Duplicate genes with RSEM counts: Which one to choose?

Question

I have Ensembl ids in the first column and samples with RSEM counts data in other columns. I converted Ensembl ids to gene symbols. Now I see there are three genes repeated twice.

Gene   S1       S2       S3
COG8  804.07  1475.16  323.80
COG8  249.23   867.94  113.64
SDHD 1464.84  3508.02    75
SDHD  4.16     3.97       0
SOGA3 81.65   30.76    32.69
SOGA3 0.00    10.77    25.65

These are the Ensembl ids:

• SOGA3: ENSG00000214338, ENSG00000255330
• SDHD: ENSG00000204370, ENSG00000255292
• COG8: ENSG00000213380, ENSG00000272617.

This is not for DE analysis, I want to do subtyping. Should I calculate mean or median on that? How should I go forward with this duplicate genes?

Answer 1

Let's look into this a bit more deeply. For instance:

• HUGO: SOGA3
• Ensembl 1: ENSG00000214338
• Ensembl 2: ENSG00000255330

The Ensembl pages (linked above) for both ENSG00000214338 and ENSG00000255330 show that these genes have 3 paralogs and each lists the other as one of the paralogs. Your other two examples are similar, they are also paralogs of each other. You can also see that the position of each gene in the genome is slightly different:

ENSG00000255330 : Chromosome 6: 127,438,406-127,519,001 reverse strand. ENSG00000214338 : Chromosome 6: 127,472,794-127,519,191 reverse strand.

So these two genes refer to two distinct regions of the genome. And, as expected, they have different transcripts. However, two of those transcripts (ENST00000481848.6 from ENSG00000255330 and ENST00000525778.5 from ENSG00000214338) code for the same protein sequence. This means that we have one protein but two different genes for it. To illustrate, here are the two transcripts aligned:

ENST00000525778.5       CCGTGTTCGAGCGGTTTTGGGATCCTCTGCCAAGTACGGGATAAGAGAAT
ENST00000481848.6       CTC-----------------------------------------------
                        *                                                 

ENST00000525778.5       AGAGCAAGGAGTTTGAGCGCTGCTGCCAATCTTCCATCTCGGGCGTGGCT
ENST00000481848.6       --------------------------------------------------


ENST00000525778.5       CTGGCCTTTTTGTCTCTTTATCCCGCCACTCCCCACCCCCGTCCCCCGTC
ENST00000481848.6       --------------------------------------------------


ENST00000525778.5       CCCCTCCCCGCCTTCTTCTCTTTCCTCTTGAAAGTAACCTCTCTTTGGTT
ENST00000481848.6       -------------------------------------------TTTGGTT
                                                                   *******

ENST00000525778.5       ACTTCTACCCTATCGTCCCTTGCAATCCCGCCTTCTCTCCTGCCCAGTTC
ENST00000481848.6       ACTTCTACCCTATCGTCCCTTGCAATCCCGCCTTCTCTCCTGCCCAGTTC
                        **************************************************

ENST00000525778.5       GGTGAGGTCAGCTCATGAACATCTCTGCACTTCCTGGGGAGCGTCTGGCC
ENST00000481848.6       GGTGAGGTCAGCTCATGAACATCTCTGCACTTCCTGGGGAGCGTCTGGCC
                        **************************************************

ENST00000525778.5       CAGCTTGGTACCTCGCGTGTTAGCCTGCTGAGAGCTGCAGCTCCAGCCCA
ENST00000481848.6       CAGCTTGGTACCTCGCGTGTTAGCCTGCTGAGAGCTGCAGCTCCAGCCCA
                        **************************************************

ENST00000525778.5       GCCGCGGACCGCCGGGAAGTCACCCGCTCTGGGGGCAGCTGAATCTTGAC
ENST00000481848.6       GCCGCGGACCGCCGGGAAGTCACCCGCTCTGGGGGCAGCTGAATCTTGAC
                        **************************************************

ENST00000525778.5       GTTACCGCCATTGTTTGGAGAAATCGAGTGGGTGTGGAACTGCGGCGAGC
ENST00000481848.6       GTTACCGCCATTGTTTGGAGAAATCGAGTGGGTGTGGAACTGCGGCGAGC
                        **************************************************

ENST00000525778.5       GAGCCCAAAGTCATGCTCAGCCGGAAAGTCGCATACAATAATATGAAGTT
ENST00000481848.6       GAGCCCAAAGTCATGCTCAGCCGGAAAGTCGCATACAATAATATGAAGTT
                        **************************************************

ENST00000525778.5       GAACTTTCCTCGGCGCAGAAAGGCACAATAATAAACCCTGAGATCCCCGG
ENST00000481848.6       GAACTTTCCTCGGCGCAGAAAGGCACAATAATAAACCCTGAGATCCCCGG
                        **************************************************

ENST00000525778.5       AATATCAGAAGGAAAGTGCTGTTGATTTGTTCAGCTACTTGGAAACCTCG
ENST00000481848.6       AATATCAGAAGGAAAGTGCTGTTGATTTGTTCAGCTACTTGGAAACCTCG
                        **************************************************

ENST00000525778.5       CCTCTGCTGAGAAGTGAGCAAGTTCTGGATTTCTAAAGGGTTGGGGATGA
ENST00000481848.6       CCTCTGCTGAGAA-------------------------------------
                        *************                                     

ENST00000525778.5       ATGATGGGCTTAGGAAGGAAGGTTGGCGGCGGTGAAGAGGGAAGAGGATG
ENST00000481848.6       --------CTTAGGAAGGAAGGTTGGCGGCGGTGAAGAGGGAAGAGGATG
                                ******************************************

ENST00000525778.5       ATCTAGTAATGGGCTCTTCCAAATCGCATCTGGTAGGTTCATAGCCATGA
ENST00000481848.6       ATCTAGTAATGGGCTCTTCCAAATCGCATCTGGTAGGTTCATAGCCATGA
                        **************************************************

ENST00000525778.5       GTCAGCCACCAATCGGGGGCGCTGCCCCTGCCACAGCAGCAGCTTCTCCC
ENST00000481848.6       GTCAGCCACCAATCGGGGGCGCTGCCCCTGCCACAGCAGCAGCTTCTCCC
                        **************************************************

ENST00000525778.5       GCCGCTGCAGCCACTGAGGCTCGTCTGCACCCGGAGGGCAGCAGCAGAAA
ENST00000481848.6       GCCGCTGCAGCCACTGAGGCTCGTCTGCACCCGGAGGGCAGCAGCAGAAA
                        **************************************************

ENST00000525778.5       GCAGCAGCGAGCTCAGTCACCCGCTAGACCGAGGGACAGTTCGCTGCGAC
ENST00000481848.6       GCAGCAGCGAGCTCAGTCACCCGCTAGACCGAGGGACAGTTCGCTGCGAC
                        **************************************************

ENST00000525778.5       AGACAATCGCGGCCACCCGGTCCCCAGTGGGGGCCGGCACTAAACTCAAT
ENST00000481848.6       AGACAATCGCGGCCACCCGGTCCCCAGTGGGGGCCGGCACTAAACTCAAT
                        **************************************************

ENST00000525778.5       TCTGTTCGGCAGCAGCAGCTGCAGCAGCAGCAACAGCAGGGTAACAAGAC
ENST00000481848.6       TCTGTTCGGCAGCAGCAGCTGCAGCAGCAGCAACAGCAGGGTAACAAGAC
                        **************************************************

ENST00000525778.5       CGGGAGCCGCACGGGGCCGCCCGCCAGCATCCGAGGAGGCGGAGGTGGGG
ENST00000481848.6       CGGGAGCCGCACGGGGCCGCCCGCCAGCATCCGAGGAGGCGGAGGTGGGG
                        **************************************************

ENST00000525778.5       CCGAGAAGGCGACGCCCCTGGCGCCCAAAGGGGCCGCTCCGGGAGCTGTC
ENST00000481848.6       CCGAGAAGGCGACGCCCCTGGCGCCCAAAGGGGCCGCTCCGGGAGCTGTC
                        **************************************************

ENST00000525778.5       CAGCCTGTGGCTGGTGCTGAAGCGGCCCCCGCCGCGACCCTGGCCGCTTT
ENST00000481848.6       CAGCCTGTGGCTGGTGCTGAAGCGGCCCCCGCCGCGACCCTGGCCGCTTT
                        **************************************************

ENST00000525778.5       GGGCGGCAGGAGGCCCGGACCGCCCGAGGAGCCGCCTCGGGAGCTAGAGT
ENST00000481848.6       GGGCGGCAGGAGGCCCGGACCGCCCGAGGAGCCGCCTCGGGAGCTAGAGT
                        **************************************************

ENST00000525778.5       CCGTGCCCTCGAAACTCGGGGAACCCCCTCCGCTCGGAGAAGGGGGAGGA
ENST00000481848.6       CCGTGCCCTCGAAACTCGGGGAACCCCCTCCGCTCGGAGAAGGGGGAGGA
                        **************************************************

ENST00000525778.5       GGGGGCGGGGAAGGAGGAGGAGCCGGCGGCGGCTCCGGGGAAAGGGAGGG
ENST00000481848.6       GGGGGCGGGGAAGGAGGAGGAGCCGGCGGCGGCTCCGGGGAAAGGGAGGG
                        **************************************************

ENST00000525778.5       GGGCGCTCCGCAGCCGCCGCCGCCCAGGGGCTGGCGAGGGAAAGGCGTAC
ENST00000481848.6       GGGCGCTCCGCAGCCGCCGCCGCCCAGGGGCTGGCGAGGGAAAGGCGTAC
                        **************************************************

ENST00000525778.5       GCGCTCAGCAGAGGGGCGGCAGCGGCGGGGAGGGGGCCTCCCCTTCTCCA
ENST00000481848.6       GCGCTCAGCAGAGGGGCGGCAGCGGCGGGGAGGGGGCCTCCCCTTCTCCA
                        **************************************************

ENST00000525778.5       TCCTCCTCTTCTGCGGGCAAAACCCCAGGAACCGGCAGCAGAAACTCCGG
ENST00000481848.6       TCCTCCTCTTCTGCGGGCAAAACCCCAGGAACCGGCAGCAGAAACTCCGG
                        **************************************************

ENST00000525778.5       AAGCGGCGTTGCGGGGGGCGGCAGCGGTGGTGGAGGGAGCTACTGGAAAG
ENST00000481848.6       AAGCGGCGTTGCGGGGGGCGGCAGCGGTGGTGGAGGGAGCTACTGGAAAG
                        **************************************************

ENST00000525778.5       AAGGATGTCTGCAGTCTGAGCTCATCCAGTTCCATCTCAAGAAGGAGCGG
ENST00000481848.6       AAGGATGTCTGCAGTCTGAGCTCATCCAGTTCCATCTCAAGAAGGAGCGG
                        **************************************************

ENST00000525778.5       GCGGCAGCGGCGGCGGCCGCGGCTCAGATGCACGCTAAGAACGGCGGCGG
ENST00000481848.6       GCGGCAGCGGCGGCGGCCGCGGCTCAGATGCACGCTAAGAACGGCGGCGG
                        **************************************************

ENST00000525778.5       CAGCAGTAGCCGCAGCTCCCCGGTGTCTGGCCCCCCTGCCGTTTGCGAGA
ENST00000481848.6       CAGCAGTAGCCGCAGCTCCCCGGTGTCTGGCCCCCCTGCCGTTTGCGAGA
                        **************************************************

ENST00000525778.5       CCCTGGCCGTCGCCTCCGCCTCCCCAATGGCGGCGGCGGCGGAGGGCCCC
ENST00000481848.6       CCCTGGCCGTCGCCTCCGCCTCCCCAATGGCGGCGGCGGCGGAGGGCCCC
                        **************************************************

ENST00000525778.5       CAGCAGAGCGCAGAGGGCAGCGCGAGCGGCGGGGGCATGCAGGCGGCAGC
ENST00000481848.6       CAGCAGAGCGCAGAGGGCAGCGCGAGCGGCGGGGGCATGCAGGCGGCAGC
                        **************************************************

ENST00000525778.5       GCCCCCTTCGTCGCAGCCGCACCCGCAGCAGCTCCAAGAGCAGGAAGAAA
ENST00000481848.6       GCCCCCTTCGTCGCAGCCGCACCCGCAGCAGCTCCAAGAGCAGGAAGAAA
                        **************************************************

ENST00000525778.5       TGCAAGAGGAGATGGAGAAGCTGCGAGAGGAAAACGAGACTCTCAAGAAC
ENST00000481848.6       TGCAAGAGGAGATGGAGAAGCTGCGAGAGGAAAACGAGACTCTCAAGAAC
                        **************************************************

ENST00000525778.5       GAGATCGATGAGCTGAGAACCGAGATGGACGAGATGAGGGACACTTTCTT
ENST00000481848.6       GAGATCGATGAGCTGAGAACCGAGATGGACGAGATGAGGGACACTTTCTT
                        **************************************************

ENST00000525778.5       CGAGGAGGATGCCTGTCAACTGCAGGAAATGCGCCACGAGTTGGAGAGAG
ENST00000481848.6       CGAGGAGGATGCCTGTCAACTGCAGGAAATGCGCCACGAGTTGGAGAGAG
                        **************************************************

ENST00000525778.5       CCAACAAAAACTGCCGGATCCTGCAGTACCGCCTCCGCAAAGCCGAGCGC
ENST00000481848.6       CCAACAAAAACTGCCGGATCCTGCAGTACCGCCTCCGCAAAGCCGAGCGC
                        **************************************************

ENST00000525778.5       AAAAGGCTCCGCTACGCCCAGACCGGGGAAATCGACGGGGAGCTGTTGCG
ENST00000481848.6       AAAAGGCTCCGCTACGCCCAGACCGGGGAAATCGACGGGGAGCTGTTGCG
                        **************************************************

ENST00000525778.5       CAGCCTGGAGCAGGACCTCAAGGTTGCAAAGGATGTATCTGTGAGACTTC
ENST00000481848.6       CAGCCTGGAGCAGGACCTCAAGGTTGCAAAGGATGTATCTGTGAGACTTC
                        **************************************************

ENST00000525778.5       ACCATGAATTAGAAAATGTGGAAGAAAAGAGAACAACAACAGAAGATGAA
ENST00000481848.6       ACCATGAATTAGAAAATGTGGAAGAAAAGAGAACAACAACAGAAGATGAA
                        **************************************************

ENST00000525778.5       AATGAGAAACTGAGGCAACAGCTCATAGAAGTTGAAATTGCAAAGCAAGC
ENST00000481848.6       AATGAGAAACTGAGGCAACAGCTCATAGAAGTTGAAATTGCAAAGCAAGC
                        **************************************************

ENST00000525778.5       TTTACAGAATGAACTGGAAAAAATGAAAGAGTTATCCTTAAAAAGAAGAG
ENST00000481848.6       TTTACAGAATGAACTGGAAAAAATGAAAGAGTTATCCTTAAAAAGAAGAG
                        **************************************************

ENST00000525778.5       GAAGCAAAGATTTGCCAAAATCTGAAAAAAAGGCTCAACAGACTCCCACA
ENST00000481848.6       GAAGCAAAGATTTGCCAAAATCTGAAAAAAAGGCTCAACAGACTCCCACA
                        **************************************************

ENST00000525778.5       GAGGAGGACAATGAAGATCTGAAGTGCCAGCTGCAGTTTGTTAAGGAAGA
ENST00000481848.6       GAGGAGGACAATGAAGATCTGAAGTGCCAGCTGCAGTTTGTTAAGGAAGA
                        **************************************************

ENST00000525778.5       AGCCGCTTTGATGAGAAAGAAAATGGCCAAGATTGATAAAGAAAAGGACA
ENST00000481848.6       AGCCGCTTTGATGAGAAAGAAAATGGCCAAGATTGATAAAGAAAAGGACA
                        **************************************************

ENST00000525778.5       GATTTGAACACGAGCTCCAGAAGTACAGATCCTTTTATGGGGATCTGGAC
ENST00000481848.6       GATTTGAACACGAGCTCCAGAAGTACAGATCCTTTTATGGGGATCTGGAC
                        **************************************************

ENST00000525778.5       AGTCCTTTGCCCAAAGGAGAAGCCGGAGGCCCTCCCAGCACTAGGGAGGC
ENST00000481848.6       AGTCCTTTGCCCAAAGGAGAAGCCGGAGGCCCTCCCAGCACTAGGGAGGC
                        **************************************************

ENST00000525778.5       CGAGCTCAAGCTACGGCTAAGGCTGGTGGAGGAAGAAGCCAACATCCTGG
ENST00000481848.6       CGAGCTCAAGCTACGGCTAAGGCTGGTGGAGGAAGAAGCCAACATCCTGG
                        **************************************************

ENST00000525778.5       GCAGGAAAATCGTCGAACTGGAGGTGGAGAACAGAGGCCTGAAGGCGGAA
ENST00000481848.6       GCAGGAAAATCGTCGAACTGGAGGTGGAGAACAGAGGCCTGAAGGCGGAA
                        **************************************************

ENST00000525778.5       CTGGACGACCTTAGGGGCGATGACTTCAACGGCTCGGCCAACCCGCTCAT
ENST00000481848.6       CTGGACGACCTTAGGGGCGATGACTTCAACGGCTCGGCCAACCCGCTCAT
                        **************************************************

ENST00000525778.5       GAGGGAGCAGAGCGAATCCCTGTCGGAGCTGCGGCAGCACCTGCAGCTGG
ENST00000481848.6       GAGGGAGCAGAGCGAATCCCTGTCGGAGCTGCGGCAGCACCTGCAGCTGG
                        **************************************************

ENST00000525778.5       TGGAAGACGAGACGGAGCTGCTGCGGAGGAACGTGGCCGACCTGGAGGAG
ENST00000481848.6       TGGAAGACGAGACGGAGCTGCTGCGGAGGAACGTGGCCGACCTGGAGGAG
                        **************************************************

ENST00000525778.5       CAGAACAAGCGCATCACGGCGGAGCTCAACAAGTACAAGTACAAGTCCGG
ENST00000481848.6       CAGAACAAGCGCATCACGGCGGAGCTCAACAAGTACAAGTACAAGTCCGG
                        **************************************************

ENST00000525778.5       CGGCCACGACAGCGCGCGGCACCACGACAACGCCAAGACCGAGGCCCTGC
ENST00000481848.6       CGGCCACGACAGCGCGCGGCACCACGACAACGCCAAGACCGAGGCCCTGC
                        **************************************************

ENST00000525778.5       AGGAGGAGCTGAAGGCGGCGCGCCTGCAGATCAACGAGCTCAGCGGCAAG
ENST00000481848.6       AGGAGGAGCTGAAGGCGGCGCGCCTGCAGATCAACGAGCTCAGCGGCAAG
                        **************************************************

ENST00000525778.5       GTCATGCAGCTGCAGTACGAGAACCGCGTGCTTATGTCCAACATGCAGCG
ENST00000481848.6       GTCATGCAGCTGCAGTACGAGAACCGCGTGCTTATGTCCAACATGCAGCG
                        **************************************************

ENST00000525778.5       CTACGACCTGGCCTCGCACCTGGGCATCCGCGGCAGCCCCCGCGACAGCG
ENST00000481848.6       CTACGACCTGGCCTCGCACCTGGGCATCCGCGGCAGCCCCCGCGACAGCG
                        **************************************************

ENST00000525778.5       ACGCCGAGAGCGACGCGGGCAAGAAGGAGAGCGACGACGACTCGCGGCCT
ENST00000481848.6       ACGCCGAGAGCGACGCGGGCAAGAAGGAGAGCGACGACGACTCGCGGCCT
                        **************************************************

ENST00000525778.5       CCGCACCGCAAGCGCGAAGGGCCCATCGGCGGCGAGAGCGACTCGGAGGA
ENST00000481848.6       CCGCACCGCAAGCGCGAAGGGCCCATCGGCGGCGAGAGCGACTCGGAGGA
                        **************************************************

ENST00000525778.5       GGTGCGCAACATCCGCTGCCTCACGCCCACTCGCTCCTTCTACCCGGCGC
ENST00000481848.6       GGTGCGCAACATCCGCTGCCTCACGCCCACTCGCTCCTTCTACCCGGCGC
                        **************************************************

ENST00000525778.5       CCGGGCCCTGGCCCAAGAGCTTCTCCGATCGGCAGCAGATGAAGGACATC
ENST00000481848.6       CCGGGCCCTGGCCCAAGAGCTTCTCCGATCGGCAGCAGATGAAGGACATC
                        **************************************************

ENST00000525778.5       CGCTCGGAGGCCGAGCGCCTGGGCAAGACCATCGACCGGCTCATCGCCGA
ENST00000481848.6       CGCTCGGAGGCCGAGCGCCTGGGCAAGACCATCGACCGGCTCATCGCCGA
                        **************************************************

ENST00000525778.5       CACGAGCACCATCATCACCGAGGCGCGCATCTACGTGGCCAACGGGGACC
ENST00000481848.6       CACGAGCACCATCATCACCGAGGCGCGCATCTACGTGGCCAACGGGGACC
                        **************************************************

ENST00000525778.5       TGTTCGGACTCATGGACGAGGAGGACGACGGCAGCCGCATCCGGGAGCAC
ENST00000481848.6       TGTTCGGACTCATGGACGAGGAGGACGACGGCAGCCGCATCCGGGAGCAC
                        **************************************************

ENST00000525778.5       GAGCTGCTCTACCGCATCAACGCTCAGATGAAGGCCTTCCGCAAGGAGCT
ENST00000481848.6       GAGCTGCTCTACCGCATCAACGCTCAGATGAAGGCCTTCCGCAAGGAGCT
                        **************************************************

ENST00000525778.5       GCAGACCTTCATCGACCGCCTCGAGGTGCCCAAGTCTGCGGACGACCGCG
ENST00000481848.6       GCAGACCTTCATCGACCGCCTCGAGGTGCCCAAGTCTGCGGACGACCGCG
                        **************************************************

ENST00000525778.5       GCGCCGAGGAGCCCATTTCCGTGAGTCAGATGTTCCAGCCTATCATTTTA
ENST00000481848.6       GCGCCGAGGAGCCCATTTCCGTGAGTCAGATGTTCCAGCCTATCATTTTA
                        **************************************************

ENST00000525778.5       CTTATTCTCATTCTTGTATTATTTTCATCACTTTCTTACACAACAATATT
ENST00000481848.6       CTTATTCTCATTCTTGTATTATTTTCATCACTTTCTTACACAACAATATT
                        **************************************************

ENST00000525778.5       TAAACTTGTCTTCCTTTTTACACTGTTTTTTGTACTGTAAATCTTTCATC
ENST00000481848.6       TAAACTTGTCTTCCTTTTTACACTGTTTTTTGTACTGTAAATCTTTCATC
                        **************************************************

ENST00000525778.5       ATTTACCATTCATTGTAGTATTTTCAGTTTGTTTATTTTGTTCACCCTTC
ENST00000481848.6       ATTTACCATTCATTGTAGTATTTTCAGTTTGTTTATTTTGTTCACCCTTC
                        **************************************************

ENST00000525778.5       AAGACAAGAAGTAAAAGAAGTATAATTTCTGTAGTAACCAATGCTATAAA
ENST00000481848.6       AAGACAAGAAGTAAAAGAAGTATAATTTCTGTAGTAACCAATGCTATAAA
                        **************************************************

ENST00000525778.5       AACACTGAAGACTGCTTATTTCTTTAAAAAGATACAACTCATCTTACCAA
ENST00000481848.6       AACACTGAAGACTGCTTATTTCTTTAAAAAGATACAACTCATCTTACCAA
                        **************************************************

ENST00000525778.5       GACCAAA-------------------------------------------
ENST00000481848.6       GACCAAATTCAATAAGAAGCCCAAACACTAAAATATTTCAGGCTTTATTT
                        *******                                           

ENST00000525778.5       --------------------------------------------------
ENST00000481848.6       TAAAGGCAAGTGAGACTGCTTCAAATAAAACAACTTCAAGCTTCCAAGAA

[. . .]

_{The ENST00000481848.6 transcript continues quite a bit after this but there is no more similarity.}

The transcripts are not identical, but are very similar. Now, look at the proteins each transcript encodes:

ENST00000481848.6  MSQPPIGGAAPATAAASPAAAATEARLHPEGSSRKQQRAQSPARPRDSSL
ENST00000525778.5  MSQPPIGGAAPATAAASPAAAATEARLHPEGSSRKQQRAQSPARPRDSSL
                   **************************************************

ENST00000481848.6  RQTIAATRSPVGAGTKLNSVRQQQLQQQQQQGNKTGSRTGPPASIRGGGG
ENST00000525778.5  RQTIAATRSPVGAGTKLNSVRQQQLQQQQQQGNKTGSRTGPPASIRGGGG
                   **************************************************

ENST00000481848.6  GAEKATPLAPKGAAPGAVQPVAGAEAAPAATLAALGGRRPGPPEEPPREL
ENST00000525778.5  GAEKATPLAPKGAAPGAVQPVAGAEAAPAATLAALGGRRPGPPEEPPREL
                   **************************************************

ENST00000481848.6  ESVPSKLGEPPPLGEGGGGGGEGGGAGGGSGEREGGAPQPPPPRGWRGKG
ENST00000525778.5  ESVPSKLGEPPPLGEGGGGGGEGGGAGGGSGEREGGAPQPPPPRGWRGKG
                   **************************************************

ENST00000481848.6  VRAQQRGGSGGEGASPSPSSSSAGKTPGTGSRNSGSGVAGGGSGGGGSYW
ENST00000525778.5  VRAQQRGGSGGEGASPSPSSSSAGKTPGTGSRNSGSGVAGGGSGGGGSYW
                   **************************************************

ENST00000481848.6  KEGCLQSELIQFHLKKERAAAAAAAAQMHAKNGGGSSSRSSPVSGPPAVC
ENST00000525778.5  KEGCLQSELIQFHLKKERAAAAAAAAQMHAKNGGGSSSRSSPVSGPPAVC
                   **************************************************

ENST00000481848.6  ETLAVASASPMAAAAEGPQQSAEGSASGGGMQAAAPPSSQPHPQQLQEQE
ENST00000525778.5  ETLAVASASPMAAAAEGPQQSAEGSASGGGMQAAAPPSSQPHPQQLQEQE
                   **************************************************

ENST00000481848.6  EMQEEMEKLREENETLKNEIDELRTEMDEMRDTFFEEDACQLQEMRHELE
ENST00000525778.5  EMQEEMEKLREENETLKNEIDELRTEMDEMRDTFFEEDACQLQEMRHELE
                   **************************************************

ENST00000481848.6  RANKNCRILQYRLRKAERKRLRYAQTGEIDGELLRSLEQDLKVAKDVSVR
ENST00000525778.5  RANKNCRILQYRLRKAERKRLRYAQTGEIDGELLRSLEQDLKVAKDVSVR
                   **************************************************

ENST00000481848.6  LHHELENVEEKRTTTEDENEKLRQQLIEVEIAKQALQNELEKMKELSLKR
ENST00000525778.5  LHHELENVEEKRTTTEDENEKLRQQLIEVEIAKQALQNELEKMKELSLKR
                   **************************************************

ENST00000481848.6  RGSKDLPKSEKKAQQTPTEEDNEDLKCQLQFVKEEAALMRKKMAKIDKEK
ENST00000525778.5  RGSKDLPKSEKKAQQTPTEEDNEDLKCQLQFVKEEAALMRKKMAKIDKEK
                   **************************************************

ENST00000481848.6  DRFEHELQKYRSFYGDLDSPLPKGEAGGPPSTREAELKLRLRLVEEEANI
ENST00000525778.5  DRFEHELQKYRSFYGDLDSPLPKGEAGGPPSTREAELKLRLRLVEEEANI
                   **************************************************

ENST00000481848.6  LGRKIVELEVENRGLKAELDDLRGDDFNGSANPLMREQSESLSELRQHLQ
ENST00000525778.5  LGRKIVELEVENRGLKAELDDLRGDDFNGSANPLMREQSESLSELRQHLQ
                   **************************************************

ENST00000481848.6  LVEDETELLRRNVADLEEQNKRITAELNKYKYKSGGHDSARHHDNAKTEA
ENST00000525778.5  LVEDETELLRRNVADLEEQNKRITAELNKYKYKSGGHDSARHHDNAKTEA
                   **************************************************

ENST00000481848.6  LQEELKAARLQINELSGKVMQLQYENRVLMSNMQRYDLASHLGIRGSPRD
ENST00000525778.5  LQEELKAARLQINELSGKVMQLQYENRVLMSNMQRYDLASHLGIRGSPRD
                   **************************************************

ENST00000481848.6  SDAESDAGKKESDDDSRPPHRKREGPIGGESDSEEVRNIRCLTPTRSFYP
ENST00000525778.5  SDAESDAGKKESDDDSRPPHRKREGPIGGESDSEEVRNIRCLTPTRSFYP
                   **************************************************

ENST00000481848.6  APGPWPKSFSDRQQMKDIRSEAERLGKTIDRLIADTSTIITEARIYVANG
ENST00000525778.5  APGPWPKSFSDRQQMKDIRSEAERLGKTIDRLIADTSTIITEARIYVANG
                   **************************************************

ENST00000481848.6  DLFGLMDEEDDGSRIREHELLYRINAQMKAFRKELQTFIDRLEVPKSADD
ENST00000525778.5  DLFGLMDEEDDGSRIREHELLYRINAQMKAFRKELQTFIDRLEVPKSADD
                   **************************************************

ENST00000481848.6  RGAEEPISVSQMFQPIILLILILVLFSSLSYTTIFKLVFLFTLFFVL
ENST00000525778.5  RGAEEPISVSQMFQPIILLILILVLFSSLSYTTIFKLVFLFTLFFVL
                   ***********************************************

As you can see, they are 100% identical. So, we have two genes (distinct regions of the DNA) which produce the same protein. Because the gene product is the same, the "function" of the genes is also the same so HUGO treats them as the same gene and gives them the same name.

Whether or not you want to treat them as one gene or two will depend on what you are doing. If you are comparing the relative abundance of each transcript, you must treat them separately. If you want to examine the expression level of the protein product and are using the RNASEM data as a proxy for protein information, then you should treat them as one "gene" and simply sum your RNASEM values.

Answer 2

There is no one-to-one mapping of gene ids from one database to the other. Ensembl (who maintain Ensembl ENSG IDs), ncbi (who maintain EntrezGene IDs and RefSeq transcript ids) and HUGO (who maintain gene symbols/names) all have different ideas about what a gene is, which part of the genome belongs to which gene etc.

In fact, it's worse than that because HUGO gene IDs refer to the abstract idea of a gene, rather than a particular part of any chromosome.

My suggestion would be to leave the IDs as Ensembl IDs (as these actually refer to a physical part of a chromosome, which is what you are quantifying), right up until you have to report the results to someone who really NEEDS gene names. If you still have duplicates, you could sum, or pick the most interesting, but I would suggest just leaving the duplicates in there, and treat it as thought there are two genes with the same name.