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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcagtttgtcctatgcttatgttggcaattggcacctgtaatttgttgcactcctgctattttactttcaatataagagctgtttctgggccttacagATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGAT

Basic information

species Oryza sativa
transcript LOC_Os05g09550.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g09550.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G117388_T03 (Zea mays), 3'ss of exon 2
-ttgcagtttgtcctatgcttatgt-tggcaattggcacctgtaatttgttgcactcctgctattttactttcaatataagagctgtttctgggccttacagATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGAT--------------------------
   |||||  ||| | |  |||||  | | |  | | || |   |||| |||||||| |||        || |||| |            ||| |||| ||||||||||||||||| ||||| |||||||||||||     ||||| || || ||||| |||||||||||||||||                          
tcggcagtcagtcatgtaattatgccttggatcttgtacattacattttttgcactc-tgcgccacacattccaatgtttttaaaacga-tggaccttgcagATATGGAGGCTATTGACAAGTTTCTTTTTCCTGGCACCATTTTCCATGAAATTTGGTATTCGCCTTCTGATGATGTAGGTTAAAGTTTTGCTGACTACTG

upper sequence: LOC_Os05g09550.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G143817_T01 (Zea mays), 3'ss of exon 2
ttgcagtttgtcctatgcttatgttggcaattggcacctgtaatttgttgcactcctgctat-----tttactttcaatataagagctgtttctgggccttacagATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGAT
   |||| | || | | |||||| | | || | | |  |   || | |||||||| ||||       || | |||| |||||  |         ||  | | ||| |||||||| |||||||||| ||||| ||||||||    ||||| || |||||||| |||||||||||||||||
---cagtctatcatgtacttatgcttggaacttgtaaattacatgttttgcactcatgcttcatatcttcattttctatatattaaaaaaaa--ggagcctgcagGTATGGAGGATATTTACAAGTTTCTTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGAT

upper sequence: LOC_Os05g09550.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G117388_T01 (Zea mays), 3'ss of exon 2
-ttgcagtttgtcctatgcttatgt-tggcaattggcacctgtaatttgttgcactcctgctattttactttcaatataagagctgtttctgggccttacagATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGAT
   |||||  ||| | |  |||||  | | |  | | || |   |||| |||||||| |||        || |||| |            ||| |||| ||||||||||||||||| ||||| |||||||||||||     ||||| || || ||||| |||||||||||||||||
tcggcagtcagtcatgtaattatgccttggatcttgtacattacattttttgcactc-tgcgccacacattccaatgtttttaaaacga-tggaccttgcagATATGGAGGCTATTGACAAGTTTCTTTTTCCTGGCACCATTTTCCATGAAATTTGGTATTCGCCTTCTGATGAT

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|441056|gb|D23616.1|D23616
EST:     ATCCACCTTTTCTTGCCTTATACTATCCCTTTGTGTTCAAGAAATTTCAG                         ATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGCAAG
genomic: ATCCACCTTTTCTTGCCTTATACTATCCCTTTGTGTTCAAGAAATTTCAGgtcagcatat ... ggccttacagATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGCAAG
EST: gi|218492921|gb|FG948483.1|FG948483
EST:     ATCCACCTTTTCTTGCCTTATACTATCCCTTTGTGTTCAAGAAATTTCAG                         ATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGGCAAGTTTTCTATCAA
genomic: ATCCACCTTTTCTTGCCTTATACTATCCCTTTGTGTTCAAGAAATTTCAGgtcagcatat ... ggccttacagATATGGAGGCTATTTACAAGCTTCTTTTTCCT-GGGCAAGTTTTCTATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgcactcctgctattttactttcaatataagagctgtttctgggccttacagATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGAT
              tattttactttcaata  TA-rich tract