Two gene name with same gene ID in Cuffdiff result

[super0925]

Hi All
I finish the Tuxedo pipeline on my data.
tophat2-cufflinks-cuffmerge-cuffdiff
I got the cuffdiff result 'gene_exp.diff', I found that some of the rows are like below:

test_id gene_id gene p_value q_value
XLOC_015858 XLOC_015858 Q27U16_BOVIN,Q3MJK3_BOVIN 5e-05 0.00449882

When I go back annotation file check , I found that in the genes.gtf
ENSBTAG00000005251 Q27U16_BOVIN
ENSBTAG00000038536 Q3MJK3_BOVIN

It seem that they are different genes...

Is it normal? I mean Two gene names with one gene ID?

Thank you!

[GenoMax]

They may be alternately spliced transcripts from same gene (or members of a family)?

CLUSTAL O(1.2.1) multiple sequence alignment

TR|Q27U16|Q27U16_BOVIN MASGILMNIQEEVTCPICLELLTEPLSLDCGHTFCQACITGNNKESIIGQEGKRSCPVCR 60
TR|Q3MJK3|Q3MJK3_BOVIN MASGILMNIQEEVTCPICLELLTEPLSLDCGHSFCQACITANNKESIIGQEGKRSCPVCR 60
                       ********************************:*******.*******************

TR|Q27U16|Q27U16_BOVIN VSFEPGNLRPNRNVANIVQRLREVKVSPEVEQERNLCAHHGEKLQLFCEQDGKVICWLCE 120
TR|Q3MJK3|Q3MJK3_BOVIN VSFEPGNLRPNRHVANIVQRLREVKVSPEVEQERNLCAHHGEKLQLFCEQDGKVICWLCE 120
                       ************.***********************************************

TR|Q27U16|Q27U16_BOVIN RSQEHRGHNTFLMEEIAPEYQKKLQSCLQRLKGKKQEAEELEIKVREEMSTWKIQIENEI 180
TR|Q3MJK3|Q3MJK3_BOVIN RSQEHRAHNTFLMEEIAPEYQKKLQSCLQRLKGKKQEAEELEIKVREEMSTWKIQIENEI 180
                       ******.*****************************************************

TR|Q27U16|Q27U16_BOVIN QNVQGKFTQLRQILDSEEMKELRKLKDELGVILKELAESENDLVQEKLLVSNLISDVERH 240
TR|Q3MJK3|Q3MJK3_BOVIN QNVQGKFTQLRQILDSEEMKELRKLKDELGVILKELAESENDLVQEKLLVSNLISDVERH 240
                       ************************************************************

TR|Q27U16|Q27U16_BOVIN LQGSTMELLQDANVIIKRSETLALKKPKSFPKEQRRVFRAPDLREILRVFNELTDVQRYW 300
TR|Q3MJK3|Q3MJK3_BOVIN LQGSTMELLQDANVIIKRSETLALKKPKSFPKEQRRVFRVPDLRQTLHVFNELTDVQRYW 300
                       ***************************************.****: *:************

TR|Q27U16|Q27U16_BOVIN VQVTLNSPRSANVVISPDQRQVRYASNDQRSNVYLIDNCEVFSVLGSPVITSGRHYWEVD 360
TR|Q3MJK3|Q3MJK3_BOVIN VQVTLNSPKSENVVISPDQRQVRYASSDQCYNAYWNDNYEDFGVLGSPVITSGRHYWEVD 360
                       ********:* ***************.**  *.*  ** * *.*****************

TR|Q27U16|Q27U16_BOVIN VSKKRAWILGVCGEN---IMIEPPIFGNFGNGNYSNVFSVYQPKNRNCGNSQNVYSRYQP 417
TR|Q3MJK3|Q3MJK3_BOVIN VSKKSAWILGVCGEKCEDIMKLPSKLGNCGNG-----------------NCQNVYSRYQP 403
                       **** *********:   **  *  :** ***                 *.*********

TR|Q27U16|Q27U16_BOVIN KNGYWVIGLKHDSVYKAFE-SSFSGPEILTLSLSVSPHRIGIFLDYEARTVLFLNVTNHG 476
TR|Q3MJK3|Q3MJK3_BOVIN KNGYWVIGLKHYCVYNAFDASSFSDPVILPLSLSVSLHRVGVFLDYEAHTVLFLNVTNHG 463
                       *********** .**:**: **** * ** ****** **:*:******:***********

TR|Q27U16|Q27U16_BOVIN FPIYKFSSCSFPQNIVPYFNPMNCDAPMTLCSPSC 511
TR|Q3MJK3|Q3MJK3_BOVIN FPICQFSSCSFPQNIVPYFNPMNCGVPMTLCSPSC 498
                       *** :******************* .*********

[super0925]

Thank you. So what is your opinion? save two names simultaneously or just need first one?