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Select or download this

$ cat file1.txt
gene1   1234    78975
...
gene1   1234    78975   abc
gene13  9876    ldlgfjk xyz
$

Select or download this

$ perl -F'\t' -lane '
>     $a{$F[0]} = $F[1], next if $#ARGV == 0;
...
gene1   1234    78975   abc
gene13  9876    ldlgfjk xyz
$