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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGCATACGCATCTTATCCAGGACATGCTTTCGATCTGCCGTGAGACATTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcattcgtttccattttctccttctgtccattttctgtatgcaagccaggttttatgattagaaattctttgatatgttaacattgcttttcttt...

Basic information

species Oryza sativa
transcript LOC_Os02g15550.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15550.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G060896_T02 (Zea mays), 5'ss of exon 9
GGTTGCATACGCATCTTATCCAGGACATGCTTTCGATCTGCCGTGAGACATTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcattcgtttccattttctccttctgtccattttctgtatgcaagccaggttttatgattagaaattctttgatat-gttaacattgcttttcttt-
|||| ||||| ||| | || ||||| |||||||| || |||||||| || |||||||||||||| | |||||| ||||| |||||||| ||||| || |||||  |  |||  |||  | || ||        | || | | ||| |   |  | ||| ||   |  || ||  ||  | | |||  |   | | |  | | 
GGTTACATACACATTTGATTCAGGATATGCTTTCAATTTGCCGTGAAACTTTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttcttcacttctctattgtcaagt--ctccttatatttatcctttcttgctttcatagctctaatttgatttttttagttttcgcagttgtggtctc

upper sequence: LOC_Os02g15550.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G120578_T02 (Zea mays), 5'ss of exon 8
GGTTGCATACGCATCTTATCCAGGACATGCTTTCGATCTGCCGTGAGACATTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcattcgtttccattttctccttctgtccattttctgtatgcaagccaggttttatgattagaaattctttgatatgttaacattgcttttcttt--
|||||||||| ||| | || |||||||||||||| || ||||||||||| |||||||||||||||| |||||| ||| | |||||||| ||||| || |||||||||||   | |  ||| |||  | ||    |  |   |||      |   ||||||    || |  | ||    ||  |      |  |     ||  
GGTTGCATACACATTTGATTCAGGACATGCTTTCAATTTGCCGTGAGACTTTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcatat-tctttattgtctggt-ctccttacctctagtactttccctccgttttaactgtatatttgctgcactaaatctggtatattacaagttaa

upper sequence: LOC_Os02g15550.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 5'ss of exon 9
GGTTGCATACGCATCTTATCCAGGACATGCTTTCGATCTGCCGTGAGACATTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcattcgtttccattttctccttctgtccattttctgtatgcaagccaggttttatgattagaaattcttt---gatatgttaacattgcttttcttt--
|| | || || |||||||| ||||| |||||||| || || ||||| |||||||||||||| ||||| ||||| ||| | ||||| || |||||||| ||||  | |||   ||     | |||   | || | | || || ||    |       | | || |        ||||   || ||| |||   || |||       
GGCTCCACACACATCTTATTCAGGATATGCTTTCTATTTGTCGTGAAACATTCAAGGGTTCGGTCCATTATGCATGGGCAAGTGTTCCTACATATCCAAGgtaat-catgtatt---gatctctatatatggctaattgctctac-tgattttttctctttggtctattgccctttccagaaatgataagggtgatttggaagat

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|29664251|gb|CB660526.1|CB660526
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|27546253|gb|CA764321.2|CA764321
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|38479602|gb|CF963699.1|CF963699
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATAGCCGAG                         TGGTGTGATTGGGTTTCTAGCTATGTGCCAAAGAAGGTCCACCAGTCAACT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCT-GCTATGTGCCAAAGAAGGTCCACCAGTCAACT
EST: gi|87027956|gb|CI276312.1|CI276312
EST:     TGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|87010799|gb|CI312491.1|CI312491
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTNTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|29667241|gb|CB663516.1|CB663516
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|86859105|gb|CI277026.1|CI277026
EST:     CGAGTGTCCCGACATATTCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: CGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|38471600|gb|CF955731.1|CF955731
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|87028025|gb|CI257185.1|CI257185
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|29657801|gb|CB654076.1|CB654076
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|88993298|gb|CI257726.1|CI257726
EST:     TCCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: T-CAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|86477600|gb|CI120233.1|CI120233
EST:     GGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: GGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|58678117|gb|CK066804.1|CK066804
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|88850542|gb|CI093223.1|CI093223
EST:     GGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: GGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|29642052|gb|CB647059.1|CB647059
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|29619281|gb|CB624293.1|CB624293
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
EST: gi|29672899|gb|CB669174.1|CB669174
EST:     TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAG                         TGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT
genomic: TTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcatt ... gcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTGCATACGCATCTTATCCAGGACATGCTTTCGATCTGCCGTGAGACATTCAAGGGTTCTGTCCACTATGCCTGGACGAGTGTCCCGACATATCCCAGgttcttcattcgtttccattttctccttctgtccattttctgtatgcaagccaggttttatgattagaaattctttgatatgttaacattgcttttcttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttc