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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgcttatgtttatctaatcaaatggttggcaaagttatcaagagaaacaagccattatctaatttgagatgtgttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCAGCCAGTGAAGAAACCTGGCCAGCAATTAGGAAGCTTCTTCAACGCGAGA

Basic information

species Oryza sativa
transcript LOC_Os01g39310.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 16
lower sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 15
gttgcttatgtttatctaatcaaatggttggcaaagttatcaagagaaacaagccattatctaat--ttgagatgtgttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCAGCCAGTGAAGAAACCTGGCCAGCAATTAGGAAGCTTCTTCAACGCGAGA
|||| |     |  |  |||  |   ||| |     | |   |    ||  || | |||||||||  || |||| |||| ||| ||| |||||||||||| || ||||  |||||||||||| ||||||||||||||||||||||||| || |||||||| ||||| |||||||||||||||||||
gttggtcccagt--ttgaattcatctgtttgtgtcatcacacaacacaaggagtccttatctaatattttagatatgttgtttcagGCACAACTTACCAAAGCTCTGGTGGAACCAGTTGAATCTCTTCTAGATTCAGCCAGTGAAGACACGTGGCCAGCTATTAGAAAGCTTCTTCAACGCGAGA

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM5G838579_T01 (Zea mays), 3'ss of exon 5
gttgcttatgtttatctaatcaaatggttggcaaagttatcaagagaaacaagccattatctaatttgagatgtgttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCAGCCAGTGAAGAAACCTGGCCAGCAATTAGGAAGCTTCTTCAACGCGAGA
|||| |     || |  | |||  || |||    |     ||  | ||   |  | |  |||||| | |||| |||| ||||||| |||||||||||| || ||||| |||||||||||| ||||||||||||||||||||||||| || |||||||| ||||| |||||||||||||||||||
gttggtcccagtt-tgcattcacctgtttgtgtcaccatgcagcacaagagaatcctcgtctaatcttagatatgttgttttagGCACAACTTACCAAAGCTCTGGCGGAACCAGTTGAATCTCTTCTAGATTCAGCCAGTGAAGATACGTGGCCAGCTATTAGAAAGCTTCTTCAACGCGAGA
















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|571771|gb|D41282.1|D41282
EST:     TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAG                         GGACAACTTACCAAGGNACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
genomic: TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAGgttgcttatg ... gttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
EST: gi|29641074|gb|CB646081.1|CB646081
EST:     TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAG                         GGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
genomic: TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAGgttgcttatg ... gttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
EST: gi|218488553|gb|FG950540.1|FG950540
EST:     TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAG                         GGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
genomic: TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAGgttgcttatg ... gttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
EST: gi|58665350|gb|CK054036.1|CK054036
EST:     TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAG                         GGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
genomic: TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAGgttgcttatg ... gttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
EST: gi|157650537|gb|EX450171.1|EX450171
EST:     TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAG                         GGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
genomic: TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAGgttgcttatg ... gttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
EST: gi|58661464|gb|CK050144.1|CK050144
EST:     TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTGGGTTCCAAATACGAG                         GGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
genomic: TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAGgttgcttatg ... gttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
EST: gi|5003388|gb|AU068537.1|AU068537
EST:     TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAG                         GGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA
genomic: TGGCATCAGTTCGTGCCAAAAAACTATCTGAACTTTGTTCCAAATACGAGgttgcttatg ... gttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaaagttatcaagagaaacaagccattatctaatttgagatgtgttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCAGCCAGTGAAGAAACCTGGCCAGCAATTAGGAAGCTTCTTCAACGCGAGA
                             atctaat  putative branch site (score: 3)
                                              ttatttt  putative PPT
                          attatctaatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgcttatgtttatctaatcaaatggttggcaaagttatcaagagaaacaagccattatctaatttgagatgtgttattttagGGACAACTTACCAAGGCACTGGCAGAACCAGTTGAAGCTCTTCTAGATTCAGCCAGTGAAGAAACCTGGCCAGCAATTAGGAAGCTTCTTCAACGCGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA