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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatcaaaagctaccattgtttgttaatttcacattattttatctctcatcaggtgaactattttgcttctcaagcttaatgtttctaaatacatggtttctgtatgactaggattatccattacctgttttttttagGATTATGGACACCGTGTGAGATTGGCAACCCATGCAAACTTTAAGGAGTTCGTTCTAACGGCTGGTCTGGAGTTTTTCCCTCTTGGCGGTGATCCAAAAA

Basic information

species Oryza sativa
transcript LOC_Os04g04254.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g04254.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G007721_T01 (Zea mays), 3'ss of exon 1
gttagatcaaaagctaccattgtttgttaatttcacattattttatctctcatcaggtgaactattttgcttctcaagcttaatgtttctaaatacatggtttctgtatgactaggattatccattacc-tgttttttttagGATTATGGACACCGTGTGAGATTGGCAACCCATGCAAACTTTAAGGAGTTCGTTCTAACGGCTGGTCTGGAGTTTTTCCCTCTTGGCGGTGATCCAAAAA
                         |||| | |  | | | | |||     ||||    |  | | |||    |  || |||   ||          | |      |   |  |   || ||  ||    |  || |  ||||| ||||| || |||||||||||||| || ||||| |||||||||||||| || ||||| ||||| ||||||||||| || ||||| || ||||| ||||
-------------------------gttagtctagcctaagtgtatt----atcaatccagttctcttgtaaattcaggttaggtttgtgcttcttgtagcagaaatgccagcatatttgtcgtttctgatccttgtcgtagGACTATGGGCATCGTGTGAGATTGGCCACTCATGCCAACTTTAAGGAGTTTGTACTAACAGCTGGCCTGGAGTTTTTTCCGCTTGGTGGAGATCCCAAAA
















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|29623072|gb|CB628083.1|CB628083
EST:     GCACAAGAGGTGATGTTCAGCCATTCATTGCTATAGGCAAACGCTTACAG                         GATTATGGACACCGTGTGAGATTGGCAACCCATGCAAACTTTAAGGAGTTC
genomic: GCACAAGAGGTGATGTTCAGCCATTCATTGCTATAGGCAAACGCTTACAGgttagatcaa ... ttttttttagGATTATGGACACCGTGTGAGATTGGCAACCCATGCAAACTTTAAGGAGTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaaatacatggtttctgtatgactaggattatccattacctgttttttttagGATTATGGACACCGTGTGAGATTGGCAACCCATGCAAACTTTAAGGAGTTCGTTCTAACGGCTGGTCTGGAGTTTTTCCCTCTTGGCGGTGATCCAAAAA
 ttctaaa  putative branch site (score: 2)
                                      ttacctgtttttttt  putative PPT
                                           tgtttttttta  TA-rich tract