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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcatgtgcttttttttaccaactctctgttctttgtttttaatttcttgtcaaagtttcttatggtaacctgacctctttgggaacttgattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG

Basic information

species Zea mays
transcript GRMZM5G859592_T01
intron # 2
splice site 3'
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|20512968|gb|BQ280154.1|BQ280154
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCGACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|60352017|gb|DN218990.1|DN218990
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|60357734|gb|DN224707.1|DN224707
EST:     GAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: GAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|60394022|gb|DN226892.1|DN226892
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|5791276|gb|AI978068.1|AI978068
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACNCG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|32840442|gb|CD980123.1|CD980123
EST:     CATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: CATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|60359543|gb|DN226516.1|DN226516
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|60342848|gb|DN209821.1|DN209821
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|61118457|gb|DN559418.1|DN559418
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|31360388|gb|CD444745.1|CD444745
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|60340221|gb|DN207194.1|DN207194
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|213192952|gb|FM183710.1|FM183710
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTCGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|60344920|gb|DN211893.1|DN211893
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|67015164|gb|CO443913.1|CO443913
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|211463894|gb|FL171640.1|FL171640
EST:     GTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: GTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|211463893|gb|FL171639.1|FL171639
EST:     GTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: GTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
EST: gi|30087353|gb|CB885559.1|CB885559
EST:     ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACG                         GCAACTTTCAGTGACATCCTTAAGAAGCTTG
genomic: ATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG

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: 31 (upstream exon), 49 (downstream exon)
Score: 708

GACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCAGCAAGGATGATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

GACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCAGCAAGGATGATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 351

GACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCAGCAAGGATGATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 239

GACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCAGCAAGGATGATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGACTTCAACACGgtgagttaca ... gattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtcaaagtttcttatggtaacctgacctctttgggaacttgattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG
            tttcttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcatgtgcttttttttaccaactctctgttctttgtttttaatttcttgtcaaagtttcttatggtaacctgacctctttgggaacttgattttgcagGCAACTTTCAGTGACATCCTTAAGAAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - -tgtgctt
- - - - - - - - - - - - - - - - - -tgttttt