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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgcatcagtttattttacctcttcaattccatatccagtagaaaaaaattgttcgtgtgattacccagtctaaataaaccttgttcgtatccatgtaagGTGCCTTTTGAAGAAGTTCCAGATCTTGTTGCCAGCCGCCGAGTATTTCTTTCAAAAGGATATGCTTATGTTGCGATGAGTCAG

Basic information

species Oryza sativa
transcript LOC_Os07g22400.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G044317_T03 (Zea mays), 3'ss of exon 7
gtatttgcatcagtttattttacctcttcaattccatatccagtagaaaaaaattgttcgtgtgattacccagtctaaataaaccttgttcgtatccatgtaagGTGCCTTTTGAAGAAGTTCCAGATCTTGTTGCCAGCCGCCGAGTATTTCTTTCAAAAGGATATGCTTATGTTGCGATGAGTCAG-------------
|||| | ||   |  | ||||| ||||| | | || | ||||        ||||  |  |||  |  |   | || || |||| | | ||   |||||  |||||| ||||| ||||||||||| |||||||||||  |||| || ||||||||||||||||| ||||||||||| || ||||| |||             
gtatgtacacttgcatgttttagctcttta-tcccttttccat-------aaatcttctgtgcaaaaattaattccaagtaaaacatattgtaatccaattaagGTACCTTTCGAAGAAGTTCCTGATCTTGTTGCTGGCCGTCGGGTATTTCTTTCAAAAGGCTATGCTTATGTGGCCATGAGCCAGGTTTGCCGTTAAC

upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G130351_T01 (Zea mays), 3'ss of exon 7
gtatttgcatcagtttattttacctcttcaattccatatccagtagaaaaaaattgttcgtgtgattacccagtctaaataaaccttgttcgtatccatgtaagGTGCCTTTTGAAGAAGTTCCAGATCTTGTTGCCAGCCGCCGAGTATTTCTTTCAAAAGGATATGCTTATGTTGCGATGAGTCAG
||||   ||     || ||||| || || | | || | |||| |   |     |  |  |||  |  |   | || || |||| | | ||   |||||  |||||| ||||||||| ||||||| |||||||||||||||||||| ||||||||||||||||| ||||||||||| ||||||| ||||
gtatggacac----ttgttttagctattta-tcccttttccatttatatcttttgttctgtgcaaaaattaattccaagtaaatcatattgtaatccaattaagGTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTTTCAAAAGGCTATGCTTATGTGGCGATGAATCAG

upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G044317_T02 (Zea mays), 3'ss of exon 7
gtatttgcatcagtttattttacctcttcaattccatatccagtagaaaaaaattgttcgtgtgattacccagtctaaataaaccttgttcgtatccatgtaagGTGCCTTTTGAAGAAGTTCCAGATCTTGTTGCCAGCCGCCGAGTATTTCTTTCAAAAGGATATGCTTATGTTGCGATGAGTCAG
|||| | ||   |  | ||||| ||||| | | || | ||||        ||||  |  |||  |  |   | || || |||| | | ||   |||||  |||||| ||||| ||||||||||| |||||||||||  |||| || ||||||||||||||||| ||||||||||| || ||||| |||
gtatgtacacttgcatgttttagctcttta-tcccttttccat-------aaatcttctgtgcaaaaattaattccaagtaaaacatattgtaatccaattaagGTACCTTTCGAAGAAGTTCCTGATCTTGTTGCTGGCCGTCGGGTATTTCTTTCAAAAGGCTATGCTTATGTGGCCATGAGCCAG

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|58665435|gb|CK054121.1|CK054121
EST:     AGCTGTTGAATCTGTGTTCTTCAAG                         GTGCCTTTTGAAGAAGTTCCAGATCTTGTTGCCAGCCGCCGAGTATTTCTT
genomic: AGCTGTTGAATCTGTGTTCTTCAAGgtatttgcat ... tccatgtaagGTGCCTTTTGAAGAAGTTCCAGATCTTGTTGCCAGCCGCCGAGTATTTCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattgttcgtgtgattacccagtctaaataaaccttgttcgtatccatgtaagGTGCCTTTTGAAGAAGTTCCAGATCTTGTTGCCAGCCGCCGAGTATTTCTTTCAAAAGGATATGCTTATGTTGCGATGAGTCAG
                       gtctaaa  putative branch site (score: 3)
                        tctaaataaa  TA-rich tract