Welcome to AnnoTrack
the Tracking System of the GENCODE project
This system is used to track and aid in the progress of the annotation of the entire human genome by HAVANA and GENCODE. As a researcher in genomics you can monitor and report on problems of the annotation.
Example entry points: a flagged transcript from the manual annotation, or a list of all transcripts flagged with "missing CCDS".
You can use the search box on this page to find specific genes or you can use filters on the transcript list to display specific regions or categories.
Here is a general introduction to this tracking system. This is the beginning of a user documentation.
Source code & instructions for the official installation of AnnoTrack are given here.
You are welcome to send bug reports or feature requests.
Lists of urgent cases:
Transcript stats | Add flags manually | Verify flags | List of all transcripts
Latest news
Mouse & Zebrafish AnnoTracks [09.11.2010]
Annotrack systems for mouse (annotrack.sanger.ac.uk/mouse) and zebrafish (annotrack.sanger.ac.uk/zfish) are now live.
Publication [07.10.2010]
A description of AnnoTrack has now been published in BMC Genomics
Last user [16.04.2010]
When logged in, you can now see the user last working on a HAVANA transcript
Resolving multiple flags [25.02.2010]
I've added the possibility to resolve related flags together using the same resolution.
RedMine update [18.11.2009]
The underlying RedMine code was updated to the latest version. Other changes include the better display of related issues.
Name change [21.08.2009]
Because of trademark issues we changed the name of the project from "GenTrack" to "AnnoTrack".
New search engine [12.06.2009]
We have just switched over to the new Sanger Lucene search engine for Annotrack.
New pages [27.05.2009]
I added pages to display stats and transcripts to be verified. Links are on the front page.
Currently loaded categories (Transcripts)
| 1319 | CCDS [ CCDS missing from HAVANA (ENSEMBL) ] |
| 2581 | CNIO_isoforms [ Principal gene products (CNIO) ] |
| 40 | CRG_U12 [ U12 predictions (CRG) ] |
| 5484 | ENSEMBL_exons [ Additional exons (ENSEMBL) ] |
| 6789 | ENSEMBL_introns [ Additional introns (ENSEMBL) ] |
| 34399 | ENSEMBL_missing_cDNA [ cDNAs not annotated (ENSEMBL) ] |
| 88 | ENSEMBL_missing_new_cDNA [ new cDNAs not annotated (ENSEMBL) ] |
| 410 | Ensembl [ Imported models (ENSEMBL) ] |
| 191302 | HAVANA [ Manual annotation (HAVANA, WTSI) ] |
| 121 | HAVANA_overlaps [ Transcripts with coding overlap (WTSI) ] |
| 60 | IDR-test-models [ Selected HUVEC RNA-Seq models with different IDRs ] |
| 175163 | MIT_CONGO [ comparative protein-coding exon predictor (MIT) ] |
| 2123 | MIT_RFC_CSF [ Evolutionary signatures (MIT) ] |
| 10547 | RNASeq_novel [ Novel locations from RNASeq data (Wold/ENSEMBL) ] |
| 228 | Scripture_novel_CDS [ Gene models with coding potential (Scripture/PhyloCSF) ] |
| 11996 | UCSC_Retro3 [ RetroFinder pseudogenes (UCSC) ] |
| 41705 | UCSC_TransMap [ TransMap cross-species alignments (UCSC) ] |
| 178200 | UCSC_exoniphy [ evolutionarily conserved protein-coding exons (UCSC) ] |
| 327 | UCSC_novel [ Novel loci predictions (Siepel, UCSC) ] |
| 130 | VERIFY [ Flags for the experimental pipeline ] |
| 22497 | YALE_pseudo [ PseudoPipe pseudogenes (YALE) ] |
| 794 | Yale-UCSC_2_way_pseudogenes [ Yale-UCSC 2-way pseudogenes not found to ovelap a Gencode model ] |
| 419 | cufflinks_CSHL [ cufflinks transcripts (GINGERAS LAB) with mass spec (GIDDINGS LAB) support ] |
| 206 | cufflinks_CSHL_CALTECH [ cufflinks transcripts overlapping bodymap transcripts ] |
| 5556 | ens_bodymap_novel [ Novel Ensembl-BodyMap loci with 5+ exons ] |
| 5489 | flagged_pseudo [ Pseudogenes predicted by YALE & UCSC only ] |
| 425 | general_issues [ Gene models imported via GTF ] |
| 1288 | lncRNAs_lipovich [ long non-coding RNA list produced by the Lipovich group (Jia et al 2010) ] |
| 2357 | mass-spec_Giddings [ Mass-spec peptides mapped by 6-frame genome translation from Giddings lab ] |
| 255 | missing_hgnc [ HGNC symbols missing from HAVANA (ENSEMBL) ] |
| 1 | putative_regions [ Unannotated regions identified to contain functional elements ] |
Current flags
| Flag descriptions | | List flagged issues |
| Unresolved flags: 586664 | | Resolved flags: 55127 |
| Unresolved flag details: | |
| Giddings_intergenic_hits_5 | 2357 |
| IDR_2 | 6 |
| IDR_3 | 20 |
| MIT_coding_lncRNAs | 401 |
| NMD_cases | 698 |
| NMD_with_missing_CDS | 5 |
| SomewhatSim | 648 |
| VQCG_duplicated_root_name | 1 |
| VQCG_transcript_gaps | 1 |
| VQCT_wrong_biotype | 14 |
| VerySim | 64 |
| all_cds_start_NF_transcripts | 7 |
| assembly_transformation | 5 |
| bidirectional | 4 |
| ccds_reflag | 3 |
| check_status | 34 |
| cnio_structures | 46 |
| congo_nc | 896 |
| crg_nc_splicing | 205 |
| cuffl_ms_spec_overlap_gencode | 309 |
| cufflinks_mass_spec_novel | 110 |
| ens_pseudogene_ovrlp | 7 |
| false_intron | 5 |
| flagged_pseudogene | 5442 |
| hgnc_update | 1 |
| isolated_polyA_sites-signals | 2 |
| lncRNA_ovlp_coding_exon | 264 |
| low_complexity | 182 |
| manual_selection | 11 |
| missing_ccds | 1267 |
| missing_cdna | 449084 |
| missing_evidence | 627 |
| missing_exon | 9370 |
| missing_hgnc | 239 |
| missing_ig | 123 |
| missing_intron | 11353 |
| missing_mhc | 3 |
| missing_new_cdna | 303 |
| no_pseudo_polyA_signal | 6912 |
| no_stop_codon | 75 |
| non-organism-support | 777 |
| novel_RNASeq_loc | 8834 |
| novel_coding_exon_MIT | 45 |
| novel_cufflinks_bodymap | 206 |
| novel_ensembl_bodymap | 89 |
| novel_ensembl_bodymap_mt4_exon | 200 |
| novel_lncRNA_lipovich | 857 |
| novel_locus | 317 |
| novel_retro | 301 |
| other_problem | 3 |
| overlapping_cds | 44 |
| proc_trans_to_lincrna_in_merge | 743 |
| processed_transc_in_merge | 1322 |
| processed_transcript_to_noncod | 3844 |
| race_454 | 360 |
| race_454_positive_control | 50 |
| race_454_positive_ctrl_25 | 32 |
| selected_targets | 222 |
| short_NMD | 169 |
| splice_AT_AC_alnDiff | 36 |
| splice_AT_AC_none | 1 |
| splice_AT_AC_suspect | 1 |
| splice_AT_AC_weak | 47 |
| splice_GC_AG_alnDiff | 121 |
| splice_GC_AG_none | 182 |
| splice_GC_AG_suspect | 18 |
| splice_GC_AG_weak | 1592 |
| splice_GT_AG_alnDiff | 1879 |
| splice_GT_AG_none | 3278 |
| splice_GT_AG_suspect | 1900 |
| splice_GT_AG_weak | 63584 |
| splice_gap_alnDiff | 5 |
| splice_gap_none | 5 |
| splice_gap_weak | 2 |
| splice_other_alnDiff | 738 |
| splice_other_moderate | 188 |
| splice_other_none | 472 |
| splice_other_strong | 328 |
| splice_other_suspect | 24 |
| splice_other_weak | 632 |
| translation_missing | 27 |
| verify | 1577 |
| wrong_biotype | 508 |