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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagttctctcttctacaccattatttctcatctacaccaacttctgttgagtttgaactgctgtgaattgtactcaagttatcttctcatgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT

Basic information

species Oryza sativa
transcript LOC_Os02g12800.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 7
ttagttctctcttctacaccattatttctcatctaca--ccaacttctgttgagtttgaactgctgtg---aattgtactcaagttatcttctcatgtattg-cagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT
      |  |     || ||||||          | |       || || |  ||| | | |||| ||   || |  ||| || | | || | ||||||||  ||||||||||||| |||||||||||||| || ||||||||||||||||| |||||||| |||||||| |||||||| ||||| || ||||| |||||||||||
-----gcatttaaacaccccattaagcggttctcaaagttttgtttttgatctgttagtagtgctatgcacaagtcaactgaactcaactcc-catgtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACAGTGTCGTTTGTGACTATGAACAAGGT

upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G134582_T01 (Zea mays), 3'ss of exon 7
--ttagttctctcttctacaccattatttctcatctacaccaacttctgttgagtttgaactgctgtgaattgtactcaagttatcttctcatgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT
  || ||      || |      |||        |||        |||||      || | || |  |||    ||| || | |   |||||||||||  |||||||||||||||||| |||||||| || ||||||||||||||||| |||||||| ||||||||||||||||| ||||| || |||||||||||||||||
gtttggtatatctttttggtgttttaagcagttcctaagttttgatctgtcagtagtgcaatg-tacgaacca-actgaactcaaactctcatgtattttagGTTTCTGGGATATGTACGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGATGAGAACACAGTGTCGTTTGTGACCATGAACAAGGT

upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
----ttagttctctcttctacaccattatttctcatctacaccaacttctgttgagtttga-actgctgtgaattgtactcaagt-tatcttctcatgt------attgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT
     | ||  | |||||  |  | |  ||| ||| ||   | | |      | | || |  | ||   | ||||||  |  |   | |||  |  |||      | |||||| |||||||| |||||||||||||| || ||||| || |||||||| |||||||| ||||| ||||||||||  ||||| || || ||  | ||||||||
gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT

upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G57720.1 (Arabidopsis thaliana), 3'ss of exon 7
ttagttctctcttctacaccatt-atttctcatctaca--ccaacttctgttgagtttgaactgctgtgaattgtactcaagttatcttctcatgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT
||||     |  ||   |   || ||    ||| ||    |||   ||||   |||     ||  |  |     | |       || || |  |  |||||||| |||||||| ||||||||||| || || ||||| || |||||||| ||||| || ||||| ||||||||||  || ||||| || ||  | ||||||||
ttagaggggtactcactatggtttatgggacatgtatggcccagagtctga-aagtacattctattaagctcaatgccttga--atgtttttcttcattgcagGATTCTGGGACATGTATGACCCGGAGGGGTACTCACTATGGTTCTGTGACTATAAGTACAACGATGAGAACATGGTCTCCTTTGTTACACTCAACAAGGT

upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
ttagttctctcttctacaccattatttctcatctacaccaacttctgttgagtttgaactgctgtgaattgtactcaagttatcttc----tcatgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT
   |  || | |  | ||   |  | |      |        |||| |   || |     | |  |   ||      || ||  ||     |  | | | ||||| |||||||| ||||  ||| | |||||||||||  |||||||||| || ||||| |||||||| ||||||   ||  |||| ||||| ||||| || ||
---gcactttttagt-cattctagtctgcagagtcagagtgtttctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT

upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S132_188V6.1 (Physcomitrella patens), 3'ss of exon 6
ttagttctctcttctacaccatt-atttctcatctacac-caacttctgttgagtttgaactgctgtgaattgtactcaagttatc--ttctcatgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT
   ||| |    ||| |||  |  |||||  |  | | | | || |   |  | ||| || |  ||   |    | | |  ||     |  |    | |  ||||||||||||| ||||  ||  | |||||||||||  |||||||||| || ||||| ||||||||||| |||   ||  | || |||||||||||||||||
---gtttttgaatctgcactctggatttcgaaaatgccctctacgttcctgaaatttaaatttgtgccgacc-cattaatattgctgatgattgcttgtgacagGTTTCTGGGAGATGTTCGATGCTGAAGGTTACTCATTGTGGTTCTGTGATTACAAGTACAATGATGAAAACCAAGTTACGTTTGTGACCATGAACAAGGT

upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ14564 (Selaginella moellendorffii), 3'ss of exon 6
ttagttctctcttctacaccattatttctcatctacaccaacttctgttgagtttgaactgctgtgaattgtactcaagttatcttctcatgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT
                                    || || |  ||||    |||| |   ||  ||   | || |  ||     |  || | ||||||| |||||||| ||||||||||| || || |||||||||||||||||||||||||| ||||| ||||||||||| ||| | |||||||| |||||||||||
----------------------------------gtac-aagtggtgtttccattgatcgcttgaaaa---tgctgattttgatcccaaatct-ttgcagGATTCTGGGAGATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT

upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
ttagttctctcttctacaccattatttctcatctacaccaacttctgttgagtttgaactgctgtgaattgtactcaagttatcttctcatgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT
                                    || || |  ||||    |||| |   ||  |||  |  |   | | ||||| |     ||||||| |||||||| ||||||||||| || || |||||||||||||||||||||||||| ||||| ||||||||||| ||| | |||||||| |||||||||||
----------------------------------gtac-aagtggtgtttccattgatcgcttgaaaatgctgattctgatctcttccc-----ttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT

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|33687434|gb|CF315673.1|CF315673
EST:     AAAAACAAACTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT
genomic: AAAAACAAACTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... tgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT
EST: gi|5667501|gb|AU077470.1|AU077470
EST:     GAGGTTATACTCAAACAC-AAAAC-AACTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT
genomic: GAGGTTATACTCAAACACAAAAACAAACTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... tgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT
EST: gi|29678879|gb|CB675154.1|CB675154
EST:     GAGGTTATACTCAAACACAAAAACAAACTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT
genomic: GAGGTTATACTCAAACACAAAAACAAACTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... tgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT
EST: gi|38479113|gb|CF963246.1|CF963246
EST:     GAGGTTATACTCAAACACAAAAACAAACTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT
genomic: GAGGTTATACTCAAACACAAAAACAAACTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... tgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT
EST: gi|218482204|gb|FG951805.1|FG951805
EST:     GAGGTTATACTCAAACACAAAAACAAACTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT
genomic: GAGGTTATACTCAAACACAAAAACAAACTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... tgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT
EST: gi|89198471|gb|CI007531.1|CI007531
EST:     CAAACTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT
genomic: CAAACTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... tgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgagtttgaactgctgtgaattgtactcaagttatcttctcatgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT
                                     tcttctcat  CT-rich tract
                     aattgta  TA-rich tract