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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGGGCAAGCTCCTGCAAGACAAGCTGCTTTAGGTGCAGGGATACCAAACACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttcatgaggcagcctttctataaattctgttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcag

Basic information

species Oryza sativa
transcript LOC_Os09g07830.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 4
TTGGGGCAAGCTCCTGCAAGACAAGCTGCTTTAGGTGCAGGGATACCAAACACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttca-tgaggcagcctttc--tataaattctgttca--------agaaattatat-ttacctgatcatgggcttgtttttatttcctttctgcag
|||||||||||||||||||| ||||||||| | ||||| |||||||||||| | |||||||||| | | ||||||||||| || |||||||||||||||||||  | |  | |    | | || ||  | |  | |||| |||        |||| | | |  |||||||| ||||  ||||||||  |||||| | |||||
TTGGGGCAAGCTCCTGCAAGGCAAGCTGCTCTGGGTGCCGGGATACCAAACTCTGTTGTTTGCACCACTGTTAACAAAGTCTGTGCATCTGGCATGAAAGgtttgaatcgaatttatctgtctgtccttgtgtactctgctcagagttcacagaagtgagagattacctgaccatgctcttgttttcctttcctatatgcag

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 4
TTGGGGCAAGCTCCTGCAAGACAAGCTGCTTTAGGTGCAGGGATACCAAACACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgtta-----cagttcatgaggcagcctttctataaatt---------ctgttcaagaaattatatttacctgat-catgggcttgtttttatttcctttctgcag----------------------
||||| |||||||||||||| ||||| ||| | |||||||||||||||||||| |||||||||| | | ||||||||||| |||||||||||||||||||||        | |||||    |    ||| ||||| |          |||||||     || ||   |  |||    |     ||| | | | || | |   ||                       
TTGGGACAAGCTCCTGCAAGGCAAGCCGCTCTGGGTGCAGGGATACCAAACACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagctaattcatctatccatgtttgtataattgatctgcttgctgttcattgttttttacacatgtgaagtgttcaggtgtgtgtgtatcatctgaccaattactctctgcacactctgcag

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA14G00760.1 (Glycine max), 5'ss of exon 4
TTGGGGCAAGCTCCTGCAAGACAAGCTGCTTTAGGTGCAGGGATACCAAACACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttcatga-ggcagcctttctataaattctgttcaaga---aattatatttacctgatcatgggcttgtttttatttccttt-ctgcag
|||||||||||||||||||||||||||||| | || ||||| ||| | ||  ||||| | ||||   | |||||||||||||| ||||| || |||||||||    ||| || |    | |  ||||||   ||   ||  |     | ||| |  ||    |  | |   ||    || ||    ||  |||||
TTGGGGCAAGCTCCTGCAAGACAAGCTGCTCTTGGAGCAGGAATATCCAATTCAGTTATCTGCACTACCGTTAACAAAGTTTGTGCATCAGGAATGAAAGgtgt--gtttataataaaaacaattctatttgtttctttgtatttttatttaaaaatatagaaaaaggatattaaccttgttctggttattgcag

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA02G47860.2 (Glycine max), 5'ss of exon 4
TTGGGGCAAGCTCCTGCAAGACAAGCTGCTTTAGGTGCAGGGATACCAAACACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagt-tcatgaggcagcct--------ttctataaattctgttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcag
|||||||||||||||||||||||||||||| | || ||||| ||| | ||  ||||  | || |   | |||||||||||||| ||||| || ||||||||||    | | || |       |        |||| |  ||| |||| || |||| |||   |   |||  |   |||||| |  ||       |||||
TTGGGGCAAGCTCCTGCAAGACAAGCTGCTCTTGGAGCAGGAATATCCAATTCAGTAATCTGTACTACTGTTAACAAAGTTTGTGCATCAGGAATGAAAGgtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaat-ataggaaaaggatattaaacttgttctggtta-----ttgcag

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G48230.2 (Arabidopsis thaliana), 5'ss of exon 4
TTGGGGCAAGCTCCTGCAAGACAAGCTGCTTTAGGTGCAGGGATACCAAACACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttcatgaggcagc--ctttctataaattctgttcaagaaattatatttacctgatcatgggcttgtt-tttatttcct--ttctgcag
||||| |||||||||||  | |||||||||||||||||||| || || ||| | ||| | || |   |||||||||| ||||| ||||| |||||||||||| | |  |  ||   ||    |  |||  |  || |   |     |||  ||     |||  |||   || |  ||| |||  |  || | |||
TTGGGTCAAGCTCCTGCTCGTCAAGCTGCTTTAGGTGCAGGAATCCCTAACTCTGTTATCTGTACTACAGTTAACAAGGTTTGTGCATCAGGCATGAAAGgtgagaactt-tggaacatttgcgctctgcattttttagacttttgatttgatgcttttgacaatgtttttctggtttgtttggtggtttttcag

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 4
TTGGGGCAAGCTCCTGCAAGACAAGCTGCTTTAGGTGCAGGGATACCAAACACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagt---tcatgaggcagcctttctataaattctgttcaagaaattatatttacctg----atcatgggcttgtttttat-ttcctttctgcag
|| || || |||||||| ||||||||||| ||||||||||| ||||| ||  |||| || || | | |  | ||||||||||| ||||| || |||||||||  || |   |||| ||  |     ||| |   |  |   | | || | | | | |  ||    |||||||  || |||| ||  |  |   |||||
TTAGGACAGGCTCCTGCTAGACAAGCTGCATTAGGTGCAGGAATACCTAATTCAGTGGTCTGTACCACCATCAACAAAGTTTGTGCATCAGGAATGAAAGgtgccactctatcatcagaaacagcatcttttcctctttccccaaaactgacactaaagtgtaatatcatgg--ttcttttaatgctggtaattgcag

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|58685561|gb|CK074248.1|CK074248
EST:     CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAG                         CGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
genomic: CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttc ... ctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
EST: gi|29640957|gb|CB645964.1|CB645964
EST:     CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAG                         CGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
genomic: CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttc ... ctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
EST: gi|88387760|gb|CI585463.1|CI585463
EST:     CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAG                         CGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
genomic: CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttc ... ctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
EST: gi|88300828|gb|CI589820.1|CI589820
EST:     ACAGTTGTTTGCAGCCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAG                         CGACAATGTTTGCAGCAC
genomic: ACAGTTGTTTGCAGC-GCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttc ... ctttctgcagCGACAATGTTTGCAGCAC
EST: gi|58683479|gb|CK072166.1|CK072166
EST:     CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAG                         CGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
genomic: CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttc ... ctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG