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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactatataatgaagggaggtttttatgttgtactgcag

Basic information

species Oryza sativa
transcript LOC_Os03g16980.5
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 6
ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactatataatgaagggaggtttttatgttgtactgcag
|||||||||||||| ||||| || |||||||||||||| || ||||| |||||||||||||||||||  |||||  |   ||||| ||| | |  |||   ||  || ||| |||  |   | | |  | |    ||||| ||| | |||||
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttcatc--atgct-attgattcttccaccgc--ctcatgtgaaaaactcagttacagaa----tttattttgaattgcag

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 12
ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactatataatgaagggaggtttttatgttgtactgcag
|||||||||||||| ||||| || |||||||||||||| |||||||| |||||||||||||||||||  |||||  |   ||||  ||| | |  |||   ||  || ||| |||  |   | | |  | |  | |||   ||| | |||||
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcagtgttcatc--atgcc-attgattcttccagcgc--ctcatgtgaaaaactcagttactgaatttattt---ttgaattgcag

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 5
ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactatataatgaagggaggtttttatgttgtactgcag
|||||||||||||| ||||| || |||||||||||||| |||||||| |||||||||||||||||||   ||||  |   ||||  ||| | |  |||   ||  || ||| |||  |   ||| |  | |  | |||   ||| | |||||
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttcatc--atgcc-attgattcttccagcgc--ctcatgtgaaaaactcaattacagaatttattt---ttgaattgcag

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G157772_T02 (Zea mays), 5'ss of exon 3
ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactatataatgaagggaggtttttatgttgtactgcag
|||||||||||||| ||||| || |||||||||||||| |||||||| ||||||||| |||||||||  |||||  |   ||||  ||| | |  ||    ||  || ||| |||  |   | | |  | |  | |||   ||| | |||||
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTAGAGCTAGgtcagtgttcatc--atgcc-attgattcttctagcgc--ctcatgtgaaaaactcagttacagaatttattt---ttgaattgcag

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G382038_T01 (Zea mays), 5'ss of exon 7
ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactatataatgaagggaggtttttatgttgtactgcag
|||||||||||||| ||||| || |||||||||||||| |||||||| |||||||||||||||||||  |||||  |   ||||  ||| | |  ||| | ||  || ||| |||  |   | | |  | |  | |||   ||| | |||||
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcagtgttcatc--atgcc-attgattcttccaacgc--ctcatgtgaaaaactcagttactgaatttattt---ttgaattgcag

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA12G06990.1 (Glycine max), 5'ss of exon 6
ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtg--ttttttt-----aatgctgatt--aacttgtcctatgcaacttatgagaactatata-------atgaagggaggtttttatgttgtactgcag
|| || |||||||| || || || || |||||||||||||| ||||||||| ||||||| || ||||||||   || | ||     |||| | |||  | ||| |   || ||  |  |    | | | |         | |      ||| |||| || |   ||||
ACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAGgttggtaaattgtctttggaaaatgataatttcagcttctatcat-cagttggtctttattctttttcttcttgttagtcttagttcttattttat-tggcag

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 6
ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactat----ataatgaagggaggtttttatgttgtactgcag
|| || |||||||| || || || ||| |||||||| | || |||||||||||||||||||| |||||||    |  ||   ||   |    ||||   ||     |||| |  |  ||     |  |      ||  | | ||  ||  || |||
ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaactactt---gcccgtctctttgttgcattttgtttataaacataattctggtcttacttatagcatgtaataatg-gctacag

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|58659240|gb|CK047920.1|CK047920
EST:     GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG                         GATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
genomic: GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgttt ... tgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
EST: gi|58590735|gb|CF989043.1|CF989043
EST:     GTTATCGGAACCCTGAA-ATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG                         GATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
genomic: GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgttt ... tgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
EST: gi|30229035|gb|CB966926.1|CB966926
EST:     GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG                         GATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
genomic: GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgttt ... tgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
EST: gi|428184|gb|D24332.1|D24332
EST:     GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG                         GATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGNGCACCC
genomic: GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgttt ... tgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
EST: gi|30228342|gb|CB966233.1|CB966233
EST:     GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG                         GATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
genomic: GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgttt ... tgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
EST: gi|313080404|gb|HO213412.1|HO213412
EST:     GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG                         GATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
genomic: GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgttt ... tgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
EST: gi|33380802|gb|CF196145.1|CF196145
EST:     GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG                         GATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
genomic: GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgttt ... tgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
EST: gi|58656016|gb|CK044696.1|CK044696
EST:     GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG                         GATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
genomic: GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgttt ... tgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
EST: gi|58672962|gb|CK061648.1|CK061648
EST:     GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG                         GATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
genomic: GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgttt ... tgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
EST: gi|58659773|gb|CK048453.1|CK048453
EST:     GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG                         GATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC
genomic: GTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgttt ... tgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactatataatgaagggaggtttttatgttgtactgcag

- - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT