Transpose is your friend...

#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11146766
use warnings;
use List::AllUtils qw( zip_by );

my @matrix = (
    [qw(t1 t1 t2 t2 t2)], # <- transcripts
    [qw(a1 a2 a1 a1 a2)], # <- alleles
    [qw(intron intron UTR_CG UTR UTR)], # <- locations
);
use Data::Dump 'dd'; dd 'original matrix', \@matrix;

my @t = zip_by { [ @_ ] } @matrix;
use Data::Dump 'dd'; dd '@t', \@t;

my %cg = map { $_->[0] . "\n" . $_->[1] => 1 } grep { $_->[2] eq 'UTR_
+CG' } @t;
use Data::Dump 'dd'; dd '%cg', \%cg;
@t = grep { $_->[2] ne 'UTR' or not $cg{ $_->[0] . "\n" . $_->[1] } } 
+@t;
use Data::Dump 'dd'; dd 'modified @t', \@t;

my @finalmatrix = zip_by { [ @_ ] } @t;
use Data::Dump 'dd'; dd 'final matrix', \@finalmatrix;
[download]

Outputs:

(
  "original matrix",
  [
    ["t1", "t1", "t2", "t2", "t2"],
    ["a1", "a2", "a1", "a1", "a2"],
    ["intron", "intron", "UTR_CG", "UTR", "UTR"],
  ],
)
(
  "\@t",
  [
    ["t1", "a1", "intron"],
    ["t1", "a2", "intron"],
    ["t2", "a1", "UTR_CG"],
    ["t2", "a1", "UTR"],
    ["t2", "a2", "UTR"],
  ],
)
("%cg", { "t2\na1" => 1 })
(
  "modified \@t",
  [
    ["t1", "a1", "intron"],
    ["t1", "a2", "intron"],
    ["t2", "a1", "UTR_CG"],
    ["t2", "a2", "UTR"],
  ],
)
(
  "final matrix",
  [
    ["t1", "t1", "t2", "t2"],
    ["a1", "a2", "a1", "a2"],
    ["intron", "intron", "UTR_CG", "UTR"],
  ],
)
[download]