Non-canonical ORFs OpenProt Track Settings

ncORFs: OpenProt - alternative and reference proteins v2.2

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 features 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 – a consolidated catalog of ATG-initiated ncORFs of at least 16 codons, called from Ribo-seq data across seven publications and mapped to GENCODE v35. Sense-overlapping ORFs were merged, leaving a unique set; over 3,000 are found in more than one publication and so are flagged as replicated. This was the basis of the original ncORF reference release for Ensembl/GENCODE, HGNC, UniProtKB, and PeptideAtlas.
Phase II Comprehensive – the expanded catalog (GENCODE v45). Additional published Ribo-seq datasets were incorporated and the size and start-codon restrictions from Phase I were lifted, so this set includes shorter and non-AUG ORFs.
Phase II Primary – a high-confidence subset of Phase II filtered for translations with especially robust Ribo-seq signatures, comparable to canonical protein-coding genes.

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 prioritizing 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 two databases (Ribo-uORF and uORFdb), mapped to MANE Select transcripts and classified into three functional 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 if you have a prediction from the VEP plugin and want to see the context.

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 we look up, for each uORF, 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), we fall back to the full GENCODE comprehensive set and apply the same projection. 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. The nuORFdb database is a very consistent dataset, from a well-known paper.

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. Metamorf has many predictions, and not all may be relevant, but gives an example of a database with as many models as possible, and is the only complete archive of sorfs.org that we are aware of.

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 is widely known and has by far the most predictions, even more 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 (7)

Display mode: Duplicate track

Color track by codons: Help on codon coloring

Show codon numbering:

Show only transcripts with these accessions:

Display data as a density graph:

Kozak translational efficiency:

(-1 to 1.5)

Filter items by: (select multiple categories and items - Help)

Kozak motif present (+) or absent (-) (per OpenProt)	Kozak consensus strength\|Strong/Moderate/Weak per Kozak rule on -3 and +4	ORF localization relative to CDS (5'UTR, CDS, 3'UTR, ncRNA)	Start codon (ATG, CTG, GTG, TTG, ACG, other) read from genome	Protein type (AltProt, RefProt, or Isoform)
Match if all one or more match	Match if all one or more match		Match if all one or more match

Data schema/format description and download

Assembly: Human Dec. 2013 (GRCh38/hg38)
Data last updated at UCSC: 2026-05-19 11:40:21

Description

This track displays 921,170 protein-coding ORFs from OpenProt v2.2, a database that provides a comprehensive annotation of all possible protein-coding ORFs in the human genome. In addition to currently annotated coding sequences (CDSs) and their reference proteins (RefProts), OpenProt predicts alternative ORFs (AltORFs) and their corresponding alternative proteins (AltProts) that are hidden within transcripts previously considered to encode only a single protein.

A pre-filtered subtrack (OpenProt MS>=2) is also available, containing only the 377,916 ORFs with at least 2 unique mass spectrometry peptides detected across studies, matching the MS-evidence threshold used by OpenProt for their curated downloads.

OpenProt classifies proteins into three types:

RefProt (246,578) – reference proteins translated from annotated CDSs in mRNAs, representing non-redundant sequences from UniProtKB/SwissProt, Ensembl, and NCBI RefSeq
AltProt (603,586) – alternative proteins translated from AltORFs in mRNA UTRs, in frameshifted reading frames overlapping the CDS, or from ORFs in non-coding RNAs
Isoform (71,006) – novel predicted isoforms of known proteins, translated from AltORFs that share clear sequence homology with a RefProt from the same gene

AltORFs are further classified by their localization relative to the annotated CDS:

5'UTR – start codon in the 5' UTR (upstream ORFs)
CDS – overlapping the annotated CDS in a different reading frame
3'UTR – start codon in the 3' UTR (downstream ORFs)
ncRNA – ORFs in transcripts classified as non-coding RNAs

Display Conventions and Configuration

Items are displayed in bigGenePred format. Items are labeled with the protein accession number: IDs starting with IP_ are predicted AltProts, II_ are novel isoforms, and other IDs (e.g. NP_, ENSP) are RefProts from existing annotations. Color reflects the categorical Kozak consensus strength:

Strong – A/G at position −3 and G at position +4
Moderate – only one of those positions matches
Weak – neither position matches
non-ATG – near-cognate start codon; the Kozak rule does not apply
no context – chromosome edge or context unavailable

Mouseover shows the protein accession in its host gene, protein type and ORF localization, start codon, Kozak strength and TE, MS score, TE score, and InterPro domain count.

The track includes the following filter options:

Start codon, Kozak strength, Kozak TE – common Kozak filters
Protein type – AltProt, RefProt, or Isoform
Localization – 5'UTR, 3'UTR, CDS, ncRNA, multiple
MS score – minimum unique MS peptides (range)
Kozak motif – OpenProt's own +/− annotation

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can be accessed from scripts through our API; the track name is "openprot" (all ORFs) or "openprotMs" (MS-filtered).

For automated download and analysis, the genome annotations are stored in bigBed files that can be downloaded from our download server. 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 only features within a given range, e.g.

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

The original data files can be downloaded from the OpenProt download page.

Methods

The OpenProt v2.2 BED12 and TSV annotation files were downloaded from the OpenProt API. The BED file (2,846,289 rows) contains genomic coordinates for all predicted ORFs; since the same protein can be mapped through multiple transcripts to identical genomic coordinates, deduplication reduced this to 921,170 unique genomic features (3 entries with overlapping BED blocks were excluded).

Each BED entry was annotated with metadata from the TSV file by joining on protein accession. For proteins with multiple transcript entries in the TSV, the annotation with the highest MS score was retained. Extended fields include protein type (AltProt/RefProt/Isoform), ORF localization, MS score, TE (Translation Event) score, Kozak motif status, InterPro domain count, and reading frame.

The annotation is based on GRCh38.p13, Ensembl release 106, and UniProt release 2022_06_01.

Credits

Thanks to Xavier Roucou and the OpenProt team at the Université de Sherbrooke for creating OpenProt and making the data publicly available.

References

Brunet MA, Brunelle M, Lucier JF, Delcourt V, Levesque M, Grenier F, Samandi S, Leblanc S, Aguilar JD, Dufour P et al. OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. Nucleic Acids Res. 2019 Jan 8;47(D1):D403-D410. PMID: 30299502; PMC: PMC6323990

Brunet MA, Lucier JF, Levesque M, Leblanc S, Jacques JF, Al-Saedi HRH, Guilloy N, Grenier F, Avino M, Fournier I et al. OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. Nucleic Acids Res. 2021 Jan 8;49(D1):D380-D388. PMID: 33179748; PMC: PMC7779043