I wrote a command-line genome browser, ASCIIGenome, that may be handy in cases like this to find sequence motifs in a reference fasta file and show them together with an annotation file.

First load the reference sequence and an annotation file (this can be a remote file. Fasta file must be indexed):

ASCIIGenome -fa /path/to/genome.fa \
    ftp://ftp.ensembl.org/pub/release-86/gff3/homo_sapiens/Homo_sapiens.GRCh38.86.chromosome.8.gff3.gz

Then at the command prompt issue these commands:

find ENSG00000168487
grep -i \tgene\t.*ENSG00000168487 gff3
seqRegex -iupac TATAWAA
zo 8
print seqRegex
seqRegex > matches.bed
save matches.png

Explained: Find the gene ENSG00000168487, for clarity only show the "gene" feature (grep ...). Then search the motif TATAWAA as iupac code, zoom out x times (e.g. 8 times) to see some matches in the sequence.

The matches can be show on screen (print seqRegex) and saved to file (print seqRegex). Finally save a picture as png.

The resulting image should like similar to this:

Just use the cross-platform and ultrafast FASTA/Q tookit SeqKit

1. Geting GTF (time: 5s, memory: <1M)

   $ zcat Homo_sapiens.GRCh38.84.gtf.gz | grep BMP1 | awk '$3=="gene"' > BMP1.gtf
   

   Three records extracted:

   $ cat BMP1.gtf 
   2   ensembl_havana  gene    68865481    68871517    .   -   .   gene_id "ENSG00000163217"; gene_version "1"; gene_name "BMP10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000129573"; havana_gene_version "1";
   X   ensembl_havana  gene    50910784    50916607    .   +   .   gene_id "ENSG00000130385"; gene_version "5"; gene_name "BMP15"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021525"; havana_gene_version "2";
   8   ensembl_havana  gene    22164736    22212326    .   +   .   gene_id "ENSG00000168487"; gene_version "17"; gene_name "BMP1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000097761"; havana_gene_version "6";
   

2. Extracting upstram sequence (FASTA index pre-built. time: 2.6s, memory: 983M)

   $ seqkit subseq --only-flank --up-stream 1000 --gtf BMP1.gtf hsa.fa  > BMP1.usf_1k.fa
   

   Gene locations were stored in sequence header. For exmaple, 2_68865481-68871517:-_usf:1000 means 1000bp upstream flanking sequence of region 68865481-68871517 in negative strand of chromosome 2.

   $ seqkit seq --name BMP1.usf_1k.fa 
   2_68865481-68871517:-_usf:1000 ENSG00000163217
   X_50910784-50916607:+_usf:1000 ENSG00000130385
   8_22164736-22212326:+_usf:1000 ENSG00000168487
   

3. Locating pattern (time: 0.1s, memory: 0)

   $ seqkit locate --ignore-case --degenerate --pattern TATAWAA BMP1.usf_1k.fa  | column -t 
   seqID                           patternName  pattern  strand  start  end  matched
   2_68865481-68871517:-_usf:1000  TATAWAA      TATAWAA  +       578    584  TATATAA
   2_68865481-68871517:-_usf:1000  TATAWAA      TATAWAA  -       577    583  TATATAA