For anyone who comes across this problem, I figured out a solution using the UCSC table browser and extract-transcript-regions

I obtained the refseq ID for each LRG I was interested in using the xref file provided on LRG's download page. Then I used the UCSC table browser to download a GTF file using the refseq IDs. Finally I Stephen Floor's extract-transcript-regions script to convert this GTF to a bed file.

Note: this script converts to bed12 or blockbed. You can use bedtools bed12ToBed6 to convert the bed6 file. I used the -n option to use score field to track feature (exon) number; downstream I used awk to bring this number back into a label in my final bed file.

python extract_transcript_regions.py -i genes.gtf -o genes --gtf

now convert this blockbed (bed12) to bed6

cat genes_cds.bed | bed12ToBed6 -i stdin -n > genes_cds_bed6.bed

cat genes_3utr.bed | bed12ToBed6 -i stdin -n > genes_3utr_bed6.bed

cat genes_5utr.bed | bed12ToBed6 -i stdin -n > genes_5utr_bed6.bed

cat genes_introns.bed | bed12ToBed6 -i stdin -n > genes_introns_bed6.bed

I wanted my final bed to have 10bp of each intron (5' and 3').

awk '{OFS="\t"} {print $1,$2,$2+10,$4"_"$5"_L",0,$6"\n"$1,$3-10,$3,$4"_"$5"_R",0,$6}' genes_introns_bed6.bed > genes_introns_10bp_bed6.bed

I also wanted to trim UTRs to 200bp. for 3':

awk '{OFS="\t"} {if($3-$2 >200 && $6 =="-") {print $1,$3-200,$3,$4"_"$5,0,$6;} else if($3-$2 >200 && $6 =="+") {print $1,$2,$2+200,$4"_"$5,0,$6;} else {print $1,$2,$3,$4"_"$5,0,$6;}}' genes_3utr_bed6.bed > genes_3utr_200bp_bed6.bed

for 5':

awk '{OFS="\t"} {if($3-$2 >200 && $6 =="-") {print $1,$2,$2+200,$4"_"$5,0,$6;} else if($3-$2 >200 && $6 =="+") {print $1,$3-200,$3,$4"_"$5,0,$6;} else {print $1,$2,$3,$4"_"$5,0,$6;}}' genes_5utr_bed6.bed > genes_5utr_200bp_bed6.bed

now clean up the labels on the CDS bed

awk '{OFS="\t"} {print $1,$2,$3,$4"_"$5,0,$6}' genes_cds_bed6.bed > genes_cds_cleaned_bed6.bed

finally, combine and sort all of the bed files to create my final region of interest bed file

cat genes_introns_10bp_bed6.bed genes_cds_cleaned_bed6.bed genes_5utr_200bp_bed6.bed genes_3utr_200bp_bed6.bed | sortBed -i - > genes_final_roi.sorted.bed