Hello, I have a list of human genes and I'd like to retrieve the physical coordinates (GRCh37/hg19 assembly) of their 3'UTRs. Are you aware of any software that can do that? Thanks !
For RefSeq annotation, you can use the `add_utrs_to_gff` python script to first add 5' and 3' UTR features and then use unix `grep` to extract the genes of your interest. The latest RefSeq annotation of the GRCh37 assembly is here: https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/105.20190906/ 

    ## download annotation in GFF3 format
    $ curl -O https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/105.20190906/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz

    ## download the add_utrs_to_gff3 python script 
    $ curl -O https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/add_utrs_to_gff/add_utrs_to_gff.py

    ## add utr features to the gff3 file 
    $ python3 add_utrs_to_gff.py GCF_000001405.25_GRCh37.p13_genomic.gff.gz > GRCh37_with_utrs.gff3

    ## extract 5' UTR for GeneID:5768 
    $ grep 'five_prime_UTR' GRCh37_with_utrs.gff3 | grep -w 'GeneID:5768'
    NC_000001.10    BestRefSeq      five_prime_UTR  180123968       180124042       .       +       .       ID=utr00100412821;Parent=rna-NM_001004128.2;transcript_id=NM_001004128.2;Dbxref=GeneID:5768,Genbank:NM_001004128.2,HGNC:HGNC:9756,MIM:603120
    NC_000001.10    BestRefSeq      five_prime_UTR  180124004       180124042       .       +       .       ID=utr00282651;Parent=rna-NM_002826.5;transcript_id=NM_002826.5;Dbxref=GeneID:5768,Genbank:NM_002826.5,HGNC:HGNC:9756,MIM:603120
