Non-canonical ORFs 5ULTRA uORFs Track Settings

ncORFs: uORFs in MANE Select transcripts from 5ULTRA

Configure track container: Non-canonical Open Reading Frames

Description

The non-canonical ORFs supertrack contains tracks that display open reading frames (ORFs) found outside of annotated protein-coding sequences. While the human genome has approximately 20,000 annotated protein-coding genes, recent advances in ribosome profiling (Ribo-seq) and proteomics have revealed widespread translation of ORFs that do not correspond to known protein-coding genes. These non-canonical ORFs are found in regions previously considered non-coding, including 5' and 3' UTRs, long non-coding RNAs, pseudogenes, and alternative reading frames of known genes.

Several subtypes of non-canonical ORFs are commonly distinguished. Upstream ORFs (uORFs) are located in 5' UTRs and can regulate translation of the downstream main coding sequence. Ribosomes that translate a uORF may fail to reinitiate at the main start codon, reducing protein output. Small ORFs (sORFs), generally defined as encoding fewer than 100 amino acids, have been systematically overlooked by gene annotation pipelines due to their short length, but many produce functional micropeptides involved in signaling, metabolism, and development. Other types include downstream ORFs (dORFs) in 3' UTRs, out-of-frame ORFs that overlap known coding sequences in an alternative reading frame, and ORFs in transcripts annotated as non-coding RNAs or pseudogenes.

This track collection imports various databases and annotates all ORFs with their Kozak strength, and colors the items by Kozak strength.

Click any of the track names below to show their configuration/documentation page:

Track	Description	Items	Genome Coverage	Exon Coverage	Start codon		Kozak strength (ATG only)
Track	Description	Items	Genome Coverage	Exon Coverage	ATG	non-ATG	Strong	Moderate	Weak
UTRannotator uORFs	Upstream ORFs in 5' UTRs from UTRannotator	44,435	1.15%	1.15%	6,236	38,199	1,307	3,054	1,875
GENCODE ncORFs	GENCODE non-canonical ORFs supported by Ribo-seq	7,264	1.02%	0.03%	7,263	1	1,571	3,705	1,987
GENCODE ncORFs primary	GENCODE non-canonical ORFs: primary set	10,127	0.45%	0.02%	6,183	3,944	1,746	3,300	1,137
GENCODE ncORFs comprehensive	GENCODE non-canonical ORFs: comprehensive set	28,359	2.24%	0.06%	13,776	14,583	3,133	7,168	3,475
5ULTRA uORFs	uORFs in MANE Select transcripts from 5ULTRA (ATG only)	22,567	2.44%	0.09%	22,567	0	3,768	10,862	7,472
nuORFdb	Non-canonical ORFs from nuORFdb v1.2	229,251	22.14%	0.83%	51,080	178,171	10,905	25,539	14,636
MetamORF	Meta-database of small ORFs (sORFs)	664,558	33.53%	1.19%	147,490	517,068	33,481	74,267	39,742
OpenProt	Alternative and reference proteins from OpenProt v2.2	921,170	49.85%	3.36%	906,942	14,228	202,199	446,288	258,455
OpenProt (MS>=2)	OpenProt proteins with mass spectrometry evidence (≥2 peptides)	377,916	40.29%	1.85%	367,257	10,659	106,148	181,817	79,292

GENCODE ncORFs (Phase I and Phase II)

The three GENCODE ncORF tracks display non-canonical translated open reading frames identified from ribosome profiling (Ribo-seq) data and mapped to the GENCODE annotation by the GENCODE / TransCODE consortium. Phase I is a consolidated catalog of 7,264 ATG-initiated ncORFs called from seven Ribo-seq publications. Phase II expands this to a Comprehensive set of 28,359 ncORFs with the length and start-codon restrictions removed, and a high-confidence Primary set of 10,127 ncORFs selected using translation signature scores derived from Ribo-seq data. See the GENCODE ncORFs Phase I subtrack page or the Phase II primary / comprehensive pages for download URLs, methods, and references.

5ULTRA uORFs

5ULTRA is a pipeline for annotating 5' UTR variants by their impact on protein translation. As part of the project, Chaldebas et al. compiled a reference set of 22,567 ATG-initiated uORFs from three databases (Ribo-uORF, uORFdb, and sorfs.org), mapped to MANE Select transcripts and classified into three types. See the 5ULTRA uORFs subtrack page for more details.

UTRannotator uORFs

Created by the Whiffin lab, UTRannotator is a VEP plugin for annotating 5' UTR variants with respect to upstream open reading frames (uORFs). As part of the project, the authors compiled a curated reference set of uORFs in human 5' UTRs from sorfs.org, which contains ORFs supported by Ribo-Seq. See the UTRannotator uORFs subtrack page for more details. Data from sorfs.org is also part of the MetamORF track (see below). This track is useful for viewing the context of a prediction from the VEP plugin.

The UTRannotator source data is distributed as single-span features with no exon/intron structure, so the uORFs would appear as continuous blocks even across introns of their host transcripts. To recover the splicing structure, each uORF is matched to a same-strand MANE Select / MANE Plus Clinical transcript whose coordinates overlap the uORF range. The host transcript's exons are clipped to the uORF range so that any MANE intron inside the overlap is preserved as an intron of the displayed bed12 record. A uORF that extends past either end of MANE keeps the MANE introns inside the overlap and gets a single bridging block for the orphan portion. If a uORF endpoint falls inside a MANE intron (i.e. UTRannotator originally used a transcript whose UTR exon boundaries differ from MANE's), the full GENCODE comprehensive set is used as a fallback, with the same projection applied. If no donor in either pool can host the uORF, it stays single-block. The chosen donor transcript ID is recorded in the intronsSource field (or none if no host was found).

nuORFdb

nuORFdb (novel unannotated ORF database) is a Broad Institute database of non-canonical open reading frames with evidence of translation from ribosome profiling (Ribo-seq). ORF types include uORFs, dORFs, out-of-frame ORFs, pseudogene ORFs, lincRNA ORFs, and others. See the nuORFdb subtrack page for more details.

MetamORF

MetamORF is a repository of small ORFs (sORFs) in the human genome, consolidated from several primary data sources and many individual ribosome profiling datasets. It integrates bioinformatic predictions, ribosome profiling experiments, and mass spectrometry studies into a unified format. See the MetamORF subtrack page for more details.

OpenProt

OpenProt is a comprehensive annotation of all possible protein-coding ORFs in eukaryotic genomes. It distinguishes RefProts (the known canonical proteins), Isoforms (alternative products of canonical genes), and AltProts (predicted from alternative reading frames in UTRs, frameshifted CDS overlaps, and non-coding RNAs). Each ORF is annotated with mass spectrometry and ribosome profiling evidence; a pre-filtered Mass-Spec-supported subset (≥2 unique peptides) is also available. See the OpenProt subtrack page for more details. OpenProt has more predictions than MetamORF, which is why a subset exists with only the more reliable ORFs with Mass-Spec data.

To view the full description, click here.

All tracks in this collection (9)

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Kozak context strength	uORF type
Match if all one or more match	Match if all one or more match

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Data schema/format description and download

Assembly: Human Dec. 2013 (GRCh38/hg38)
Data last updated at UCSC: 2026-10-08 18:09:13

Description

This track shows 22,567 upstream open reading frames (uORFs) in the 5' untranslated regions (5' UTRs) of human protein-coding genes, compiled as part of the 5ULTRA pipeline for annotating 5' UTR variants. The uORFs are defined on MANE Select transcripts, which provide a single well-supported, clinically relevant transcript per gene matched between Ensembl/GENCODE and RefSeq. Only ATG-initiated uORFs are included.

uORFs are short open reading frames found upstream of the main protein-coding sequence. When a ribosome scans from the 5' cap, it may translate a uORF before reaching the main start codon, which often reduces production of the downstream protein. Genetic variants that create, disrupt, or alter uORFs can therefore change protein output and contribute to disease.

Each uORF is classified into one of three types based on the position of its stop codon relative to the main CDS start:

A non-overlapping uORF has its stop codon upstream of the main CDS start.
An overlapping uORF has its stop codon within the CDS but in a different reading frame.
An N-terminal extension is an upstream ATG that is in-frame with the main CDS, with no stop codon between the two start codons, producing a protein with an extended N-terminus.

Display Conventions and Configuration

Items are colored by Kozak context strength based on two specific positions in the genomic sequence, counted relative to the A of the ATG start codon: position −3 (three bases before the A) and position +4 (one base after the G).

	Strong: both position −3 (A/G) and position +4 (G) match.
	Moderate: only one of position −3 (A/G) or position +4 (G) matches.
	Weak: neither position −3 (A/G) nor position +4 (G) matches.
	NA: Kozak context could not be scored (465 uORFs).

Separately, uORFs can span multiple exons. Each uORF's exon/intron structure comes from an overlapping MANE Select transcript. If no MANE transcript has introns that match the uORF's endpoints, the GENCODE comprehensive annotation is used instead. The source transcript is recorded in the intronsSource field (none if no matching transcript was found).

The track can be filtered by:

Kozak strength
uORF type

Item names follow the pattern GENE_N, where N matches the uORF's rank within the gene (for example, KCNAB2_2 is the uORF with rank 2 of 3 for KCNAB2). Rank 1 is the uORF closest to the main CDS start. Higher ranks are progressively further upstream, toward the 5' cap.

Mouseover shows the gene symbol, uORF type, rank within the gene, Kozak strength, and the donor transcript used for intron structure.

Data Access

The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=fiveUltraUorfs.

For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called fiveUltraUorfs.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain features within a given range, e.g.

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/ncOrfs/fiveUltraUorfs/fiveUltraUorfs.bb -chrom=chr21 -start=0 -end=100000000 stdout

The original uORF reference set is distributed with the 5ULTRA software package and can be obtained by installing the package and running 5ULTRA-download-data.

Methods

Chaldebas et al. compiled a reference set of uORFs from three sources: the Ribo-uORF database (501,554 translated uORFs supported by 1,495 ribosome profiling datasets), the uORFdb database of computationally predicted uORFs, and the sorfs.org database. Only ATG-initiated uORFs were retained. These were mapped to the 5' UTRs of 18,775 MANE Select protein-coding transcripts from GENCODE v45 basic annotation, yielding 22,567 uORFs. Of these, 8,067 (35.7%) have direct ribosome profiling support. Each uORF was classified as Non-Overlapping, Overlapping, or N-terminal extension based on the relationship between its stop codon and the main CDS start. See Chaldebas et al. 2026 for full details.

The uORF reference BED file was obtained from the 5ULTRA GitHub repository (installed via 5ULTRA-download-data, file uORFs.MANE.hg38.bed). Colors were remapped to distinguish Kozak strength (see Display Conventions). To recover exon/intron structure for uORFs that span introns, each uORF was projected onto an overlapping MANE Select transcript using the addIntrons.py script in the kent source tree. A GENCODE v49 comprehensive bigBed was used as fallback when no MANE candidate could provide intact boundaries at the uORF endpoints. Of 22,567 uORFs, 3,861 received multi-block exon structure from MANE, 9 from GENCODE fallback, and 45 overlapped a GENCODE transcript but had no introns within the uORF range. 18,652 remain as single-exon uORFs whose genomic span contains no intron from any known host. Build steps are recorded in the makedoc. The processing scripts are at src/hg/makeDb/scripts/ncOrfs/.

Credits

Thanks to Matthieu Chaldebas and the 5ULTRA team for making the uORF reference data publicly available as part of the 5ULTRA package.

References

Chaldebas M, Ponsin K, Bohlen J, Conil C, Mourelatos H, Stenson PD, Cooper DN, Abel L, Casanova JL, Cobat A et al. Genome-wide detection of human 5' UTR variants that impact protein translation. Am J Hum Genet. 2026 Apr 2;113(4):809-827. PMID: 41881026; PMC: PMC13087467