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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttgtacaagttattgatttgctaatttgtattagccattaaccacatgtaccgagtttttttgggttcttattgagtagtgtatttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAATGCTGCACTTCAG

Basic information

species Zea mays
transcript GRMZM2G432566_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G432566_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g19970.1 (Oryza sativa), 3'ss of exon 5
gcaagt-tgtacaagtta-ttg-atttgctaatttgtattagccattaaccacatgtaccgagtttttttgggttcttattgagtagtgtatttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAATGCTGCACTTCAG
|||||| | |   ||||| ||| ||| |||  | |||    || ||||    |   ||      || |||   |  || |||  | || ||||||  ||||| ||||||||||||||||| |||||||| ||||||||| | ||||||||||| |||||||||
gcaagtatatttcagttagttgtattagctgctctgttactgc-attagatgc---taggttacttattttcatatttcttggcttgtttatttctccagAGACATAATGCTATGGAGCATGGTGGGCGGATGTCTCGTGCTCAGAGGAATGCCGCACTTCAG
















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|211497881|gb|FK991463.1|FK991463
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211040651|gb|FK991476.1|FK991476
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGNGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211040652|gb|FK991477.1|FK991477
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211497874|gb|FK991456.1|FK991456
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211497876|gb|FK991458.1|FK991458
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211497879|gb|FK991461.1|FK991461
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCANAGCTGAAG                         AGGCATAATGCTATGGAGCACGGNGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211040645|gb|FK991470.1|FK991470
EST:     CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGGGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211497884|gb|FK991466.1|FK991466
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211040648|gb|FK991473.1|FK991473
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211497885|gb|FK991467.1|FK991467
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211497877|gb|FK991459.1|FK991459
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCT-TGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211497878|gb|FK991460.1|FK991460
EST:     CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211497882|gb|FK991464.1|FK991464
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGNGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211040653|gb|FK991478.1|FK991478
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211497880|gb|FK991462.1|FK991462
EST:     CATGCTTGGCAAAGAAGTTTGTTGTCTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCT-TGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211040643|gb|FK991468.1|FK991468
EST:     CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
EST: gi|211040644|gb|FK991469.1|FK991469
EST:     CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAG                         AGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT
genomic: CATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAAT

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: 47 (upstream exon), 46 (downstream exon)
Score: 121

TTCAATTCAGTTGCATTTTCGAAAGGACCATTTTCTTTGTGAAGATGAAGCATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAATGCTGCACTTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 98

TTCAATTCAGTTGCATTTTCGAAAGGACCATTTTCTTTGTGAAGATGAAGCATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAATGCTGCACTTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 83

TTCAATTCAGTTGCATTTTCGAAAGGACCATTTTCTTTGTGAAGATGAAGCATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAATGCTGCACTTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 85

TTCAATTCAGTTGCATTTTCGAAAGGACCATTTTCTTTGTGAAGATGAAGCATGCTTGGCAAAGAAGTTTGTTGTTTTTCTGAGTGAAGCAGAGCTGAAGgcaagttgta ... atttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAATGCTGCACTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaccacatgtaccgagtttttttgggttcttattgagtagtgtatttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAATGCTGCACTTCAG
 cattaac  putative branch site (score: 85)
                agttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagttgtacaagttattgatttgctaatttgtattagccattaaccacatgtaccgagtttttttgggttcttattgagtagtgtatttcaacagAGGCATAATGCTATGGAGCACGGTGGGCGAATGTCTCGTTCCCAGAGGAATGCTGCACTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC