How can i find a gene list in .bed with all hemoglobin/ globin genes in Human Genome ?

Question

[dzisis1986]

I would like to find/create a .bed which will include all hemoglobin/ globin genes for human GRCh38 similar to rRNA.bed which can be found for example in http://rseqc.sourceforge.net/#fetch-chromsome-size-file-from-ucsc

Answer 1

[Pierre Lindenbaum]

i wrote this tool http://lindenb.github.io/jvarkit/GoUtils.html to map gene ontology terms , annotations and GFF3 files.

So with "GO:0005344" oxygen carrier activity

I got:

$ gunzip -c  Homo_sapiens.GRCh38.105.chr_patch_hapl_scaff.gff3.gz |\
java  dist/goutils.jar -A "GO:0005344" --action gff3  |\
awk '($3=="gene") {printf("%s\t%d\t%d\n",$1,int($4)-1,$5);}' |\
bedtools merge

chr11   5225463 5229395
chr11   5232677 5243657
chr11   5248268 5249857
chr11   5253187 5505652
chr14   77265482    77271206
chr16   142727  166764
chr16   176679  177522
chr16   180458  181179
chr17   76527355    76551175
chr22   35606763    35637951
chr6    154154495   154356803

[dzisis1986]

The problem is that i dont find any proper list of hemoglobin genes. I need first the globin genes.

[GenoMax]

NCBI (globin): https://www.ncbi.nlm.nih.gov/gene/?term=globin+AND+human+%5Borgn%5D
NCBI (hemoglobin): https://www.ncbi.nlm.nih.gov/gene/?term=hemoglobin+AND+human+%5Borgn%5D
Genecards: https://www.genecards.org/Search/Keyword?queryString=globin&startPage=0

[dzisis1986]

i Have lets say my list with globin genes:

ENSG00000086506
ENSG00000130656
ENSG00000188536
ENSG00000196565
ENSG00000206172
ENSG00000206177
ENSG00000206178
ENSG00000213931
ENSG00000213934
ENSG00000223609
ENSG00000229988
ENSG00000244734
ENSMUSG00000052187
ENSMUSG00000052217
ENSMUSG00000052305
ENSMUSG00000073940
ENSMUSG00000078621
ENSMUSG00000083216
ENSMUSG00000085700

But with Table browser, I can't download or create a .bed file for those genes. Can you help me with the creation of .bed file for this list?