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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGAACGGACATTGAAGACTACAAGTGCTCATGGTTAGTTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtattattaactttgtagtttttatcaacccatgggcaccatctgaatcctttatgtctaattgacag

Basic information

species Oryza sativa
transcript LOC_Os01g50760.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G098569_T01 (Zea mays), 5'ss of exon 9
ATTGGAACGGACATTGAAGACTACAAGTGCTCATGGTTAGTTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtattattaactttgt-agtttttatcaacccatgggcaccatct-----gaatcctttatgtctaattga-cag
|| ||||| ||||||||||||||||| || || ||| |||||||||||||||| ||||||||||  ||||||||||||  |||||| |||||||| | ||||||  | |  | | ||| |||   |||   |  ||         ||||||| ||||||  |  | |||
ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcactattaaactggccaatctttttcacaacataaacgacaaagtaagaaaatccttcatgtctgttcaaacag

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 9
ATTGGAACGGACATTGAAGACTACAAGTGCTCATGGTTAGTTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtattattaactttgtagtttttatcaacccatgggcaccatct----------gaatcctttatgtctaattga-cag
|| ||||| |||||||||||||||||||| || ||| |||| ||||||||||| || |  ||||| ||||| |||||| ||||||| |||||||| | |||||| || |  | |||| |||   ||||  |  ||              ||||||| ||||||  |  | |||
ATCGGAACTGACATTGAAGACTACAAGTGTTCCTGGCTAGTCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcactattaaattggccgattttttcacaacatgaacgacaaagtaagaaaaaaaaatccttgatgtctgttcaaacag
















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|88965695|gb|CI006596.1|CI006596
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCTAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|86600966|gb|CI356723.1|CI356723
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATTCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|88380218|gb|CI516205.1|CI516205
EST:     CACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: CACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|27577652|gb|CB000347.1|CB000347
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|4714704|gb|AU055821.1|AU055821
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGANCCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCNGATCCTGAATGTGTTGCAAAAGTGANGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|88266799|gb|CI368575.1|CI368575
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|86852882|gb|CI323191.1|CI323191
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|86419076|gb|CI053877.1|CI053877
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|27576092|gb|CA998786.1|CA998786
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGT
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGT
EST: gi|86836476|gb|CI348358.1|CI348358
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|33820604|gb|CF336113.1|CF336113
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|87011492|gb|CI279401.1|CI279401
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCTAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|33822342|gb|CF336983.1|CF336983
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|86535251|gb|CI175457.1|CI175457
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|29620886|gb|CB625897.1|CB625897
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTTTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|86527820|gb|CI168026.1|CI168026
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|29682410|gb|CB678685.1|CB678685
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|86252127|gb|CI055864.1|CI055864
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|86426167|gb|CI071264.1|CI071264
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCCAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|89169652|gb|CI110011.1|CI110011
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCGGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|86834085|gb|CI340224.1|CI340224
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|8856728|gb|AU094046.1|AU094046
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|88974804|gb|CI023100.1|CI023100
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|29688203|gb|CB684478.1|CB684478
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|27554346|gb|CA998246.1|CA998246
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAG
EST: gi|89166650|gb|CI103936.1|CI103936
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|88970717|gb|CI385383.1|CI385383
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         G-AAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|58681411|gb|CK070098.1|CK070098
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCCAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCCAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|86521107|gb|CI161313.1|CI161313
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|29684202|gb|CB680477.1|CB680477
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|88829676|gb|CI074546.1|CI074546
EST:     TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: TTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
EST: gi|86598572|gb|CI355189.1|CI355189
EST:     GTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTT                         GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG
genomic: GTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 107

ATTGGAACGGACATTGAAGACTACAAGTGCTCATGGTTAGTTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtatta ... taattgacagGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGAACGGACATTGAAGACTACAAGTGCTCATGGTTAGTTGTGCAAGCTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTgtaagtattattaactttgtagtttttatcaacccatgggcaccatctgaatcctttatgtctaattgacag

- - - - - - - - - - - - - - - - - - - - - -  CAAGCT