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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagccttttcttactacgtacatgatattaagggcttcttttcttgttctctttattgtgtacatttattatcctttgatctgaaatcacctgactc...

Basic information

species Zea mays
transcript GRMZM5G883149_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G883149_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 4
GAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagccttttcttactacgtacatgatattaagggcttcttttcttgttctctttattgtgtacatttattat-cctttgatctgaaatcacctgactc------
 || |  || |||||||| ||||||||||| ||| |||| || ||||||||||| || ||||||||||||||||||||||||| |||  ||| |||        ||| | ||  | |  | ||| | |  | | |||  |   | || ||    |  || ||      |   |||          
AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatcctagtctcactg-------gatgtcaaatgttcttattcctttcgtttgtatgtttggctttcatggcacgctttataatcggttgtctgctctagtaat

upper sequence: GRMZM5G883149_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G01000.1 (Glycine max), 5'ss of exon 4
GAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaa-gccttttcttactacgtacatgatattaagggcttcttttcttgttctctttattgtgtacatttattatcctttgatctgaaatcacctgactc
|| ||  |||||||||||    ||||| ||||| ||||| || || || ||||||||||| || |||||||||||||||||      | ||  |   ||     |  | |    |      ||  ||  | | || || ||    ||||||| | | ||||                  
GAGCAATGTTGACAAAAGAGAGGCACTTGAGAACTTGGATCTCATTCTCTTGTGTCTTGACGAGATTGTTGATGGAGGgtatgcatatatttctgtcacaatttttctttcccagataagcttaatttattttttaatagt----atttatttttccttgaag----------------

upper sequence: GRMZM5G883149_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G13190.3 (Glycine max), 5'ss of exon 4
GAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagc-----cttttcttactacgtacatgatattaagg-gcttcttttcttgttctctttattgtgtacatttattatcctttgatctgaaatcacctgactc
   ||  || ||||| | |  |||||| ||||| ||||| || || ||||||||  ||||||||||||||||||| |||||         || ||| ||  |  |  ||    || ||  |  | |||  ||| |    | | | |   |||  | |  ||| |      ||  ||        
AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATTGATGAAATTGTTGATGGCGGgtatgctatatgctattcatatgaaatttatctccttcagttgtgtgtttgtttgcttctctaaatcttctcatgcacttccctcttcctccaatacaaa------

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|67020825|gb|CO449574.1|CO449574
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
EST: gi|211335317|gb|FL100773.1|FL100773
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
EST: gi|60344091|gb|DN211064.1|DN211064
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
EST: gi|32937965|gb|CF042784.1|CF042784
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGTTGAAAAGGTGCCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
EST: gi|50324980|gb|CO520106.1|CO520106
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
EST: gi|50324981|gb|CO520107.1|CO520107
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
EST: gi|211477574|gb|FL100774.1|FL100774
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
EST: gi|116827357|gb|EC871252.1|EC871252
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
EST: gi|40303119|gb|CK347506.1|CK347506
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
EST: gi|211529711|gb|FL481418.1|FL481418
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
EST: gi|211477578|gb|FL100778.1|FL100778
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGG
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGG
EST: gi|5714079|gb|AI944064.1|AI944064
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
EST: gi|113703727|gb|EE681231.1|EE681231
EST:     GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA

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), 36 (downstream exon)
Score: 28

GAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 44

GAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 30

GAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 44

GAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGGgtaaagccttttcttactacgtacatgatattaagggcttcttttcttgttctctttattgtgtacatttattatcctttgatctgaaatcacctgactc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG