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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggttttttacagttcatttgatttatacttcagataactattgtatgttttgtaaagacatatatttttcaataaattgctatttcggatagcatgcaatttttcatgtacgacagtcatgatcttttccatcatttacttatttctcatgattgttcttcctttttctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG

Basic information

species Oryza sativa
transcript LOC_Os02g42320.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G850355_T08 (Zea mays), 3'ss of exon 5
gtggttttttacagttcatttgatttatacttcagataactattgtatgttttgtaaagacatatatttttcaataaattgctatttcggatagcatgcaatttttcatgtacgacagtcatgatcttttccatcatttacttatttctcatgattgttcttcctttttctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG
                                                     ||| | | || | ||||     |||||  | ||||              || |||  | |   |   ||       | | | |  ||| |||     ||  ||||| ||   || || |||||||||   ||| ||||| || |||||||| ||||| ||||||||||| |||||||||||||||||||| ||
----------------------------------------------------agtagaaaaatgtgtttt-----aaattattgtttca-------------ttgtcaaatgcaggaaatata------tacctaaggtacctatgctaaattgttgttatt--gttgtcaaatgcagGAGCATATACCTGTAACACAGCTTGTGCGAGAGACTGCTGCTGTGATGCAGGAGTTCACACAGTCAGG

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 6
gtggttttttacagttcatttgatttatacttcagataactattgtatgttttgtaaagacatatatttttcaataaattgctatttcggatagcatgcaatttttcatgtacgacagtcatgatcttttccatcattta-cttatttctcatgattgttcttcctttttctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG
                                                                                                                    ||  ||  || |  |  |||  || |  || | |  | ||| || || | ||| | ||||||||||  ||| ||||| || |||||||| ||||| ||||||||||| |||||||||||||||||||| ||
-------------------------------------------------------------------------------nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgatctagagatcgtcctcgctgtcaggtagcaaatgtgttttaattattgtttcatttccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G115948_T01 (Zea mays), 3'ss of exon 2
gtggttttttacagttcatttgatttatacttcagataactattgtatgttttgtaaagacatatatttttcaataaattgctatttcggatagcatgcaatttttcatgtacgacagtcatgatcttttccatcatttacttatttctcatgattgttcttcctttttctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG
                                                                  | ||  | | ||||  || ||   |        ||| | |    | |  ||  |  |    | ||    |   |  | | | | |  ||| || || | ||| | ||||||||||  ||| ||||| || |||||||| ||||| ||||||||||| |||||||||||||||||||| ||
------------------------------------------------------------------tattgaagtgaatttgtaatttaaa--------aatgtattccctgctgcaacctcg---ctgtcaggtagcaaagtgtgtttta-aattattgtttcatttccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G850355_T02 (Zea mays), 3'ss of exon 6
gtggttttttacagttcatttgatttatacttcagataactattgtatgttttgtaaagacatatatttttcaataaattgctatttcggatagcatgcaatttttcatgtacgacagtcatgatcttttccatcatttacttatttctcatgattgttcttcctttttctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG
                                                     ||| | | || | ||||     |||||  | ||||              || |||  | |   |   ||       | | | |  ||| |||     ||  ||||| ||   || || |||||||||   ||| ||||| || |||||||| || || ||||||||||| |||||||||||||||||||| ||
----------------------------------------------------agtagaaaaatgtgtttt-----aaattattgtttca-------------ttgtcaaatgcaggaaatata------tacctaaggtacctatgctaaattgttgttgtt--gttgtcaaatgcagGAGCATATACCTGTAACACAGCTTGTGCGGGAGACTGCTGCTGTGATGCAGGAGTTCACACAGTCAGG

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G824831_T02 (Zea mays), 3'ss of exon 6
gtggttttttacagttcatttgatttatacttcagataactattgtatgttttgtaaagacatatatttttcaataaattgctatttcggatagcatgcaatttttcatgtacgacagtcatgatcttttccatcatttacttatttctcatgattgttcttcctttttctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG
                                                                  | ||  | | ||||  || ||   |        ||| | |    |    ||  |  |    | ||    |   |  | | | | |  ||| || || | ||| | ||||||||||  ||| ||||| || |||||||| ||||| ||||||||||| |||||||||||||||||||| ||
------------------------------------------------------------------tattgaagtgaatttgtaatttaaa--------aatatattccctgttgcaacctcg---ctgtcaggtagcaaaatgtgtttta-aattattgtttcatttccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG

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|56550165|gb|CX056269.1|CX056269
EST:     TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG                         GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
genomic: TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAGgtggtttttt ... tctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
EST: gi|27554138|gb|CA998038.1|CA998038
EST:     TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG                         GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
genomic: TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAGgtggtttttt ... tctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
EST: gi|86493119|gb|CI135752.1|CI135752
EST:     TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG                         GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
genomic: TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAGgtggtttttt ... tctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
EST: gi|88852675|gb|CI008868.1|CI008868
EST:     AGCACAGCAGTATTATCGGTTGTACAAG                         GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
genomic: AGCACAGCAGTATTATCGGTTGTACAAGgtggtttttt ... tctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
EST: gi|88236034|gb|CI235236.1|CI235236
EST:     GAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG                         GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
genomic: GAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAGgtggtttttt ... tctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
EST: gi|86494880|gb|CI137513.1|CI137513
EST:     AACAAGCACAGCAGTATTATCGGTTGTACAAG                         GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
genomic: AACAAGCACAGCAGTATTATCGGTTGTACAAGgtggtttttt ... tctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
EST: gi|27578244|gb|CB000939.1|CB000939
EST:     TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG                         GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
genomic: TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAGgtggtttttt ... tctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
EST: gi|29613823|gb|CB618836.1|CB618836
EST:     TATTATCGGTTGTACAAG                         GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
genomic: TATTATCGGTTGTACAAGgtggtttttt ... tctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
EST: gi|27576119|gb|CA998813.1|CA998813
EST:     TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG                         GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
genomic: TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAGgtggtttttt ... tctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
EST: gi|396941624|gb|HO188281.1|HO188281
EST:     TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG                         GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
genomic: TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAGgtggtttttt ... tctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
EST: gi|25797837|gb|CA753798.1|CA753798
EST:     TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG                         GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG
genomic: TTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAGgtggtttttt ... tctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttttccatcatttacttatttctcatgattgttcttcctttttctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG
                                            ttctaat  putative branch site (score: 2)
                     tttctcatgattgttc  CT-rich tract
         atcatttacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggttttttacagttcatttgatttatacttcagataactattgtatgttttgtaaagacatatatttttcaataaattgctatttcggatagcatgcaatttttcatgtacgacagtcatgatcttttccatcatttacttatttctcatgattgttcttcctttttctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT