019-A/130002: Polycomb-Associated Non-Coding RNAs. MA558075 - JP 2018138019-A/130001: Polycomb-Associated Non-Coding RNAs. MA558074 - JP 2018138019-A/130000: Polycomb-Associated Non-Coding RNAs. MA558073 - JP 2018138019-A/129999: Polycomb-Associated Non-Coding RNAs. MA558072 - JP 2018138019-A/129998: Polycomb-Associated Non-Coding RNAs. MA558067 - JP 2018138019-A/129993: Polycomb-Associated Non-Coding RNAs. MA558065 - JP 2018138019-A/129991: Polycomb-Associated Non-Coding RNAs. MA558064 - JP 2018138019-A/129990: Polycomb-Associated Non-Coding RNAs. MA558063 - JP 2018138019-A/129989: Polycomb-Associated Non-Coding RNAs. MA558062 - JP 2018138019-A/129988: Polycomb-Associated Non-Coding RNAs. MA558059 - JP 2018138019-A/129985: Polycomb-Associated Non-Coding RNAs. MA558055 - JP 2018138019-A/129981: Polycomb-Associated Non-Coding RNAs. MA558054 - JP 2018138019-A/129980: Polycomb-Associated Non-Coding RNAs. MA558053 - JP 2018138019-A/129979: Polycomb-Associated Non-Coding RNAs. MA558051 - JP 2018138019-A/129977: Polycomb-Associated Non-Coding RNAs. MA558050 - JP 2018138019-A/129976: Polycomb-Associated Non-Coding RNAs. JD477895 - Sequence 458919 from Patent EP1572962.

Biochemical and Signaling Pathways


	BioCyc Knowledge Library PWY-7894 - procollagen hydroxylation and glycosylation Reactome (by CSHL, EBI, and GO) Protein P13674 (Reactome details) participates in the following event(s): R-HSA-1650808 Prolyl 4-hydroxylase converts collagen prolines to 4-hydroxyprolines R-HSA-1650814 Collagen biosynthesis and modifying enzymes R-HSA-1474290 Collagen formation R-HSA-1474244 Extracellular matrix organization

Other Names for This Gene


	Alternate Gene Symbols: C9JL12, ENST00000394890.1, ENST00000394890.2, ENST00000394890.3, ENST00000394890.4, ENST00000394890.5, ENST00000394890.6, NM_001142595, P13674, P4HA, P4HA1_HUMAN, Q15082, Q15083, Q5VSQ5, uc318wzn.1, uc318wzn.2 UCSC ID: ENST00000394890.7_6 RefSeq Accession: NM_001017962.3 Protein: P13674 (aka P4HA1_HUMAN or P4H1_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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