This track represents the gene models for the T2T CHM13 assembly generated using the CAT (Compartive Annotation Toolkit) software with genes that CAT could not be mapped as well as novel paralogs, filled in from the LiftOff mappings. The reference annotations are from GENCODE V35.
This track follows the display conventions for gene prediction tracks. The exons for putative non-coding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. Gene names are displayed in 'pack' or 'full' mode. More information about each gene can be found by clicking on the specific gene/transcript model.
The following color key is used:
This tracks combines gene annotations generated by two methods. First the Comparative Annotation Toolkit (CAT) was used to Liftoff was then used as a second annotation method to map genes missed by CAT and additional gene paralogs.
Genome annotation for T2T CHM13 assembly was performed using Comparative Annotation Toolkit (CAT). CAT leverages whole-genome alignments generated by Cactus to transfer annotations from one source genome to one or more target genomes. For this annotation set, CAT lifted over the reference GENCODE v35 annotations onto the T2T genome. CAT also incorporated Iso-Seq data, first assembled into transcripts with StringTie2, to make the final consensus annotation set.
Liftoff uses Minimap2 to align reference gene DNA sequences to the target genome and selects the alignment(s) concordant with the intron/exon structure with the highest sequence identity. A minimum sequence identity of 95% was required to annotate gene paralogs. After running Liftoff, we identified genes that did not overlap any CAT annotations using bedtools intersect. These were combined with the CAT annotation to create the final annotation.
This track was provide by Marina Haukness <mhauknes@ucsc.edu> of UC Santa Cruz and Alaina Shumate <ashumat2@jhmi.edu> of Johns Hopkins University.
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