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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctaagactagaaactggaacctgccatcttccttttttaaccaaaataggttaacatgtcattttattatttgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGCCATTAAACTCGTTTGGTCTTGCCACAGGGAGATCATATATGACATTGGC

Basic information

species Oryza sativa
transcript LOC_Os05g45960.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G090087_T03 (Zea mays), 3'ss of exon 14
gtgagctaagactagaaactggaacctgccatcttcctttt--------------ttaaccaaaataggttaacatgtcattt---tattatt-tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGCCATTAAACTCGTTTGGTCTTGCCACAGGGAGATCATATATGACATTGGC
|||||| | |||   ||| |  | | || |||   |  ||               | || | | ||| |  ||| |  |||||   |   | |    ||| ||||||||| || || ||||||||  |||| ||||||||||| ||||| |||||||| ||||| || ||||| |||||||||||  ||||||||||| | || 
gtgagccaggacccaaaaattcagcttggcatgcacggttacaagtaggcatacatgaaactatatacggcaacgtaacatttccgtcccactgcaaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGCCATCAAACTTGTCTGGTCCTGCCACAGGGAAGTCATATATGACGTCGGG

upper sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA05G01290.1 (Glycine max), 3'ss of exon 15
gtgagctaagactagaaactggaacctgccatcttccttttttaaccaaaatagg-----ttaacatgtc-attttattatttgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGCCATTAAACTCGTTTGGTCTTGCCACAGGGAGATCATATATGACATTGGC
|| |  | | | |      |  ||| ||   |   |  |   |||| || | | |     ||||  |||  |   || || ||  | | ||||||||| || ||||||||| | ||||||||||| || ||||| ||||| || || ||||| || |||||||||||||| || || || |||||  |||| 
gtaaattgatattt---ttttaaacttgtt-ttacctgtacataactaagaaatgattctttaatttgttgaaaataataatttcattgcagGTTTGGACCCGCTGGTGATGCTAGAGGTGCAGGAATTGGAACACCAGAGGCTATAAAACTTGTATGGTCTTGCCACAGAGAAATAATCTATGATTTTGGG

upper sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA17G10610.1 (Glycine max), 3'ss of exon 15
gtgagctaagactagaaactggaacctgccatcttccttttttaaccaaaataggttaacat-gtcattt-----tattatttgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGCCATTAAACTCGTTTGGTCTTGCCACAGGGAGATCATATATGACATTGGC
|| |  | | | |      |  ||| ||   |      |   |||| || | | | |    | || | ||     || || ||  | |  |||||||| || ||||||||| | ||||||||||| || ||||| ||||| || || ||||| || |||||||||||||| || || || |||||  |||| 
gtaaattgatattt---ttttcaacttgtt-ttacttgtacataactaagaaatgatgctttagttagttgaaaataataatttcattgtagGTTTGGACCCGCTGGTGATGCTAGAGGTGCAGGAATTGGAACACCAGAGGCTATAAAACTTGTATGGTCTTGCCACAGAGAAATAATCTATGATTTTGGG

upper sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 14
lower sequence: EFJ29772 (Selaginella moellendorffii), 3'ss of exon 14
gtgagctaagactagaaactggaacctgccatcttccttttttaaccaaaataggttaacatgtcattttattatttgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGCCATTAAACTCGTTTGGTCTTGCCACAGGGAGATCATATATGACATTGGC
                           |  | ||||     ||   | | |||    |  | |  |   |||| ||| | || ||||||||| || ||||| ||||||   ||||| || |||||||||||||||||||| ||||| || |||||||||||| | ||||||||  | ||| |||| 
---------------------------gtaagcttctcgagttttgcgagataa-cgaggaagaaac--tattgttt-tgatacagGTTTGGACCCGCTGGAGATCCACTTGGTGCTGGAATCGGAACTCCAGAAGCCATCAAACTGGTGTGGTCTTGCCACCGTGAGATCATCCAAGACTTTGGA

upper sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 14
lower sequence: EFJ08918 (Selaginella moellendorffii), 3'ss of exon 14
gtgagctaagactagaaactggaacctgccatcttccttttttaaccaaaataggttaacatgtcattttattatttgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGCCATTAAACTCGTTTGGTCTTGCCACAGGGAGATCATATATGACATTGGC
                           |  | ||||     ||   | | |||    |  | |  |   |||| ||| | || ||||||||| |||||||| ||||||  |||||| || |||||||||||||||||||| ||||| || |||||||||||| | ||||||||  | ||| |||| 
---------------------------gtaagcttctcgagttttgcgagata----acgaggaaaaactattgttt-tgatacagGTTTGGACCTGCTGGAGATCCACTAGGTGCTGGAATCGGAACTCCAGAAGCCATCAAACTGGTGTGGTCTTGCCACCGTGAGATCATCCAAGACTTTGGA

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|87028745|gb|CI349464.1|CI349464
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         TTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|86496475|gb|CI139108.1|CI139108
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGNTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|86486168|gb|CI128801.1|CI128801
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|86436669|gb|CI118391.1|CI118391
EST:     ACATATGCCGGCATCCGAGCTAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|44673853|gb|CR287287.1|CR287287
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|88251843|gb|CI349080.1|CI349080
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|8956651|gb|BE230326.1|BE230326
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|86487725|gb|CI130358.1|CI130358
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|88848173|gb|CI086695.1|CI086695
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|9865361|gb|AU101111.1|AU101111
EST:     ACATATGCCGGNATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|88962017|gb|CI097170.1|CI097170
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGGACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|89180443|gb|CI044722.1|CI044722
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|88907945|gb|CI090541.1|CI090541
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|88269212|gb|CI380510.1|CI380510
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|88282820|gb|CI402020.1|CI402020
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTT                         GTTTGGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAG
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTT-GGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAG
EST: gi|89162486|gb|CI099178.1|CI099178
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|29632954|gb|CB637963.1|CB637963
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAAAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|86851512|gb|CI314095.1|CI314095
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|89161684|gb|CI100844.1|CI100844
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|58656949|gb|CK045629.1|CK045629
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|29617924|gb|CB622936.1|CB622936
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|88968032|gb|CI098274.1|CI098274
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|218484591|gb|FG954366.1|FG954366
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAG
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAG
EST: gi|88277860|gb|CI398662.1|CI398662
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAG
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTT-GGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAG
EST: gi|88908314|gb|CI090907.1|CI090907
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|88976781|gb|CI257525.1|CI257525
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|88275300|gb|CI395904.1|CI395904
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAG-A--ACTG                         TTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
EST: gi|86493002|gb|CI135635.1|CI135635
EST:     ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG                         GTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC
genomic: ACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTGgtgagctaag ... tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttccttttttaaccaaaataggttaacatgtcattttattatttgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGCCATTAAACTCGTTTGGTCTTGCCACAGGGAGATCATATATGACATTGGC
                        ttaacatgtcatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctaagactagaaactggaacctgccatcttccttttttaaccaaaataggttaacatgtcattttattatttgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGCCATTAAACTCGTTTGGTCTTGCCACAGGGAGATCATATATGACATTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA