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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatccgtgcatgtctatgcagagttgaatgttgtagtccattttagacaatctcagctatatcttcactttgcag

Basic information

species Zea mays
transcript GRMZM2G114861_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114861_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os04g53760.2 (Oryza sativa), 5'ss of exon 16
CAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatccgtgca------tgtctatgcagag---ttgaatgttgtagtccattttagaca-atctcagctat-atcttcactttgcag
||||||||||||||| ||| | |||||||| ||||| || || || |||||||| || || || || ||||| || ||||||||||||||||| |||||||| ||||| ||||| || || || | | ||| | | |||| | ||| || || ||| | ||| ||||||
CAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCGAAAGGAGACGATCATGTGCCCTTCAGGAACTCAAAACTTACATACCTTTTGCAGgtgagtgacttgtgcaaatggatggtaatacaaaaacctgcaatccctgaatttatttgaaacatatttcttatatcaactttctattgcag
















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|211045020|gb|FL382451.1|FL382451
EST:     GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
genomic: GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
EST: gi|4646828|gb|AI621903.1|AI621903
EST:     CCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACC-
genomic: CCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
EST: gi|71757388|gb|DR955325.1|DR955325
EST:     GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
genomic: GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
EST: gi|211412934|gb|FL480489.1|FL480489
EST:     GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
genomic: GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
EST: gi|14244176|gb|BG841853.2|BG841853
EST:     GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
genomic: GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
EST: gi|32945905|gb|CF050724.1|CF050724
EST:     GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
genomic: GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
EST: gi|4646866|gb|AI621941.1|AI621941
EST:     GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
genomic: GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
EST: gi|18167051|gb|BM336890.1|BM336890
EST:     GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
genomic: GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
EST: gi|18167204|gb|BM337043.1|BM337043
EST:     GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
genomic: GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
EST: gi|5607865|gb|AI901532.1|AI901532
EST:     GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTTAACATTTCCCCT
genomic: GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
EST: gi|211207046|gb|FL397891.1|FL397891
EST:     GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
genomic: GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
EST: gi|37383658|gb|CF628853.1|CF628853
EST:     GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAG                         CCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG
genomic: GAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCG

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), 49 (downstream exon)
Score: 80

CAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCGGAGGCATCCTCCGTTGGTGAGACGATATGCTCGTTGAGGTTTGCTTCAA


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 29

CAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCGGAGGCATCCTCCGTTGGTGAGACGATATGCTCGTTGAGGTTTGCTTCAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 26

CAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCGGAGGCATCCTCCGTTGGTGAGACGATATGCTCGTTGAGGTTTGCTTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

CAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatc ... cactttgcagCCTTGCCTTGGAGGTGACTCGAAAGCTCTCATGTTTGTCAACATTTCACCGGAGGCATCCTCCGTTGGTGAGACGATATGCTCGTTGAGGTTTGCTTCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTATTGCAGgttagtgatccgtgcatgtctatgcagagttgaatgttgtagtccattttagacaatctcagctatatcttcactttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGATG