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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgaaagaatgctctttaactatctggttatcattgttttgttgtacatcatcattagaagttggtattgatgctctattacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG

Basic information

species Oryza sativa
transcript LOC_Os09g24650.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24650.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 8
gtgagtgaaagaatgctctttaactatctggttatcattgttttgttgtacatcatcattagaagttggtattgatgctctattacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG
|| ||||||| ||   |||| ||  || |    ||  |||      |||| |  | || | |    |  | || ||| | |   | |||| |||||||||| |||||||||||||| || ||||| || ||||| || |||||||||||| | |||||||||||||||||||||||| |||||
gtaagtgaaataaccatcttgaaaaatat----attgttggc--aatgtataataacacttg----tttttttaatggtttgcaa-ttgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG

upper sequence: LOC_Os09g24650.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 5
gtgagtgaaag-aatgctctttaactatctggttatcattgt-tttgttgtacatcatcattagaagttgg-------tattgatgctctattacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG
||||||||    | | |  |||   ||  |||||| ||  || |||||  | |||    ||     || ||       || | |  |      |||   ||||||||  |  | ||||||||||| |||||  |||| | |||||| |||||||||||| | ||||| ||||| |||||  ||||  |||| 
gtgagtgactttagttcattttggataagtggttaacacagtatttgtattgcattcaaatacattgtcggcctaacctaattacacaaccaaactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA

upper sequence: LOC_Os09g24650.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
gtgagtgaaagaatgctctttaactatctggttatcattgttttgttgta-catcatcattagaagt-tggtattgatgctcta--ttacttgac---------agCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG
|| ||   |   | |||  ||   | | |  || || ||  ||| ||||  ||    ||||  |  | |   |   |  | | |  ||   |||          ||||| | ||  | || |||||||||||||| || |||| |||||| |||||||||||  | |||||  | |||||||| |||||| |||||
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaaccacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG

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|38471428|gb|CF955559.1|CF955559
EST:     CGCTGACTCTAACTGATGAAGATGACGATAATACTTCTGCAATGTTTTCA                         CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
genomic: CGCTGACTCTAACTGATGAAGATGACGATGATACTTCTGCAATGTTTTCAgtgagtgaaa ... tacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
EST: gi|86831029|gb|CI295513.1|CI295513
EST:     GACGATGATACTTCTGCAATGTTTTCA                         CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
genomic: GACGATGATACTTCTGCAATGTTTTCAgtgagtgaaa ... tacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
EST: gi|29626393|gb|CB631404.1|CB631404
EST:     CGCTGACTCTAACTGATGAAGATGACGATGATACTTCTGCAATGTTTTCA                         CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
genomic: CGCTGACTCTAACTGATGAAGATGACGATGATACTTCTGCAATGTTTTCAgtgagtgaaa ... tacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
EST: gi|29626392|gb|CB631403.1|CB631403
EST:     CGCTGACTCTAACTGATGAAGATGACGATGATACTTCTGCAATGTTTTCA                         CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
genomic: CGCTGACTCTAACTGATGAAGATGACGATGATACTTCTGCAATGTTTTCAgtgagtgaaa ... tacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
EST: gi|163925422|gb|EG711559.1|EG711559
EST:     CGCTGACTCTAACTGATGAAGATGACGATGATACTTCTGCAATGTTTTCA                         CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
genomic: CGCTGACTCTAACTGATGAAGATGACGATGATACTTCTGCAATGTTTTCAgtgagtgaaa ... tacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
EST: gi|218496676|gb|FG944369.1|FG944369
EST:     CGCTGACTCTAACTGATGAAGATGACGATGATACTTCTGCAATGTTTTCA                         CTTTTTATATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
genomic: CGCTGACTCTAACTGATGAAGATGACGATGATACTTCTGCAATGTTTTCAgtgagtgaaa ... tacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
EST: gi|88223285|gb|CI223134.1|CI223134
EST:     CAATGTTTTCA                         CTTTTTCTAGTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT
genomic: CAATGTTTTCAgtgagtgaaa ... tacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgttgtacatcatcattagaagttggtattgatgctctattacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG
                               tattgat  putative branch site (score: 3)
                                       ctctatt  CT-rich tract
                                          tattactt  TA-rich tract