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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttgtgtattctacctgctatgatccttcaaaaatcatgtgagatgctgtgtcacttattgatctcctttttagAGGCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCAAGATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTT

Basic information

species Oryza sativa
transcript LOC_Os01g16970.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16970.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 9
gtaggttgtgtattctacctgcta------tgatccttcaaaaatcatgtgagatgctgtgtcacttattgatct-cctttttagAGGCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCAAGATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTT
|||  |||| ||| |||  | |||        ||||||||  | | ||| | |   |  |  ||  |    || | ||  | |||||||||||| |||||| ||||||||||||||||| ||||||||||| || || |||||||||| |||||||| |||  | || ||||||||||| || ||
gtaatttgtatatgctagtttctaatcagccaatccttcatgagttatgagggg-acactaacatctgcatatttacccatctagAGGCTTCTCATGTTCGTAAGGAGTATGATGATGCTAGCTCAAAGCTTTCAAAAATTCAGTCTAAGATATCCAGTCTAGCTGAGAAGCTAAAACATGATTT

upper sequence: LOC_Os01g16970.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 9
gtaggttgtgtattctacctgcta------tgatccttcaaaaatcatgtgag-atgctgtgtcacttattgatc--tcctttttagAGGCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCAAGATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTT
|||  |||| |||  |   | |||       ||| |||||  | ||||| | | ||| | |  || |     |||     ||||||||||||||||||||||| ||||||||||| ||||| | ||||||||| || || |||||||||| |||||||| | |  | || ||||||||||| || ||
gtaatttgtatatagtggtttctaatcagtcgattcttcatgagtcatgagggtatgttataacattcgcatatcaactttttttagAGGCTTCTCGTGTTCGTAAGGAGTATGACGATGCCAACTCAAAGCTTTCAAAAATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTT
















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|38481101|gb|CF965190.1|CF965190
EST:     AATGTTTTACGAACATTCAACTTTTTCAAGACCCCTGTGGATTGTGTCTG                         AGGCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCC
genomic: AATGTTTTACGAACATTCAACTTTTTCAAGACCCCTGTGGATT-TATCTGgtaggttgtg ... tcctttttagAGGCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCC
EST: gi|88371457|gb|CI602635.1|CI602635
EST:     GAATGTTTTACGAACATTCAACTTTTTCAAGACCCCTGTGGATTTATCTG                         AGGCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCA
genomic: GAATGTTTTACGAACATTCAACTTTTTCAAGACCCCTGTGGATTTATCTGgtaggttgtg ... tcctttttagAGGCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCA
EST: gi|58589761|gb|CF988069.1|CF988069
EST:     GAATGTTTTACGAACATTCAACTTTTTCAAGACCCCTGTGGATTTATCTG                         AGGCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCA
genomic: GAATGTTTTACGAACATTCAACTTTTTCAAGACCCCTGTGGATTTATCTGgtaggttgtg ... tcctttttagAGGCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatccttcaaaaatcatgtgagatgctgtgtcacttattgatctcctttttagAGGCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCAAGATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTT
                                     tattgat  putative branch site (score: 3)
                                       ttgatctccttttt  CT-rich tract
       ttcaaaaat  TA-rich tract