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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcatgctcctaactttctaatttatttatgctattgatttttcttttggatctatctcatcgtgtaaatatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG

Basic information

species Oryza sativa
transcript LOC_Os08g45240.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g45240.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G016106_T01 (Zea mays), 3'ss of exon 1
---------gtatgtcatgctcctaactttctaatttatttatg--ctattgatttttcttttggatctatctcatcgtgtaaatatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG
          ||  | ||      |  || ||   |  || |||    |    | |||  ||||  | | ||||| |   |||  |||| |||| ||||| ||  | || ||||||||||| ||||| ||||| ||||| || || || || ||||| || |||||||| || ||||||||||||||||||
gtagctaacataacttattaattcagtttcctttgtgtttaatggatcacccttatttggtttgcttgtgtctcaactcctaacaatttgcagACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTATCCAAAGCATTCTCACGGTTTCCATCCTTCAACATGGCAAGG

upper sequence: LOC_Os08g45240.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 1
------------gtatgtcatgctcctaactttctaatttatttatgctattgattt--ttcttttggatctatctcatcgtgtaaatatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG
             ||    ||    | |  || ||  ||  ||||||||  |   ||  ||| |||   | | | ||| |   |||  |||| |||| ||||| ||  | || ||||||||||| ||||| ||||| ||||| || || ||||| ||||| ||||||||||| || ||||||||||||||||||
gtagcagccaacataacctattaatccagtttcct--ttgttttatgcttctcccttatttcatttccttgtgtttcaactcttaacaatttgcagACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG

upper sequence: LOC_Os08g45240.4 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 3'ss of exon 2
--------------gtatgtcatgctcctaactttctaat---ttatttatgc-tattgatttttcttttggatctatctcatcgtgtaaatatt-tacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG
                 | | |||||    |  |||  |    |  ||| ||| |    ||  |||| |     ||  |  | | |||    ||  | ||||||| ||||| ||||||||||| ||||| |||||||| || ||||| || || || |||||||| |||||||| || || |||||||| ||||| |  
ttcattgacattattcctatgatgctgtatatgttcctacccctcctttttgcctggatatgcttctctcatgcctggcagaac-tgttggcatcctgcagATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAATGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCTAAA

upper sequence: LOC_Os08g45240.4 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 3'ss of exon 2
--------------gtatgtcatgctcctaactttctaatttatttatgctattg----atttttcttttggatctatctcatcgtgtaaatatt-tacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG
               | | | |||||  | |  |||  |  | |   |  |        ||  |||| |      |     | | |||    ||| | ||||||| ||||| ||||||||||| ||||| |||||||| || || || || || || |||||||| |||||||| || || |||||||| ||||| || 
ttcattcacactgtttctatgatgctatttatgttcctacctctcctttttgcctggatatgcttctctcatgcttggaagaac-tgttggcattctgcagATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAACGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCCAGA

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|33684393|gb|CF312632.1|CF312632
EST:     CGCCGCCGGCCAATTCTGGGAGGATCCCACCCTCACCGACTGGCCCGACA                         ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
EST: gi|58599191|gb|CK009719.1|CK009719
EST:     CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACA                         ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
EST: gi|88368173|gb|CI575055.1|CI575055
EST:     CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGAGTGGCCCGACA                         ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
EST: gi|88742490|gb|CI765998.1|CI765998
EST:     CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCAACGACTGGCCCGACA                         ATGACTATCGCTTATTTGGTGGAGAT
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGAT
EST: gi|38475426|gb|CF959559.1|CF959559
EST:     CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACA                         ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
EST: gi|86829522|gb|CI286725.1|CI286725
EST:     CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACA                         ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttatgctattgatttttcttttggatctatctcatcgtgtaaatatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG
         tattgat  putative branch site (score: 3)
         tattgatttttctttt  TA-rich tract