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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAAACGTTCCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgtttctttagtgataagagttagtttatctatttccgatatttttttcattctcaaacgctagttggtttgttcgctaagatgtcttccatataatgttaactactattattgcattacatgaaagctgaacgtctctacgtcttattttgctgttcctgataacacccaaccaatcttccttgctcctcctag

Basic information

species Zea mays
transcript GRMZM2G135132_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 12
GTGAAAACGTTCCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgtttctttagtgataa-gagttagtttatctatttccgatatttttttcattctcaaacgctagttggtttgttcgctaagatgtcttccatataatgttaactactattattgcattacatgaaagctgaacgtctctacgtcttattttgctgttcctgataacacccaaccaatcttccttgctcctcctag
|||||||| ||||||||||||||| |||| ||||||||||||||||||||||| ||||| |||| || |||||||  |   |  || ||  |  || |||||| |  ||||  || |     |||| | |       | ||    ||||  |||| |  |       |   | |||||||                                                                                  
GTGAAAACATTCCCTGTGATCCTACTGCCAAAGGAGAAGCTTGTTGACACCAATGGCGCTGgta-atatttcttttatagcattgaattgat--atttatttctggcatttccttaaa----aaactcaa-------tattttacaaga-atcttactca----accagtcagtattatt----------------------------------------------------------------------------------

upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 11
GTGAAAACGTTCCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgtttctttagtgataa-gagttagtttatctatttccgatatttttttcattctcaaacgctagttggtttgttcgctaagatgtcttccatataatgttaactactattattgcattacatgaaagctgaacgtctctacgtcttattttgctgttcctgataacacccaaccaatcttccttgctcctcctag
                                                  ||| || |||| | |   | |  ||   ||  | |    |||  |   ||| ||  |  | || | |  | |||     || |||||  |   | ||     |    ||  | | |    |   |||||| |||  |  ||  ||||||  |  | |    | ||   | | | | |  ||      |  || |  ||||  || ||     
--------------------------------------------------CAA-GGTGCAGATCCTGTTGTAGTTGCAGAGGATGGAAAAGTGAAGTCATTCCCTGTGATCTTGTTA--CCCAAGGAGAAGCTGGTTGAT--ACCAATGGAGCAGgtatgaactctcttatttcattatt-catgcctagagtgctgaaaatgaccaaccttcataaaggtttgcatcgtattgag-attcagtgctcctgtcttct-----

upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 5'ss of exon 11
GTGAAAACGTTCCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgtttctttagtgataa-gagttagtttatctatttccgatatttttttcattctcaaacgctagttggtttgttcgctaagatgtcttccatataatgttaactactattattgcattacatgaaagctgaacgtctctacgtcttattttgctgttcctgataacacccaaccaatcttccttgctcctcctag
                                                  ||| || |||| | |   | |  ||   ||  | |    |||  |   ||| ||  | |  | ||  | | |||     || |||||  |   | ||     |    ||  | | |    |   |||||| |||  |  ||  ||||||  |  | |    | ||   | | | | |  ||      |  || |  |||   || ||     
--------------------------------------------------CAA-GGTGCAGATCCTGTTGTAGTTGCAGAGGATGGAAAAGTGAAGTCATTCCC--TGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGAT--ACCAATGGAGCAGgtatgaactctcttatctcattatt-catgcctagagtgctgaaaatgaccaaccttcataaaggtttgcatcgtattgag-attcagtgctcccgtcttct-----

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|4775994|gb|AI664997.1|AI664997
EST:     CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAG                         GTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
genomic: CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
EST: gi|60340226|gb|DN207199.1|DN207199
EST:     CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAG                         GTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
genomic: CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
EST: gi|211259748|gb|FL311234.1|FL311234
EST:     CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAG                         GTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
genomic: CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
EST: gi|60355835|gb|DN222808.1|DN222808
EST:     CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAG                         GTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
genomic: CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
EST: gi|14243818|gb|BG841519.2|BG841519
EST:     CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAG                         GTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
genomic: CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
EST: gi|86473077|gb|DY239447.1|DY239447
EST:     TGCCCAAGGAGAAGCTTGTTGACACCAACGGCCCAG                         GTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGTTGGTCCAGGGCAAGAGCA
genomic: TGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
EST: gi|60337076|gb|DN204049.1|DN204049
EST:     CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAG                         GTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
genomic: CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
EST: gi|60395531|gb|DN228401.1|DN228401
EST:     CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAG                         GTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA
genomic: CCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCA

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), 46 (downstream exon)
Score: 376

GTGAAAACGTTCCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCATCGAGGACTGCGTGACGGCTGGTTGCTACGCCGCCAATGTTGTCATCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

GTGAAAACGTTCCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCATCGAGGACTGCGTGACGGCTGGTTGCTACGCCGCCAATGTTGTCATCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

GTGAAAACGTTCCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCATCGAGGACTGCGTGACGGCTGGTTGCTACGCCGCCAATGTTGTCATCCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 511

GTGAAAACGTTCCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgttt ... ctcctcctagGTGACGCTTTCGTCGGAGGCTTTCTCTCTCGGCTGGTCCAGGGCAAGAGCATCGAGGACTGCGTGACGGCTGGTTGCTACGCCGCCAATGTTGTCATCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAAACGTTCCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgtttctttagtgataagagttagtttatctatttccgatatttttttcattctcaaacgctagttggtttgttcgctaagatgtcttccatataatgttaactactattattgcattacatgaaagctgaacgtctctacgtcttattttgctgttcctgataacacccaaccaatcttccttgctcctcctag

- - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - AGAAGC