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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcaaatgttatgcaacttgacactgatgatcatatatactctgtgggcttattgatggaatctaatttcttctttgtgcttcccttaaagACGAAGGCAGAGCTTGAGGAGATTGCTCTTGCGGAGGCTGATGTTGCAAGGTTAAAGCAGAAGGTTGCGGAGCTCCATCTCCAACTCAACCAGCAGCGTC

Basic information

species Oryza sativa
transcript LOC_Os07g46450.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G340359_T01 (Zea mays), 3'ss of exon 18
-gtactcaaatgttatgcaacttga-cactgatgatcatatatactctgtgggcttattg-atggaatctaatttcttctttgtgcttcccttaaagACGAAGGCAGAGCTTGAGGAGATTGCTCTTGCGGAGGCTGATGTTGCAAGGTTAAAGCAGAAGGTTGCGGAGCTCCATCTCCAACTCAACCAGCAGCGTC
  |||| ||||  || |||| | |  |  ||||  | | ||| | |  | |||||||||   |||   || || | |||| ||  |  | ||| | ||| ||||||||||||||||| |||||||| || || |||||||||||||| ||||| ||||||||||| ||||| |||||||||||||| || ||||| |
gttactgaaatcataagcaagtagttctttgatagttacata-attgcg-gggcttattctgtggtggcttatgtattctatgcacaactcttta-gACAAAGGCAGAGCTTGAGGAAATTGCTCTCGCAGAAGCTGATGTTGCAAGATTAAAACAGAAGGTTGCAGAGCTGCATCTCCAACTCAATCAACAGCGCC

upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G036872_T02 (Zea mays), 3'ss of exon 18
gtactcaaatgttatgcaacttga-cactgatgatcatatatactctgtgggcttattg-atggaatctaatttcttctttgtgcttcccttaaagACGAAGGCAGAGCTTGAGGAGATTGCTCTTGCGGAGGCTGATGTTGCAAGGTTAAAGCAGAAGGTTGCGGAGCTCCATCTCCAACTCAACCAGCAGCGTC
||| |  |||  || |||| |||  |  |||   |  ||  ||||   |  |||||||  |||   ||   | | |||| ||  ||||  ||| |||| ||| ||||||||||||| |||||||| || || |||||||||||||| ||||| ||||||||||| ||||| ||| |||||||||| || ||||| |
gtattggaattgtaagcaagttgttctttgacagt--tacgtacttgctcagcttattttatgatgtcctctgttttctatgcacttct-ttatagACAAAGTCAGAGCTTGAGGAAATTGCTCTCGCAGAAGCTGATGTTGCAAGATTAAAACAGAAGGTTGCAGAGCTGCATTTCCAACTCAATCAACAGCGCC
















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|25800836|gb|CA756797.1|CA756797
EST:     TAAGCATGTCTTCTGCACAGATTTCTAGTTCACGTTCTATGGATTCAAAG                         ACGAAGGCAGAGCTTGAGGAGATCGCTCTTGCGGAGGCTGATGTTGCAAGG
genomic: TAAGCATGTCTTCTGCACATATTTCTAGTTCACGTTCTATGGATTCAAAGgtactcaaat ... tcccttaaagACGAAGGCAGAGCTTGAGGAGATTGCTCTTGCGGAGGCTGATGTTGCAAGG
EST: gi|218499410|gb|FG963726.1|FG963726
EST:     TAAGCATGTCTTCTGCACATATTTCTAGTTCACGTTCTATGGATTCAAAG                         ACGAAGGCAGAGCTTGAGGAGATTGCTCTTGCGGAGGCTGATGTTGCAAGG
genomic: TAAGCATGTCTTCTGCACATATTTCTAGTTCACGTTCTATGGATTCAAAGgtactcaaat ... tcccttaaagACGAAGGCAGAGCTTGAGGAGATTGCTCTTGCGGAGGCTGATGTTGCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactctgtgggcttattgatggaatctaatttcttctttgtgcttcccttaaagACGAAGGCAGAGCTTGAGGAGATTGCTCTTGCGGAGGCTGATGTTGCAAGGTTAAAGCAGAAGGTTGCGGAGCTCCATCTCCAACTCAACCAGCAGCGTC
                        atctaat  putative branch site (score: 3)
                              tttcttctttgtgctt  CT-rich tract
                       aatctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcaaatgttatgcaacttgacactgatgatcatatatactctgtgggcttattgatggaatctaatttcttctttgtgcttcccttaaagACGAAGGCAGAGCTTGAGGAGATTGCTCTTGCGGAGGCTGATGTTGCAAGGTTAAAGCAGAAGGTTGCGGAGCTCCATCTCCAACTCAACCAGCAGCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT