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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattggtgaatcctgaagtacagttcactccttaaagatatgaatatatgatgtaaccgaatttctgaggcatgactcacggccaacttgtttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAATGGCCCACAGCTGTATCAG

Basic information

species Oryza sativa
transcript LOC_Os02g42320.3
intron # 5
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 5
lower sequence: GRMZM2G085243_T01 (Zea mays), 3'ss of exon 7
gattggtgaatcctgaagtacagttcactccttaaa-gat--atgaatatatgatgtaaccgaatttctgag-gcatgactcacggccaacttgtttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAATGGCCCACAGCTGTATCAG
  |||    | |||  | |        ||  | |   |||   ||||    |||  ||     || |    | |  | |||   |  |  ||| |||||| |||||||||||||||||||||||||||  | |||||||| ||||| |||||||||||||||||| ||||||||
--ttgtactagcctctattgtctggggctgttaaggtgattagtgaaagcctgagatacgtatatgttaatgagttttacttgtgatc--cttatttgtttcagTGGTGTAAGACCATTTGGAGTATCGCTGTTGATTGCTGGGTATGATGACAATGGCCCACAGTTGTATCAG

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G850355_T02 (Zea mays), 3'ss of exon 7
gattggtgaatcctgaagtacagttcactccttaaa-gat--atgaatatatgatgtaaccgaatttctgag-gcatgactcacggccaacttgtttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAATGGCCCACAGCTGTATCAG
  |||    | |||  | |        ||  | |   |||   ||||    |||  ||     || |    | |  | |||   |  |  ||| |||||| |||||||||||||||||||||||||||| | |||||||| ||||| |||||||||||||||||| ||||||||
--ttgtactagcctctattgtctggggcttttaaggtgattagtgaaagcctgagatacgtatatgttaatgagttttacttgtgatc--cttatttgtttcagTGGTGTAAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCACAGTTGTATCAG

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G824831_T02 (Zea mays), 3'ss of exon 7
-gattggtgaatcctgaagtacagttcactccttaaagatatgaatatatgatgtaaccgaatttctgaggcatgactcacggccaacttgtttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAATGGCCCACAGCTGTATCAG
    |  |     ||   ||   |     |      |    ||||    |||  ||     ||  || | |  |    |  |     |||| ||||  ||||||||| |||||||||||||||||| | |||||||| ||||| |||||||||||||| ||| ||||||||
catgtactagcctctattgtttggggtgttaaggtgattagtgaaagcttgagataggtatatg-ctaatgagttttacttgttatccttgcttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G850355_T08 (Zea mays), 3'ss of exon 6
gattggtgaatcctgaagtacagttcactccttaaa-gat--atgaatatatgatgtaaccgaatttctgag-gcatgactcacggccaacttgtttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAATGGCCCACAGCTGTATCAG
  |||    | |||  | |        ||  | |   |||   ||||    |||  ||     || |    | |  | |||   |  |  ||| |||||| |||||||||||||||||||||||||||  | |||||||| ||||| |||||||||||||||||| ||||||||
--ttgtactagcctctattgtctggggcttttaaggtgattagtgaaagcctgagatacgtatatgttaatgagttttacttgtgatc--cttatttgtttcagTGGTGTAAGACCATTTGGAGTATCGCTGTTGATTGCTGGGTATGATGACAATGGCCCACAGTTGTATCAG

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|88956166|gb|CI092454.1|CI092454
EST:     CTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCNGGGTACGATGACAA
genomic: CTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|56550165|gb|CX056269.1|CX056269
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|88985654|gb|CI016363.1|CI016363
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|3766855|gb|AU030965.1|AU030965
EST:     GTTCACACAGTCTGG                         TGGTNTAAGCCCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAN
genomic: GTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|88239782|gb|CI238944.1|CI238944
EST:     AGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: AGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|86422896|gb|CI060469.1|CI060469
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|33661637|gb|CF292604.1|CF292604
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|88243911|gb|CI243033.1|CI243033
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|27554138|gb|CA998038.1|CA998038
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|86493119|gb|CI135752.1|CI135752
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|88852675|gb|CI008868.1|CI008868
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|89197364|gb|CI009984.1|CI009984
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|88236034|gb|CI235236.1|CI235236
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|86494880|gb|CI137513.1|CI137513
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|87029179|gb|CI276447.1|CI276447
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|88995615|gb|CI022938.1|CI022938
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|27578244|gb|CB000939.1|CB000939
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|29613823|gb|CB618836.1|CB618836
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|27576119|gb|CA998813.1|CA998813
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|88201510|gb|CI201865.1|CI201865
EST:     TGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: TGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|396941624|gb|HO188281.1|HO188281
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|88240749|gb|CI239911.1|CI239911
EST:     AGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: AGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|25797837|gb|CA753798.1|CA753798
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACNA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
EST: gi|88901506|gb|CI008934.1|CI008934
EST:     CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG                         TGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA
genomic: CAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctact ... tttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgatgtaaccgaatttctgaggcatgactcacggccaacttgtttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAATGGCCCACAGCTGTATCAG
                            gactcac  putative branch site (score: 2)
                                         cttgttt  putative PPT
              aatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattggtgaatcctgaagtacagttcactccttaaagatatgaatatatgatgtaaccgaatttctgaggcatgactcacggccaacttgtttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAATGGCCCACAGCTGTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - tgaatcc
- - - - - - - - - - - - - - - - - - - - - - - -atgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaccgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcatga