5 mouse genes cause errors referencing very large genes on the same chromosome

[sreichl]

used mouse genome 12-column BED file:
mm10 from UCSC as gzip https://genome.ucsc.edu/cgi-bin/hgTables assembly:mm10 -> track:NCBI RefSeq -> table:refFlat; output format: BED

error genes

• Ccl19 -> chr4:42,754,525-42,756,543 2,019 bp
• Ccl21a -> chr4:42,772,860-42,773,993 1,134 bp
• Ccl21c -> chr4:42,612,123-42,613,253 1,131 bp
• Il11ra2 -> chr4:42,656,001-42,665,763 9,763 bp
• Rarres2 -> chr6:48,546,630-48,549,721 3,092 bp

Mdn1 pops up in all Chr4 error messages:
chr4:32,657,119-32,775,217
118,099 bp

Sspo pops up in Rarres2 (on Chr6) error message
chr6:48,425,163-48,478,169
53,007 bp

Ccl19 (error)
chr4:42,754,525-42,756,543
2,019 bp

Cxcl17 not correctly displayed! no gene not correct coordinates
chr7:25,099,478-25,112,311
12,834 bp

Ccl17 completely fine
chr8:95,537,081-95,538,664
1,584 bp

https://www.informatics.jax.org/marker/MGI:109123

https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm39&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr6%3A48425163-48478169&hgsid=1597741285_OPZS1OsEmzcw5yAStALoyZTLcBbj

[sreichl]

• print gene_annot_df next time such an error occurs

[sreichl]

one more odd/weird observation in Corce's RNA-seq data for CD14 -> 4 gene tracks but without any information on introns/exons...