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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgcttccttgctctcgcctgaaaaagattatccctttttttttgccttagctttttgcggaggtgttctggttttaggttctcgtgtttgtgctagtagctcgaatctacttactgtaggcaatctaagagagctgtttaatcgaattgtgtttactttttgccttggcgcagGGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATTCTCCCATCACGATCTTCTCGTCGCGAGTGAATGATGGTATCTGTG

Basic information

species Oryza sativa
transcript LOC_Os01g16970.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16970.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 2
--gttgcttccttgctctcgcctgaaaaagattatccctttttttttgccttagctttttgcggaggtgtt-ctggttttaggttctcgtg---tttgtgctagtagctcgaatctacttactgtaggcaatctaagagagctgtttaatcgaattgtgtttactttttgccttg-gcgcagGGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATTCTCCCATCACGATCTTCTCGTCGCGAGTGAATGATGGTATCTGTG
    |||| | ||   || ||||||||             ||| | |    | |  |  || ||| | ||| || || |||  ||         || |     ||   |   || |   |    |  |  |||     | | |  ||  |   || |  |  | | |    ||||   ||||||||||| || ||||| |||| ||| ||||||||| ||||||| || ||  ||||  |||||||||||||||| ||||||||||| || || ||||
gtactgct-cattctccttgcctgaaagga----------tttctctattctgggctactgtggacgcgttgctagtcttaaattgcgagagatttaggatctgtcatttagatttttgtgtgttgtgacatcactatgtgtttgtttgttatatagc-tgaattatgactcttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG

upper sequence: LOC_Os01g16970.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 2
--gttgcttccttgctctcgcctgaaaaagattatccctttttttttgccttagctttttgcggaggtgt-tctggttttaggttctcgtgtttgtgctagtagctcgaatctacttactgtaggcaatctaagagagctgtttaatcgaattgtgtttactttttgccttggcgcagGGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATTCTCCCATCACGATCTTCTCGTCGCGAGTGAATGATGGTATCTGTG
    ||| || ||   ||    ||||     || ||   | ||  | |  |    || |||     |||| | ||   | |  |     ||| | || | || | | |||        ||||||| |  |  | | || | | ||   ||||| ||  |     ||||      ||||||||||| |||||||| |||| ||||||||||||| ||||||| || ||  ||||  ||||||||||||| || ||||||||||| || || ||||
gtactgcctcattctccttatttgaatggatttctc---tattcatcgtgtagatttcttgtttttgtgtgtgtgtcatgacatcactatgtgtttgtt-gttgttggaa--------ctgtaggaatacagatacagttatgtagctgaattatgact----cttgc----atgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG
















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|88963686|gb|CI029464.1|CI029464
EST:     CAAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCAG                         GGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATT
genomic: CAAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCAGgttgcttcct ... cttggcgcagGGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATT
EST: gi|86423164|gb|CI060737.1|CI060737
EST:     CAAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCAG                         GGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATT
genomic: CAAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCAGgttgcttcct ... cttggcgcagGGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATT
EST: gi|88212111|gb|CI211751.1|CI211751
EST:     CAAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCAG                         GGACATCGGCGTGCCCGGAGGGGAGGTTCTACTGCCAGAATGCTGGGCATT
genomic: CAAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCAGgttgcttcct ... cttggcgcagGGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATT
EST: gi|88903472|gb|CI089010.1|CI089010
EST:     CAAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCAG                         GGAAATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATT
genomic: CAAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCAGgttgcttcct ... cttggcgcagGGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaatctaagagagctgtttaatcgaattgtgtttactttttgccttggcgcagGGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATTCTCCCATCACGATCTTCTCGTCGCGAGTGAATGATGGTATCTGTG
                 gtttaat  putative branch site (score: 4)
                                 tttactttttgcctt  putative PPT
                                 tttacttttt  TA-rich tract