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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttatatttcttgagctcaacaaaactagtcggcataacaaacagagattcaattgtttgttgactgttgaacactgaattttattttgtttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGACGATGAGACCACGAAAGCATGATCTGCGTTAGTTGGATATTTATTTCTAA

Basic information

species Zea mays
transcript GRMZM2G093535_T01
intron # 3
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|211192189|gb|FL404823.1|FL404823
EST:     AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG                         CCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
genomic: AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
EST: gi|211213892|gb|FL469120.1|FL469120
EST:     AAGRCAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG                         CCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
genomic: AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
EST: gi|32837519|gb|CD977197.1|CD977197
EST:     AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG                         CCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
genomic: AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
EST: gi|213167496|gb|FM196281.1|FM196281
EST:     AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG                         CCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
genomic: AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
EST: gi|211273115|gb|FL373254.1|FL373254
EST:     AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG                         CCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
genomic: AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
EST: gi|12970294|gb|BG266911.1|BG266911
EST:     AAGACAGCAAAGGGCTGATGCTGCAAAGAA-CGCGATGAGGAGAAAGCTG                         CCAAGGAGCAGAGGAAGTCCGAAGCACGGAAGTAACTGCAATATCATGGAC
genomic: AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
EST: gi|32937462|gb|CF042281.1|CF042281
EST:     AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG                         CCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
genomic: AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
EST: gi|32944737|gb|CF049556.1|CF049556
EST:     AAGGCAGCAAAGGGCTGATACTGCAAAGAAACGCGATGAGGAGAAAGCTG                         CCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
genomic: AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
EST: gi|32856684|gb|CD996365.1|CD996365
EST:     AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG                         CCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
genomic: AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC
EST: gi|78026071|gb|DV494458.1|DV494458
EST:     AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG                         CCAAGGAGCAGAGGAAGTCCGAAGCACGGAAGTAACTGCAATATCATGGAC
genomic: AAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGAC

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: 735

AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGACGATGAGACCACGAAAGCATGATCTGCGTTAGTTGGATATTTATTTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 493

AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGACGATGAGACCACGAAAGCATGATCTGCGTTAGTTGGATATTTATTTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 574

AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGACGATGAGACCACGAAAGCATGATCTGCGTTAGTTGGATATTTATTTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 443

AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTGgtacatccct ... tttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGACGATGAGACCACGAAAGCATGATCTGCGTTAGTTGGATATTTATTTCTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagattcaattgtttgttgactgttgaacactgaattttattttgtttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGACGATGAGACCACGAAAGCATGATCTGCGTTAGTTGGATATTTATTTCTAA
              tgttgac  putative branch site (score: 443)
                                        ttttgttt  putative PPT
                             actgaattttattttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttatatttcttgagctcaacaaaactagtcggcataacaaacagagattcaattgtttgttgactgttgaacactgaattttattttgtttatcgcagCCAAGGAGCAGAGGAAGTCGGAAGCACGGAAGTAACTGCAATATCATGGACGATGAGACCACGAAAGCATGATCTGCGTTAGTTGGATATTTATTTCTAA

- - - -tttcttg
- - - - - - - - - -aacaaaa
- - - - - - - - - - - - - - - - - - taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactgaa