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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTGAATTTGTGCATGAATTGAATCGCAGCGGAAATCAATTCCACTCGTGTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccctagttgtgtaagggcttgttcgttttgctctcgattcatgtgggttgggtgtgattgggtggatttaaatctcaaacaagttaaaatctt...

Basic information

species Zea mays
transcript GRMZM2G425377_T01
intron # 9
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71304828|gb|DR788528.1|DR788528
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|78115254|gb|DV533642.1|DV533642
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|37398903|gb|CF636771.1|CF636771
EST:     TTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: TTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|95107721|gb|EB739950.1|EB739950
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|5607689|gb|AI901356.1|AI901356
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|37392475|gb|CF633489.1|CF633489
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|32931898|gb|CF036710.1|CF036710
EST:     GTGTTTTCCGCCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|5860417|gb|AW011639.1|AW011639
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|78115253|gb|DV533641.1|DV533641
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|60400574|gb|DN233381.1|DN233381
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|6742462|gb|AW313277.1|AW313277
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|60344594|gb|DN211567.1|DN211567
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|37393934|gb|CF634234.1|CF634234
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
EST: gi|32930799|gb|CF035611.1|CF035611
EST:     GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAG                         TCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT
genomic: GTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 264

AGGTGAATTTGTGCATGAATTGAATCGCAGCGGAAATCAATTCCACTCGTGTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAATGCGCATGACGGTTTGGTTGCAGCCCTGGCATCATCCAGTGCTACAGGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 169

AGGTGAATTTGTGCATGAATTGAATCGCAGCGGAAATCAATTCCACTCGTGTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAATGCGCATGACGGTTTGGTTGCAGCCCTGGCATCATCCAGTGCTACAGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

AGGTGAATTTGTGCATGAATTGAATCGCAGCGGAAATCAATTCCACTCGTGTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAATGCGCATGACGGTTTGGTTGCAGCCCTGGCATCATCCAGTGCTACAGGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 200

AGGTGAATTTGTGCATGAATTGAATCGCAGCGGAAATCAATTCCACTCGTGTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccc ... tgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAATGCGCATGACGGTTTGGTTGCAGCCCTGGCATCATCCAGTGCTACAGGGA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTGAATTTGTGCATGAATTGAATCGCAGCGGAAATCAATTCCACTCGTGTGTTTTCCACCCAACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGgtaagttccctagttgtgtaagggcttgttcgttttgctctcgattcatgtgggttgggtgtgattgggtggatttaaatctcaaacaagttaaaatctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacaag