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I was browsering the UCSC viewer of the genome at this region.

UCSC genes label two genes as Hba-a2 while GENCODE thinks the left one is Hba-a1

Which annotation is correct?

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Gencode is correct (when in doubt, always assume Gencode/Ensembl is correct when it differs from UCSC). What presumably happened is that the UCSC annotation pipeline noticed that Hba-a1 and Hba-a2 are nearly identical (they produce the same protein and have minimal nucleotide difference) and just misannotated.

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    $\begingroup$ As a general rule, it is usually safe to believe Gencode over RefSeq and RefSeq over UCSC (not because UCSC is bad, but because it isn't manually curated). $\endgroup$ – terdon Jan 5 '18 at 17:27

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