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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatatgtcactgtttatccgcattgaataataggttatgctgatatatacattttctccttttgccacatgttagctgaattaaatctgtttagGTTTCTCTGGGGTACTTCATCGCTGACCTTGCTATGTTATCCTGGGCTTATCCTTCCCTTGGCGGAATGGAGTAT

Basic information

species Oryza sativa
transcript LOC_Os01g56230.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56230.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G825226_T04 (Zea mays), 3'ss of exon 5
---------gtaacatatgtcactgtt-tatccgcattgaataataggttatgctgatatatacattttctccttttgccacatgttagctgaatt-aaatctgtttagGTTTCTCTGGGGTACTTCATCGCTGACCTTGCTATGTTATCCTGGGCTTATCCTTCCCTTGGCGGAATGGAGTAT
         |  ||  | | |  |||| | |   ||   || || ||| | ||          || |   |  | ||||| ||| ||  ||||||| |||| |||  |||||||| | ||||| |||||| |||||||||||||| |||  |||||||||||||| ||||| ||||||||||||
aactttcttgggactaaaggctttgttgttttttcaagaaaaaaaaggctttgt---------cagtcgttgttattgcctcatatttactgaatttaaatttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTATCCTTCTCTTGGTGGAATGGAGTAT
















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|29660431|gb|CB656706.1|CB656706
EST:     ATGGCCCAGTAACAGTTCGGAGTTCAAACCTCTCCAATTTTACACTGGGG                         GTTTCTCTGGGGTACTTCATCGCTGACCTTGCTATGTTATCCTGGGCTTAT
genomic: ATGGCCCAGTAACAGTTCGGAGTTCAAACCTCTCCAATTTTACACTGGGGgtaacatatg ... atctgtttagGTTTCTCTGGGGTACTTCATCGCTGACCTTGCTATGTTATCCTGGGCTTAT
EST: gi|300215972|gb|HO088598.1|HO088598
EST:     ATGGCCCAGTAACAGTTCGGAGTTCAAACCTCTCCAATTTTACACTGGGG                         GTTTCTCTGGGGTACTTCATCGCTGACCTTGCTATGTTATCCTGGGCTTAT
genomic: ATGGCCCAGTAACAGTTCGGAGTTCAAACCTCTCCAATTTTACACTGGGGgtaacatatg ... atctgtttagGTTTCTCTGGGGTACTTCATCGCTGACCTTGCTATGTTATCCTGGGCTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatatatacattttctccttttgccacatgttagctgaattaaatctgtttagGTTTCTCTGGGGTACTTCATCGCTGACCTTGCTATGTTATCCTGGGCTTATCCTTCCCTTGGCGGAATGGAGTAT
 tgctgat  putative branch site (score: 3)
                                              tctgttt  putative PPT
                                       aattaaatctgttta  TA-rich tract