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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatgcttatccaattttattgaaaccatatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcattcag

Basic information

species Oryza sativa
transcript LOC_Os02g54340.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 4
GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatgcttatccaattttattgaaaccatatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcattcag
||||| |||||||| ||||| ||||| |||||||| |||||||| |||||||| || |||||||||||||| ||||| |||| |||||||  |   |||||  | |   |||  |    |        ||| |||  | |   || | || |  | |  || ||| | |||
GTGGCAAGGTGTACAAAGATCATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatgctcgtgtcatttttctcatctcatgccaccta-------gaatttgtgcagc---tttttatgccttgtaatgaatcctgcag

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 4
GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatgcttatccaattttattgaaaccatatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcattcag-------------
||||| || || || ||||| || || || ||| |||| ||||| ||||||||||| ||||| ||||||||||||||||||  |     || |   | | | ||       |  || |    |     || |  | ||     || |  |  |   |||||| |  ||||              
GTGGCAAGATGCACAAAGATAATTAGCCCCAATTCTGAGGATGCCAAATATGTGATAAATGTTAAACAAATTGCAAAGgtaagcttcaattttaagactctgtt-----tcttcctatagaaacttgtaaagcatggactttctttttctgtt-ccttttgttttgttcaaacgcaaaattttt
















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|58603359|gb|CK013887.1|CK013887
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|29684844|gb|CB681119.1|CB681119
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|58685776|gb|CK074463.1|CK074463
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|58602175|gb|CK012703.1|CK012703
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATCAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|58675342|gb|CK064029.1|CK064029
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|88574346|gb|CI666115.1|CI666115
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCCTCCA-CTGACATTGAGGAA
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTC-TCCAACTGACATTGAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatgcttatccaattttattgaaaccatatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG