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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggtgaatatttttgctaatatattttttagttgtagaccatcatgtggtaattgcattagcttgccctaaaagtggaggagatatgttattttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCAGCAAGGATGATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGA

Basic information

species Zea mays
transcript GRMZM5G859592_T01
intron # 1
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|60352017|gb|DN218990.1|DN218990
EST:     GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGNNNNNNNGTCATCAG                         GCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
genomic: GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
EST: gi|60394022|gb|DN226892.1|DN226892
EST:     GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGNNNNNNNGTCATCAG                         GCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
genomic: GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
EST: gi|60359543|gb|DN226516.1|DN226516
EST:     GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGNNNNNNNGTCATCAG                         GCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
genomic: GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
EST: gi|60342848|gb|DN209821.1|DN209821
EST:     GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGNNNNNNNGTCATCAG                         GCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
genomic: GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
EST: gi|61118457|gb|DN559418.1|DN559418
EST:     GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGNNNNNNNGTCATCAG                         GCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
genomic: GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
EST: gi|60340221|gb|DN207194.1|DN207194
EST:     GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGNNNNNNNGTCATCAG                         GCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
genomic: GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
EST: gi|213192952|gb|FM183710.1|FM183710
EST:     GAAGAAG-AACCCACAGCGGAAAAGGAGATCAAAGNNNNNNNGTCATCAG                         GCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
genomic: GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
EST: gi|60344920|gb|DN211893.1|DN211893
EST:     GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGNNNNNNNGTCATCAG                         GCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
genomic: GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
EST: gi|30087353|gb|CB885559.1|CB885559
EST:     GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGNNNNNNNGTCATCAG                         GCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA
genomic: GAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCA

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), 49 (downstream exon)
Score: 517

ATTCATGAGGAAAAAGAAAGCCCCAATAATAGTGCAAAGGTTTTTTCTAGGAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCAGCAAGGATGATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 160

ATTCATGAGGAAAAAGAAAGCCCCAATAATAGTGCAAAGGTTTTTTCTAGGAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCAGCAAGGATGATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 271

ATTCATGAGGAAAAAGAAAGCCCCAATAATAGTGCAAAGGTTTTTTCTAGGAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCAGCAAGGATGATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 206

ATTCATGAGGAAAAAGAAAGCCCCAATAATAGTGCAAAGGTTTTTTCTAGGAAGAAGAAACCCACAGCAGAAAAGGAGATCAAAGAAAAAAAGTCATCAGgtaaagtagt ... ttttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCAGCAAGGATGATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtaattgcattagcttgccctaaaagtggaggagatatgttattttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCAGCAAGGATGATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGA
                    ccctaaa  putative branch site (score: 206)
 ttatttt  putative PPT
 atatgttattttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggtgaatatttttgctaatatattttttagttgtagaccatcatgtggtaattgcattagcttgccctaaaagtggaggagatatgttattttatgtagGCAAAAAGGTGACAAAGGGTAAAGGAGAATCCGTTGAAGCAGTTCTTCCCAGCAAGGATGATCTGAGGAAGACCATTACTGAAATCCTCAAGAAAGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - ttttgct
- - - - - - - - - - - - - - - - - - - - - catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - ttgcatt