Same transcript coordinates in gtf file, different transcript ID I have a gtf file from Ensembl, and I noticed that several "transcript" annotations have the exact same coordinates. See for instance the third and fourth transcripts ("Y74C9A.2b.1" and "Y74C9A.2b.4") for this gene:

$ grep "WBGene00022276" genes.gtf | awk '$3 == "transcript" {print}'
I   ensembl transcript  10413   16842   .   +   .   gene_biotype "protein_coding"; gene_id "WBGene00022276"; gene_name "nlp-40"; gene_source "ensembl"; gene_version "1"; p_id "P24752"; transcript_biotype "protein_coding"; transcript_id "Y74C9A.2a.2"; transcript_name "Y74C9A.2a.2"; transcript_source "ensembl"; transcript_version "1"; tss_id "TSS7921";
I   ensembl transcript  11495   16793   .   +   .   gene_biotype "protein_coding"; gene_id "WBGene00022276"; gene_name "nlp-40"; gene_source "ensembl"; gene_version "1"; p_id "P22572"; transcript_biotype "protein_coding"; transcript_id "Y74C9A.2b.2"; transcript_name "Y74C9A.2b.2"; transcript_source "ensembl"; transcript_version "1"; tss_id "TSS9220";
I   ensembl transcript  11499   16842   .   +   .   gene_biotype "protein_coding"; gene_id "WBGene00022276"; gene_name "nlp-40"; gene_source "ensembl"; gene_version "1"; p_id "P22572"; transcript_biotype "protein_coding"; transcript_id "Y74C9A.2b.1"; transcript_name "Y74C9A.2b.1"; transcript_source "ensembl"; transcript_version "1"; tss_id "TSS9215";
I   ensembl transcript  11499   16842   .   +   .   gene_biotype "protein_coding"; gene_id "WBGene00022276"; gene_name "nlp-40"; gene_source "ensembl"; gene_version "1"; p_id "P22572"; transcript_biotype "protein_coding"; transcript_id "Y74C9A.2b.4"; transcript_name "Y74C9A.2b.4"; transcript_source "ensembl"; transcript_version "1"; tss_id "TSS9215";
I   ensembl transcript  11505   16842   .   +   .   gene_biotype "protein_coding"; gene_id "WBGene00022276"; gene_name "nlp-40"; gene_source "ensembl"; gene_version "1"; p_id "P24752"; transcript_biotype "protein_coding"; transcript_id "Y74C9A.2a.3"; transcript_name "Y74C9A.2a.3"; transcript_source "ensembl"; transcript_version "1"; tss_id "TSS16820";
I   ensembl transcript  11618   16842   .   +   .   gene_biotype "protein_coding"; gene_id "WBGene00022276"; gene_name "nlp-40"; gene_source "ensembl"; gene_version "1"; p_id "P24752"; transcript_biotype "protein_coding"; transcript_id "Y74C9A.2a.1"; transcript_name "Y74C9A.2a.1"; transcript_source "ensembl"; transcript_version "1"; tss_id "TSS43845";
I   ensembl transcript  11623   16842   .   +   .   gene_biotype "protein_coding"; gene_id "WBGene00022276"; gene_name "nlp-40"; gene_source "ensembl"; gene_version "1"; p_id "P22572"; transcript_biotype "protein_coding"; transcript_id "Y74C9A.2b.3"; transcript_name "Y74C9A.2b.3"; transcript_source "ensembl"; transcript_version "1"; tss_id "TSS49800";


What does it mean? Do these two "transcripts" actually correspond to an exon, belonging to two different isoforms?
As Ian explained, these are different transcripts which happen to have the same start and end positions. You have no information on their exonic structure in that file. However, if you look them up at EnsEMBL, you will see:

Transcript Y74C9A.2b.1 :



1   Y74C9A.2b.1.e1  11,499  11,561  -   -   63
    Intron 1-2      11,562  11,617          56
2   Y74C9A.2b.1.e2  11,618  11,689  -   -   72
    Intron 2-3      11,690  14,950          3,261
3   Y74C9A.2b.1.e3  14,951  15,160  -   1   210
    Intron 3-4      15,161  16,472          1,312
4   Y74C9A.2a.1.e3  16,473  16,842  1   -   370


This has 4 exons, two of which are non-coding (UTR). The second starts at 

Transcript Y74C9A.2b.4



1   Y74C9A.2b.4.e1  11,499  11,557  -   -   59
    Intron 1-2      11,558  11,617          60
2   Y74C9A.2b.1.e2  11,618  11,689  -   -   72
    Intron 2-3      11,690  14,950          3,261
3   Y74C9A.2b.1.e3  14,951  15,160  -   1   210
    Intron 3-4      15,161  16,472          1,312
4   Y74C9A.2a.1.e3  16,473  16,842  1   -   370


Granted, the two transcripts are very simlar, they both have 4 exons, the first 2 of which are non coding (UTR). However, the 1st exon of transcript 
Y74C9A.2b.1 is 63 nt long and ends at 11,561 while the 1st exon of transcript Y74C9A.2b.4 is 59 nts and ends at 11,557.

So there you go: two (slightly) different transcripts.