Transcript not seen in results

[JohmaChroc]

Hi,
Results for my gene transcript of interest (ENST00000450313) are not being displayed whereas results for other transcripts for the same gene are. Is there a limit on the number of transcripts displayed in the results output? If so, is there a way of selecting a specific gene transcript for analysis? The impacted exon in question is present in the majority of transcripts so I may expect to see somewhat similar results (the exon in my transcript is concordant with the gnomAD canonical transcript - ENST00000372098). Thank you in advance.

[bw2]

Hi @JohmaChroc , thanks for reporting this issue.
To reduce the number of transcripts in the results, I excluded most non-protein-coding transcripts that overlapped protein-coding ones. ENST00000450313 falls in this category as its transcript type is "nonsense_mediated_decay" rather than "protein_coding" in gencode 36.

My current set of GRCh38 annotations includes 176,560 transcripts, and excludes the follow transcripts by type:

     37121: lncRNA
      4085: processed_pseudogene
      3469: processed_transcript
      2077: retained_intron
      1415: miRNA
      1340: nonsense_mediated_decay
      1332: misc_RNA
      1068: snRNA
       827: transcribed_unprocessed_pseudogene
       658: snoRNA
       611: TEC
       573: unprocessed_pseudogene
       418: transcribed_processed_pseudogene
       283: rRNA_pseudogene
       128: transcribed_unitary_pseudogene
        34: scaRNA
        28: pseudogene
        26: unitary_pseudogene
        13: IG_V_pseudogene
        10: rRNA
         9: Mt_tRNA
         6: polymorphic_pseudogene
         6: IG_V_gene
         5: non_stop_decay
         3: ribozyme
         3: IG_C_pseudogene
         2: sRNA
         2: Mt_rRNA
         1: translated_processed_pseudogene
         1: scRNA
         1: IG_C_gene
         1: TR_V_gene
         1: TR_V_pseudogene

Since you (and probably others) want to see some of these, I'll try adding all transcripts.

[JohmaChroc]

A follow up question: Is there any difference with the included transcripts for GRCh37/hg19?

[bw2]

There's no difference in how SpliceAI-lookup treats GRCh37 and GRCh38 transcripts.
In Gencode though, there are currently 236230 GRCh37 transcripts vs. 234486 GRCh38.
(GRCh37 transcripts are downloaded from https://www.gencodegenes.org/human/release_37lift37.html
and GRCh38 transcripts from https://www.gencodegenes.org/human/)

Also, even after showing all non-coding transcripts, ENST00000450313 still doesn't appear because 1-45797036-GCCTGTGGATATAGCCTCAAAAGCCAACATC-G is ~800bp to the left of the transcript. Here's the relevant line from gencode.v37lift37.annotation.gtf:

chr1	HAVANA	transcript	45797868	45806071	.	-	.	gene_id "ENSG00000132781.19_12"; transcript_id "ENST00000450313.6_6"; gene_type "protein_coding"; gene_name "MUTYH"; transcript_type "nonsense_mediated_decay"; transcript_name "MUTYH-210"; level 2; protein_id "ENSP00000408176.2"; transcript_support_level 5; hgnc_id "HGNC:7527"; tag "mRNA_end_NF"; tag "RNA_Seq_supported_only"; havana_gene "OTTHUMG00000007682.11_12"; remap_num_mappings 1; remap_status "full_contig"; remap_target_status "overlap";

This transcript was quite different in the earlier gencode.v19.annotation.gtf:

chr1	ENSEMBL	transcript	45794915	45806142	.	-	.	gene_id "ENSG00000132781.13"; transcript_id "ENST00000450313.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "MUTYH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "MUTYH-202"; level 3; protein_id "ENSP00000408176.1"; tag "basic"; havana_gene "OTTHUMG00000007682.5";