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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttaccctgcgccatctgatgcgagtaaatacgccactgtttttgttcttgtctcacacatttgctttgtttgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGA

Basic information

species Oryza sativa
transcript LOC_Os01g55500.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55500.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G437859_T04 (Zea mays), 3'ss of exon 12
gttggttaccctgcgccat--ctgatg-cgagtaaatacgccactgtttttgttcttgtctcacacatttgctttgtt-tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGA
|||||| | ||||   | |  ||||||  | |       |  |     |    |  || ||         |||||  | ||||| ||||| || |||||||| |||||| | ||||| |||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| || || || ||
gttggtcatcctgtttccttcctgatgatgtgctttggtgtaatgcaatgcaatgctgcctgggctgacggcttttctctgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA

upper sequence: LOC_Os01g55500.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA06G06840.1 (Glycine max), 3'ss of exon 11
gttggttaccctgcgccatctgatgc---gagtaaatacgccactgtttttgttcttgtctcacacatttgctttgtttgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGA
||  ||  | |     || ||   |    |  |||  | | |  || ||   |   | | |   |       ||| | | | || ||||  | |||||||| || ||||||||||| |||||||||||||| ||| | |||||||||||  | |||||  || | ||  | ||  | ||||| || ||
gtgagtatcaccatttcacctatggtttagtttaagcatgtctttgcttcc-tctatcttttttatgacaattttctct-atttgcagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTCTTGGTGTAGCCCTTTTCTTAGGTTTTTCTGTTCCTGA

upper sequence: LOC_Os01g55500.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA04G06750.1 (Glycine max), 3'ss of exon 11
gttggttaccctgcgccatctgatgc---gagtaaatacgccactgtttttgttcttgtctcacacatttgctttgtttgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGA
||  ||  | |  |  |  |||  |    |  |||| |   |  || ||    | |  | |  |  |   ||||  |||   || ||||  | |||||||| || ||||||||||| |||||||||||||| ||| | ||||||||||| || |||||  || | ||  | ||  | ||||| || ||
gtgagtatcaccacttctcctgtggtttagtttaaacatctctttgcttcctctatcttatttctaacaagcttatttt--tttgcagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTGTTGGTGTTGCCCTTTTCTTAGGTTTTTCTGTTCCTGA

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|58669485|gb|CK058171.1|CK058171
EST:     CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTG                         CGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
genomic: CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttacc ... tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
EST: gi|33793472|gb|CF322619.1|CF322619
EST:     CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTG                         CGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
genomic: CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttacc ... tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
EST: gi|25807066|gb|CA763027.1|CA763027
EST:     CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTG                         CGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
genomic: CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttacc ... tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
EST: gi|87026155|gb|CI256898.1|CI256898
EST:     CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTG                         CGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
genomic: CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttacc ... tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
EST: gi|58670557|gb|CK059243.1|CK059243
EST:     CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTG                         CGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
genomic: CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttacc ... tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatacgccactgtttttgttcttgtctcacacatttgctttgtttgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGA
                                      ctttgttt  CT-rich tract
             tttttgtt  TA-rich tract