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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtattactgattcttaactaacataacatttgtaaattactgcttgcaaatttgtacagcaattgatgttctattttgtctttcttttgattatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 48
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 48
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 31
gtagtattactgattcttaactaacataacatttgtaaattactgcttgcaaatttgtacagcaattgatgttctattttgtctttctttt----gattatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG
  |  ||| |  |  || | | |      |  |   ||||    ||||| | |||  | |||   || |  | ||||||| |  |||| ||    |  ||||   ||||||||||||||||||| ||||||||||| || ||||| ||||||||||| |||||  | || ||||| || |||||||| || || ||||| |||
--atcatttcccagcctcagccactgggtctctgtcaaat----gcttg-agattaatgcagtgtttcacatgctatttttttgttctcttttgtggctatgaacagCAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 48
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 49
gtagtattactgattcttaactaacataacatttgtaa-attactgcttgcaaatttgtacagcaattg---atgttctattttgtctttcttttgattatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG
   |||   ||| |  || | |     |   |||||      | |||||  | |||  |||||  |||    ||| | | |||  ||| | || ||  |||||  ||||||||||||||||| | |||||||||||||||||||| ||||||||||| ||||| || |||||||| || |||||||| || || ||||| |||
---gtacagctgttcttttagtcgttcatgctttgtggtgcaaatgctta-agattaatacagtgatttcacatgctatttttgttctcttttgtggctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 48
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 51
gtagtattactgattcttaactaacataacatttgtaaattactgcttgcaaatttgtacagcaattgatgttctattttgtctttcttttgattatgg----gtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG
 |  | ||| |  |  |    |  | ||| |||  ||  ||||||    ||||||   |  || ||| |   |  | | |||   | |  | |  ||      | ||||||||||||||||| |||| ||||| ||||| || || ||||| || ||||||||||| |||||||| || ||||| |||||| ||||||| |||
-tgtttttatttgtgttattttgccctaatattc-tattttactg----caaattca-aaggctatttacccttgactctgttcctatccttaaaattaaattgcagCAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 48
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 50
gtagtattactgattct-taactaacataacatttgtaaattactgcttgcaaatttgtacagcaattgatgttctattttgtctttcttttgattatgggt---agCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG
 |  | ||| |  |  | | | | || ||| |||  ||  |||||||     || ||  |  || |||     |  | | ||| | | |  | |   |   |   |||||||||| |||||| |||| ||||| ||||| || || ||||| || ||||||||||| |||||||| || || || |||||| ||||||| |||
ttgtttttatttgtgttattatttac-taatattc-tattttactgc-----aacttcaaaggctatttgcccttgactctgtttctgtcctcaaattaaatttcagCAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGTATTACCCAATTGTACCCAAAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 48
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 20
----------------------------------------------------------------gtagtattactgattcttaactaacataacatttgtaaattactgcttgcaaatttgtacagcaattgatgtt--ctattttgtctttcttttgattatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG
                                                                ||  |||   |   | | || |    ||    | ||  ||      |  ||  ||          ||||   |   | | |||| ||| |||  | |    | |||| || ||||||||| |||||||||||||||||||||| |||||||| || |||||| | |||||||| ||||| || || |||||||||||||||
gtactataatgtttttattttcttcatttattgttttgaagatcatatttgaggttgttcatgggtgttatgttttgctttcaatttctttagtggt-gtgtatattcaatctcattttctcctgttgcttgacaatgattctcttgtttttatttcaactt---gcagCAGGAACTTGCTGCTATATTCAAGAAAATTGGTGACAAGCAAACATGCACTATTGGTTTATATGAACTATACCGTATTACTCAACTGTACCCCAAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 48
lower sequence: PP1S66_170V6.1 (Physcomitrella patens), 3'ss of exon 49
---------------------------gtagtattactg-----attcttaactaacataacatttgtaaattactgcttgcaa-atttgtaca---gcaattgatgttctattttgtctttcttttgattatgg----gtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG
                               | || |||     |  |||||  ||  |   | ||  || |        ||   ||||| | |   |  |||    |  |    ||  ||| | |||||   |     |||||||||||||||||| || |||||||| || ||||| || || || || |||||||||||||| || || || || || || || || || ||  ||
gtaagttatgcacttttcttctttacaactttttttctgtgtgtacgcttaatcaatctggtaattagaagtcttcttcagcttcatttgcatatatgtgattacaatctttggctgagtttttgttgatctcgttgttgtagCAAGAGCTTGCTGCAGTGTTCAAGAAGATCGGTGATAAGCAGACTTGCACAATTGGTCTTTACGAGCTTTATCGTATCACACAGCTTTATCCTCAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 48
lower sequence: PP1S131_18V6.1 (Physcomitrella patens), 3'ss of exon 49
--------------------gtagtattactgattcttaactaacataacatttgtaaa-ttactgcttgcaa-atttgtacagcaattgatgttctattt---tgtctttcttttgatta----tgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG
                     | ||||||   |  || || |  |||    |  ||| | ||| || || ||  |  |        |||  ||   |  ||   ||| | |  |||||       | || |||||||||||||||| || || ||||| || ||||| || || || |||||||||||||| ||||| || || || || ||||| || || ||  ||
gtaagttttgcgctccttctatggtattat--acgctgaatt--catcgggtcagtagacttattgtttacagcaccttcgtgttcattactgcaatccttgactgtgtattctttgacctccacttggcagCAAGAGCTTGCTGCAGTGTTTAAGAAGATCGGTGATAAGCAGACTTGTACAATTGGTCTCTATGAGCTATATCGTATCACCCAGCTATATCCTCAG

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|58658439|gb|CK047119.1|CK047119
EST:     GGTCCAATAATCCAAACCCATCAACTCATTCAACTGATGCACAGTTGAAG                         CAAGAGCTTGCTGCTGTATTCAAGAAAATCGGTGACAAACAAACATGTACA
genomic: GGTCCAATAATCCAAACCCATCAACTCATTCAACTGACGCACAGTTGAAGgtagtattac ... ttatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
EST: gi|58601380|gb|CK011908.1|CK011908
EST:     GGTCCAATAATCCAAACCCATCAACTCATTCAACTGATGCACAGTTGAAG                         CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
genomic: GGTCCAATAATCCAAACCCATCAACTCATTCAACTGACGCACAGTTGAAGgtagtattac ... ttatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
EST: gi|58600986|gb|CK011514.1|CK011514
EST:     GTCCAATAATCCAAACCCATCAACTCATTCAACGTGATGCACAGTTGAAG                         CAAGAGCTTGCTGCTGTATCCAAGAAAATTGGTGACAAACAAACATGTACA
genomic: GTCCAATAATCCAAACCCATCAACTCATTCAAC-TGACGCACAGTTGAAGgtagtattac ... ttatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
EST: gi|29680245|gb|CB676520.1|CB676520
EST:     GGTCCAATAATCCAAACCCATCAACTCATTCAACTGACGCACAGTTGAAG                         CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
genomic: GGTCCAATAATCCAAACCCATCAACTCATTCAACTGACGCACAGTTGAAGgtagtattac ... ttatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
EST: gi|218497579|gb|FG955134.1|FG955134
EST:     GGTCCAATAATCCAAACCCATCAACTCATTCAACTGATGCACAGTTGAAG                         CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
genomic: GGTCCAATAATCCAAACCCATCAACTCATTCAACTGACGCACAGTTGAAGgtagtattac ... ttatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
EST: gi|88344329|gb|CI655723.1|CI655723
EST:     GGTCCAATAATCCAAACCCATCAACTCATTCAACTGACGCACAGTTGAAG                         CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
genomic: GGTCCAATAATCCAAACCCATCAACTCATTCAACTGACGCACAGTTGAAGgtagtattac ... ttatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
EST: gi|58677253|gb|CK065940.1|CK065940
EST:     GGTCCAATAATCCAAACCCATCAACTCATTCAACTGATGCACAGTTGAAG                         CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
genomic: GGTCCAATAATCCAAACCCATCAACTCATTCAACTGACGCACAGTTGAAGgtagtattac ... ttatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
EST: gi|58690696|gb|CK079383.1|CK079383
EST:     GGTCCAATAATCCAAACCCATCAACTCATTCAACTGATGCACAGTTGAAG                         CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA
genomic: GGTCCAATAATCCAAACCCATCAACTCATTCAACTGACGCACAGTTGAAGgtagtattac ... ttatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaatttgtacagcaattgatgttctattttgtctttcttttgattatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG
                                       ttttgat  putative branch site (score: 4)
                                 tctttcttttgatt  CT-rich tract
                                   tttcttttgattat  TA-rich tract