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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctggttctgttctattattgggagactctacaatatactagcaccatagcaccaatagactatctatacgtatcgttttttgaagacttttgatctattgtgatgaatcaaccttatctccacttatccagGGATTTGAGGCTGCTGTTGCAGCTGGTGCAAAAGAAGTTGCAGTTTTCGCATCTGCCTCTGAATCCTTTTCTAAGTCAAACCTTAATTGTACCATCAAGG

Basic information

species Oryza sativa
transcript LOC_Os12g04020.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtctggttctgttctattattgggagactctacaatatactagcaccatagcaccaatagactatctatacgtatcgttttttgaagacttttgatctattgtgatgaatcaaccttatctccacttatc-cagGGATTTGAGGCTGCTGTTGCAGCTGGTGCAAAAGAAGTTGCAGTTTTCGCATCTGCCTCTGAATCCTTTTCTAAGTCAAACCTTAATTGTACCATCAAGG
                                             || |  || |   | | | |      | |      |  ||   |  | || ||      ||||| | |     || || || |||  |   |||||||||| || ||| ||||||||||||| || ||||||||  | || || || || ||||| |||||||| ||||||||| | |||||||  ||  | |
------------------------------------------gtgagta--attgtttccagaaaaaggggaaaaaccatgagttcaaagcaattctgtctgtatgtgagggaatt-tctcatatcaactacttgtagGGATTTGAAGCAGCTATTGCAGCTGGTGCTAAGGAAGTTGCCATCTTTGCTTCAGCTTCTGAGTCCTTTTCAAAGTCAAACATCAATTGTAGTATTGAAG
















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|86848655|gb|CI293960.1|CI293960
EST:     TTAAGCATGTGCCAGATGTGCGGTTTCCAGTGTTAACTCCTAACCTCAGA                         GGATTTGAGGCTGCTGTTGCAGCTGGTGCAAAAGAAGTTGCAGTTTTCGCA
genomic: TTAAGCATGTGCCAGATGTGCGGTTTCCAGTGTTAACTCCTAACCTCAGAgtatgtctgg ... acttatccagGGATTTGAGGCTGCTGTTGCAGCTGGTGCAAAAGAAGTTGCAGTTTTCGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgaagacttttgatctattgtgatgaatcaaccttatctccacttatccagGGATTTGAGGCTGCTGTTGCAGCTGGTGCAAAAGAAGTTGCAGTTTTCGCATCTGCCTCTGAATCCTTTTCTAAGTCAAACCTTAATTGTACCATCAAGG
           ttttgat  putative branch site (score: 4)
                                   ccttatctccactt  putative PPT
           ttttgat  TA-rich tract