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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtccagatttgctgtgacctatcctaggttgttcttttttgggacggatggagtacttctgaagcgttcgtccttatagttctgtttcattgtttcagGTTGCAAGCCATGAAACTTTTGGTACTTTGGGTGCAATTGTGAAACGGCGCACTGGCAACAAGCAGGTTGGTTTCCTCACTAACCATCATGTCGCGGTTG

Basic information

species Oryza sativa
transcript LOC_Os04g52479.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G033724_T02 (Zea mays), 3'ss of exon 3
-ttgtccagatttgctg-tgacctatcctaggttgttcttttttgggacggatggagtacttctgaagcgttcgtccttata-gttctgtttcattgtttcagGTTGCAAGCCATGAAACTTTTGGTACTTTGGGTGCAATTGTGAAACGGCGCACTGGCAACAAGCAGGTTGGTTTCCTCACTAACCATCATGTCGCGGTTG
 |  |  | |   |||| | |    ||   |  || |    | |      || ||  | ||| ||||   ||  |||||  |  |  ||||||| | || ||||||||||| || || |||||||| |||||||| || ||||| |||||| | ||||||||||||| ||| |||||| |||| ||||  ||||| || ||||
ttacttaaaagcagctggtaaggcttctcggaatgatgcaatgtcaa---gaaggcatgcttttgaaaactttctccttgcacatcttgtttcactcttccagGTTGCAAGTCAGGACACTTTTGGAACTTTGGGCGCCATTGTAAAACGGAGAACTGGCAACAAGCTGGTAGGTTTCGTCACCAACCGACATGTTGCTGTTG

upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G102346_T01 (Zea mays), 3'ss of exon 3
-ttgtccagatttgctgtgacctatcctaggttgttcttttttgggacggatggagtacttctgaagcgttcgtccttatagttctgtttcattgtttcagGTTGCAAGCCATGAAACTTTTGGTACTTTGGGTGCAATTGTGAAACGGCGCACTGGCAACAAGCAGGTTGGTTTCCTCACTAACCATCATGTCGCGGTTG
 ||    | |   ||||  |    | || ||   |  |    ||  | | |  |  | ||| || |   ||  |||||| | |  ||||||| | |||||||||||||| || || |||||||| |||||||| || ||||| |||||||| ||||||||||||||| | ||||||||||| ||||  ||||| || ||||
attacttaaaaaagctgataagacttcttggaaatggtgcaatgtcaagca-agcatgcttttggaatctttctccttacactcttgtttcactctttcagGTTGCAAGTCAGGACACTTTTGGAACTTTGGGCGCCATTGTAAAACGGCGAACTGGCAACAAGCAGATAGGTTTCCTCACCAACCGACATGTTGCTGTTG
















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|58659200|gb|CK047880.1|CK047880
EST:     TTGTTGATAAGTTATGTGGCAGTGACGAATGTATTGGTTCAGGCTCTCAG                         GTTGCAAGCCATGAAACTTTTGGTACTTTGGGTGCAATTGTGAAACGGCGC
genomic: TTGTTGATAAGTTATGTGGCAGTGACGAATGTATTGGTTCAGGCTCTCAGgtactcgtgt ... attgtttcagGTTGCAAGCCATGAAACTTTTGGTACTTTGGGTGCAATTGTGAAACGGCGC
EST: gi|58605986|gb|CK034019.1|CK034019
EST:     TTGTTGATAAGTTATGTGGCAGTGACGAATGTATTGGTTCAGGCTCTCAG                         GTTGCAAGCCATGAAACTTTTGGTACTTTGGGTGCAATTGTGAAACGGCGC
genomic: TTGTTGATAAGTTATGTGGCAGTGACGAATGTATTGGTTCAGGCTCTCAGgtactcgtgt ... attgtttcagGTTGCAAGCCATGAAACTTTTGGTACTTTGGGTGCAATTGTGAAACGGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggatggagtacttctgaagcgttcgtccttatagttctgtttcattgtttcagGTTGCAAGCCATGAAACTTTTGGTACTTTGGGTGCAATTGTGAAACGGCGCACTGGCAACAAGCAGGTTGGTTTCCTCACTAACCATCATGTCGCGGTTG
                                         tttcatt  CT-rich tract
                              ttatagtt  TA-rich tract