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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctagactgtttgtttgcctcttaggattatttaatccagattatataatctggggggtaaacaaacaggccctaagtaaccaatgttgaatgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT

Basic information

species Zea mays
transcript GRMZM2G108225_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108225_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g59040.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------------------------------gctagactgtttgtttgcctcttaggattatttaatc-----cagattatataatctggggggtaaacaaacaggccctaagtaaccaatgt-tgaatgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT
                                                                                         | |    ||||||    |  || | |||||| |||        | || | |  | |      |  ||  |||  |  |   |      |   ||  ||  ||||||||||||||||||||| ||  ||| |||||||||||| |||||  |||||||| | ||||| |||||||||||||||||||||||||| |
gtcagcaatttctctgaactactttgtacttttcaattgctttttgactttaccacgatttggtgatttggtgaatttttcttttcaaacaaagtggtttgtggcgccttttgaattattgaattacccatggtttttgtgttttcctttatcgacttacatactatgtttttttttttcatgggtgcgtgcagAGGACGACACTAGCATTCCTGCCGCGGTGAAGGTGCCGATCCTTAAGGAATTCCATCGGCATATCTACAACCGCGACTGGCATTATTCAT
















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|211235616|gb|FL131352.1|FL131352
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|211062222|gb|FL131347.1|FL131347
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGC
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGC
EST: gi|211235613|gb|FL131349.1|FL131349
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGNTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|149098979|gb|EE184992.2|EE184992
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|211062221|gb|FL131346.1|FL131346
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|149089299|gb|EE178514.2|EE178514
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|148959751|gb|EC905647.2|EC905647
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|74240348|gb|DT648262.1|DT648262
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|149000700|gb|EE037914.2|EE037914
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|148941371|gb|EC886282.2|EC886282
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|211062220|gb|FL131345.1|FL131345
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|148954555|gb|EC899993.2|EC899993
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|211062219|gb|FL131344.1|FL131344
EST:     GTGTGCATCTTCTACCTCGTGCTCCCGTGCCCTCGACACCGTTS                         AGGACGACACTAGCATCCCGACCGANGGTGAAGGGTGCCCATCCTCCAGGA
genomic: GTGTGCATCTTCTACCTCGTGCTCC-GTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGA-GGTGAAGG-TGCCCATCCTCCAGGA
EST: gi|211235614|gb|FL131350.1|FL131350
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|148966228|gb|EE017184.2|EE017184
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCTTCCTC
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTC
EST: gi|149010292|gb|EE042121.2|EE042121
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|211235615|gb|FL131351.1|FL131351
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
EST: gi|211235617|gb|FL131353.1|FL131353
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCA
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCA
EST: gi|148940819|gb|EC885646.2|EC885646
EST:     GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG                         AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT
genomic: GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAAT

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: 40 (upstream exon), 48 (downstream exon)
Score: 163

GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 61

GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 93

GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 79

GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTGgtcagtagtc ... atgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatctggggggtaaacaaacaggccctaagtaaccaatgttgaatgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT
                             aagtaac  putative branch site (score: 79)
             taaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctagactgtttgtttgcctcttaggattatttaatccagattatataatctggggggtaaacaaacaggccctaagtaaccaatgttgaatgactgcagAGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT

- - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caggccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgttga