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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattctactccttcctctctctccccaatccgtctgattctcgctatctgtgaacgttttggtctaatttccccccctttttttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC

Basic information

species Oryza sativa
transcript LOC_Os12g44000.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g44000.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 1
gtattattctactccttcctctctctccccaatccgtc---tgattctcgctatctgtgaa---cgttttggtctaatttccccccc--tttttttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC
|||     || | ||| || |  ||      || || |    |     |||     |||     ||| | | | |   |  |    |  | | |   | | |    | |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||  ||||||| ||  | || |||||| ||| ||||||||||||||| |
gtaccgggct-cacctcccccagtccattggattcgccgctcggggagcgccccgggtgtttttcgtctcgatttggctaacaattcgatctatcccttttctcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAACTCGCCGAGTGGCAACTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTAC

upper sequence: LOC_Os12g44000.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 1
gtat-tattctactccttcctctctctccccaatc--cgtctgattctcgct--atctgtgaacgttttggtctaatttccccccctttt-------tttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC
|||  |  ||| ||||  ||     |  |  | ||  || | |     |||     | ||     ||  |  |  |||   |   |  ||       |   | | |    | ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||   | ||| |||  |||||||||| ||| |||||||||||||||||
gtacgtgctctcctcccccccaatccatcggattcgccgcccggggagcgcccaggcggttggttttccgtcccgattcggctaacaattcgatcgatcccttttcgcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGGCAGCAAAACCCCCCCGTCGGGTTCAAGCACAAGGTCTCCGATAACCTCC

upper sequence: LOC_Os12g44000.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------------------gtattattctactccttcctctctctccccaatccgtctgattctcg------ctatctgtgaacgttttggtctaatttccccccctttttttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC
                                                       ||  | || | ||      | |  |||         || |   || |       |   ||  ||    ||  ||| || |       || |  |||||          |||| || ||||| ||||||||||||||||| ||||| ||||| |  |||||||||||||  || ||| |||| |||||  |||  ||| |||| || || |
gtctgttcctctctcctgatgtctagccctaatttttgtcatgtctttgtgatttgtggtgtttt-ctaggaaattttgctctggtgattttcaggcacttggcaagattgcttgcaaattgatttttctcatctggttgtattgtgatttgtggtgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGGCAGGTCAATCCACCCGCCGGTTTCAAACACAAAGTCACCGACAATCTTC

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|163920049|gb|EG709843.1|EG709843
EST:     CATCATCATCAATCAACGCCATGACGAGCTCCTCATCTCCTTCCCGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGG
genomic: CATCATCATCAATCAACGCCATGACGAGCTCCTCATCTCCTTCCCGAAAGgtattattct ... ctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGG
EST: gi|8857593|gb|AU094911.1|AU094911
EST:     ATCATCAATCAACGCCATGACGAGCTCCTCATCTCCTTCCCGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGG
genomic: ATCATCAATCAACGCCATGACGAGCTCCTCATCTCCTTCCCGAAAGgtattattct ... ctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGG
EST: gi|58593809|gb|CF992117.1|CF992117
EST:     CATCATCATCAATCAACGCCATGACGAGCGGGGGATCTCCTTCCCGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGG
genomic: CATCATCATCAATCAACGCCATGACGAGCTCCTCATCTCCTTCCCGAAAGgtattattct ... ctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGG
EST: gi|5851049|gb|AU078221.1|AU078221
EST:     ATCATCAATCAACGCCATGACGAGCTCCTCATCTCCTTTCCCGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGG
genomic: ATCATCAATCAACGCCATGACGAGCTCCTCATCTCC-TTCCCGAAAGgtattattct ... ctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgtgaacgttttggtctaatttccccccctttttttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC
                gtctaat  putative branch site (score: 3)
                 tctaatttccccccct  CT-rich tract
                                tttttttttgta  TA-rich tract