Scary Exon Sizes

Question

[Jitendra]

Hi BioStars,

Followings are the part of Cufflinks output (transcripts.gtf). The last column, added by me, is the length of the transcripts and exons. Can we get an exon of size 7 and transcripts of 124700 size?

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Chr1    Cufflinks    transcript    210626    210717    1000    91
Chr1    Cufflinks    exon    210626    210717    1000    91
Chr1    Cufflinks    transcript    201666    206408    1000    4742
Chr1    Cufflinks    exon    201666    201875    1000    209
Chr1    Cufflinks    exon    206401    206408    1000    7
Chr1    Cufflinks    transcript    11401    11679    1000    278
Chr1    Cufflinks    exon    11401    11679    1000    278
Chr1    Cufflinks    transcript    14805    15101    1000    296
Chr1    Cufflinks    exon    14805    15101    1000    296
Chr1    Cufflinks    transcript    17030    17199    1000    169
Chr1    Cufflinks    exon    17030    17199    1000    169
Chr1    Cufflinks    transcript    19583    144283    1000    124700
Chr1    Cufflinks    exon    19583    19627    1000    44
Chr1    Cufflinks    exon    144258    144283    1000    25

Answer 1

[Gww]

I don't see any problems with your exon sizes or transcript sizes. If your transcript has one or more large introns its size could be quit large. Small exons (also known as microexons) are known to exist, for example, see Carlo et al (2000).