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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_Os09g24650.4
intron # 6
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 56 (downstream exon)
Score: 27

TTAATGGCTCTGTTATTATTGAGACATGCGCTGACTCTAACTGATGAAGATGACGATGATACTTCTGCAATGTTTTCAgtgagtgaaa ... tacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgttgtacatcatcattagaagttggtattgatgctctattacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG
                               tattgat  putative branch site (score: 27)
                                       ctctatt  CT-rich tract
                                          tattactt  TA-rich tract