You are mistaken!

This

• $split_topodom[0]

is only printing the part before the first "TOPO_DOM" which is an empty string ""

"TOPO_DOM 1 ...
^^
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You have to inspect the full array

• @split_topodom

Debugger-Demo

> perl -de0
...
  DB<21> $string="TOPO_DOM 1; /note=Cytoplasmic; /evidence=ECO:0000269
+|PubMed:24744376; TOPO_DOM 25..74; /note=Extracellular;..."

  DB<22> x split /TOPO_DOM/, $string
0  ''
1  ' 1; /note=Cytoplasmic; /evidence=ECO:0000269|PubMed:24744376; '
2  ' 25..74; /note=Extracellular;...'
  DB<23>
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