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Series GSE30017 Query DataSets for GSE30017
Status Public on Jan 05, 2012
Title Widespread regulated alternative splicing of single codons accelerates proteome evolution
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Thousands of human genes contain introns ending in NAGNAG motifs (N any nucleotide), where both NAGs can function as 3' splice sites, yielding isoforms differing by inclusion/exclusion of just three bases. However, the functional importance of NAGNAG alternative splicing is highly controversial. Using very deep RNA-Seq data from sixteen human and eight mouse tissues, we found that approximately half of alternatively spliced NAGNAGs undergo tissue-specific regulation and that regulated events have been selectively retained: alternative splicing of strongly tissue-specific NAGNAGs was ten times as likely to be conserved between species as for non-tissue-specific events. Further, alternative splicing of human NAGNAGs was associated with an order of magnitude increase in the frequency of exon length changes at orthologous mouse/rat exon boundaries, suggesting that NAGNAGs accelerate exon evolution. Together, our analyses show that NAGNAG alternative splicing constitutes a major generator of tissue-specific proteome diversity and accelerates evolution of proteins at exon-exon boundaries.
Overall design mRNA-Seq of sixteen human and eight mouse tissues.

Supplementary files:
human.nagnag.junctions.gff and mouse.nagnag.junctions.gff are the annotation files (in GFF3 format) corresponding to the 'bwtout' mapped reads files linked to the Sample records.

Raw data files provided for Samples GSM742937-GSM742952 only.
Contributor(s) Bradley RK, Merkin J, Burge CB
Citation(s) 22235189
Submission date Jun 16, 2011
Last update date May 15, 2019
Contact name Robert K Bradley
Organization name MIT
Department Biology
Street address 77 Massachusetts Avenue, 68-223A
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platforms (3)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (48)
GSM742921 human_adipose.paired
GSM742922 human_adrenal.paired
GSM742923 human_brain.paired
SRA SRP007338
BioProject PRJNA143693

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE30017_RAW.tar 2.4 Gb (http)(custom) TAR (of TXT)
GSE30017_human.nagnag.junctions.gff.gz 432.3 Kb (ftp)(http) GFF
GSE30017_mouse.nagnag.junctions.gff.gz 347.0 Kb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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