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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttcttctctttaattctcatctcacctgtggatataacaccacccatttaaatttctaaaataccttgtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGC

Basic information

species Oryza sativa
transcript LOC_Os03g25940.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G113873_T02 (Zea mays), 3'ss of exon 9
--gtactttcttctct--ttaattctcatctcacctg---tggatataacaccacccatttaaatttctaaaataccttgtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGC
    | ||  ||||    |||||| |  | |   ||    ||   | ||||  ||  | || | |     | |||     |||||  |||||||||||||||||||||| || |||| ||| || ||||||||||||||||||||||||||||| || || || |||||||||||||| ||||||||||
gtaaatttaattcttgaattaattgtactttgtactaagttgttgagaacatgacatagttcagtgatatacatattccttctgt--agGTTGCTGGAGACTTTGATGCCACAAGGAAATTCATCGATTCTGTTAAGATACCCTATCATGCCCCTTCTTTCGGAGGCTGTGAGAGCATAATTGATCAGC

upper sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G075153_T03 (Zea mays), 3'ss of exon 10
gtactttcttctctttaatt---ctcatctcacctgtggatataacaccacccatttaaatttctaaaataccttgtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGC
|||  |     |||| |||       | ||  |       | |          |  | | ||| ||  |||  |  | |||| ||||||||||||||||||||||||| |||| ||| |||||||||||||| |||||||||||||| || || ||||| |||||||||||||| ||||||||||
gtaaatatagttcttgaatcagatataccttgcactaaattgttgggaacatgacatgattttttatgatatat--tttgtgtagGTTGCTGGAGACTTTGATGCTACGAGGAAATTCATTGATTCTGTTAAAATACCCTATCATGCGCCTTCTTTTGGAGGCTGTGAGAGCATAATTGATCAGC

upper sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 9
----gtactttcttctcttta---attctcatctcac-ctgtggatataacaccacccatttaaatttctaaaataccttgtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGC
    | | ||    |  |||     | ||  | | |   |||  || |   |       ||||| |   ||       ||   | ||||||||| |||||||||     | || |  |  ||| ||||| |  | || || || |||  ||||||||| || || ||||||||||||||| |||||||||
gtaagcatttgtaaccattttcatgtgctggtgtgaggttgttcatctggaagttggattttaagtgcttattgctatttaaatttgcagGTTGATGGAGACTTAACCACCACCATCAAGTTTGTTGATGCATTGAAAATCCCTTATATTGCCCCATCCTTCGGAGGCTGTGAGAGCATTGTTGATCAGC

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|25803371|gb|CA759332.1|CA759332
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCGTTAGTTNTGAG                         GTTTCTGGAGACTNTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|89184572|gb|CI006997.1|CI006997
EST:     GTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: GTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|15855064|gb|BI807876.1|BI807876
EST:     CATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTCGTCATTAGTTTTGAG                         GTTCGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGAT
genomic: CATTGCCAAGAGTCAGATGACCGGCTTTGGTGGT-GTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTT-GCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGAT
EST: gi|29673041|gb|CB669316.1|CB669316
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|88903949|gb|CI006182.1|CI006182
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|86530519|gb|CI170725.1|CI170725
EST:     TGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: TGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|29660677|gb|CB656952.1|CB656952
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|29686154|gb|CB682429.1|CB682429
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|58585673|gb|CF983981.1|CF983981
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|29625315|gb|CB630326.1|CB630326
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCGTTAGTTTTGAG                         GTTTCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|29671055|gb|CB667330.1|CB667330
EST:     ACATTGCCCAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACT
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACT
EST: gi|29641911|gb|CB646918.1|CB646918
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|428295|gb|D24443.1|D24443
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|88397733|gb|CI684672.1|CI684672
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTT
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTT
EST: gi|29639161|gb|CB644170.1|CB644170
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|29688489|gb|CB684764.1|CB684764
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGAT
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGAT
EST: gi|86413644|gb|CI019229.1|CI019229
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTCTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|29645225|gb|CB650232.1|CB650232
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|29614166|gb|CB619179.1|CB619179
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|2798534|gb|AA751828.1|AA751828
EST:     TGGTGGTCTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: TGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|29614914|gb|CB619927.1|CB619927
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|29613257|gb|CB618270.1|CB618270
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|88998108|gb|CI037993.1|CI037993
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
EST: gi|38475493|gb|CF959626.1|CF959626
EST:     ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG                         GTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA
genomic: ACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAGgtactttctt ... gtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacctgtggatataacaccacccatttaaatttctaaaataccttgtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGC
                               ttctaaa  putative branch site (score: 2)
                                         ccttgtct  putative PPT
                       atttaaatttctaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttcttctctttaattctcatctcacctgtggatataacaccacccatttaaatttctaaaataccttgtctgtgcagGTTGCTGGAGACTTTGATGCTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA