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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcag

Basic information

species Oryza sativa
transcript LOC_Os12g27520.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G063792_T06 (Zea mays), 5'ss of exon 7
GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcag
||| ||||||||||||||| |||||||| ||||||||||||||||| || |||||||| |||||||||||||  ||||    |  || | ||  | |   ||   |  |  | ||||   | |||||||| || | |   ||||
GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaatggg----accttggcttcatttggcat-gtacaagtaccaggggatctgagttaccaaggttgt-gcag

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G063792_T01 (Zea mays), 5'ss of exon 4
-----------------------------------GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcag
                                   ||| ||||||||||||||| |||||||| ||||||||||||||||| || |||||||| |||||||||||||  ||||    |  || | ||  | |   ||   |  |  | ||||   | |||||||| || | |   ||||
TGGTGATATTTTATGATTGTGTGGATCTTGTTCAGGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaatggg----accttggcttcatttggcat-gtacaagtaccaggggatctgagttaccaaggttgt-gcag

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G179308_T03 (Zea mays), 5'ss of exon 8
GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcag
||||||||||||||||||| |||||||| ||||||||||||||||| || |||||||| ||||||||||||| ||| |        |||||||| ||| |      ||||   |||    | |||||||| || | | | ||||
GACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttattgtgc------cttggtttg-attttgcatgtacaagtacagaggatctgagttaccaaggtt-ctgcag

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 7
-----------------------------------GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgtt--gttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttt------tgagttacgaaagc-taccgcag
                                   ||||||| ||||| || || |||||||| |||||||| || |||||  |||||||| |||||||||||||||  | |   |  |||  |   |    |   |||     || |     |||| |      | | ||  |||    ||   |||
GCAAGCTAAAGTTGATTTTGGCAATGATGTTTTAGGACTTGGCTGGAGCTATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacag

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA04G36360.1 (Glycine max), 5'ss of exon 8
GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgtt--gttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgag-ttacgaaag-ctaccgcag
||||||| ||||| || || ||||||||||||||||| || |||||| |||||||  ||||||| ||| |||  | |   ||  ||| ||  |  | | | |    ||         |  |   | || ||| |     |||  ||||
GACTTGGGTGGAGCTATCCATGTGATATATGGAGTGTGGGCTGTATATTGGTTGAATTATGCACTgtaagtttggctctctg-gatactttttaggcaattttatccagttttgtttgtttaaatcagcttatgggcttctattgcag

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA05G02740.1 (Glycine max), 5'ss of exon 8
GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttg-------ttgggtgcaatatttggtttgtattc-----tatcacaacaacagcaggatttt-tgagttacgaaagc-taccgcag
||||||| ||||| || || ||||||||||||||||| || |||||| |||||||  ||||||| |||||||        |      |  |||         |||      | ||| | ||      | ||| | | | | | |||    ||   |||
GACTTGGCTGGAGCTATCCATGTGATATATGGAGTGTGGGATGTATATTGGTTGAATTATGCACAgtatgtttggctctttcaaaacctttatacaaagcacatttatccatctcatatcatagattgtattctataattcatgaatttgtattacag

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA06G18530.1 (Glycine max), 5'ss of exon 8
GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgtt--gttgggtgca-atatttggtttgtattctatcacaacaacagcaggatttttgag-ttacgaaag-ctaccgcag
||||||| ||||| || || ||||||||||||||||| |||||||||||||||||  ||||||| ||| |||  | |   || | |  ||||   |  ||  |||| ||      |  |  |   | || ||| ||    |||  ||||
GACTTGGGTGGAGCTATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACTgtaagtttggctctctggatacttttgaggttaatattatc-cagtttttgttgtttaaatcagcttatgagtttctattgcag

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA17G13440.2 (Glycine max), 5'ss of exon 8
GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgtt--gttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttt------tgagttacgaaagc-taccgcag
||||||| ||||| || || |||||||| |||||||| || |||||  |||||||| |||||||||||||||  | |   |  |||  |   |    |   |||     || |     |||| |      | | ||  |||    ||   |||
GACTTGGCTGGAGCTATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacag

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 5'ss of exon 9
GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttg---ttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagc-taccgcag-------------------------
| |||||||||||||| || ||||| || ||||| |||||||||||| |||| || |||||  ||||||| |     |   || | ||||   |     ||  |||| |      |  ||   |    || | |||  | ||  |||                          
GGCTTGGATGGAGTTATCCATGTGACATGTGGAGCGTTGGTTGTATATTGGTGGAACTATGTTCGgtatgcttaatctctctgtagtatt-aatgatctttgcatcaaatggctggatggtaatacatgtcatgaagtcctaatgcaaaacatgtggctgcttcctgttgcag

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 9
GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagca--ggatttttgagttacgaaagctaccgcag------------
| |||||||||||||| || |||||||||||||||||||| |||||  |||| ||| ||||||||||| |||  |   |  ||| |    |   | || | ||       | |||  ||| |  |||| |    | || ||                 
GGCTTGGATGGAGTTATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttattaattaaat-tgcaatgcatgttgtctctttttgtcggcattggaatgatgaggttatgatgcaacatttattcattacacag

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|58030560|gb|CX728103.1|CX728103
EST:     GTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: GTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|86250790|gb|CI007653.1|CI007653
EST:     GTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACG                         GGAGAAGCATTTTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: GTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|29632958|gb|CB637967.1|CB637967
EST:     ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|86421246|gb|CI057235.1|CI057235
EST:     AGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: AGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|29670716|gb|CB666991.1|CB666991
EST:     GGTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: GGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|88841022|gb|CI000984.1|CI000984
EST:     ACTGGTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: ACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|86416061|gb|CI030072.1|CI030072
EST:     TATGGAGTGTTGGTTGTATACTGNTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: TATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|88958327|gb|CI095846.1|CI095846
EST:     GAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: GAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|88845676|gb|CI008673.1|CI008673
EST:     ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTTGAGCATCTTGCTATGATG
genomic: ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
EST: gi|29675908|gb|CB672183.1|CB672183
EST:     ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG
genomic: ACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgtt ... gctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATG