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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttaccagtttcactgtcaagtattctattacacataacattgtgttttgactgatcgctgaaacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCA

Basic information

species Oryza sativa
transcript LOC_Os12g40880.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40880.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G035338_T01 (Zea mays), 3'ss of exon 7
gtgt-taccagtttcactgtcaagtattctattacacataacattgtgttttgactgatcgctgaaacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCA
|| | |||||||  | |||  |   |   | ||  | |   |||  | |||   ||||||    ||||||||| || || |||||||||||||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||||| ||
gtatctaccagtgcc-ctgcaatacaaattcttgaatactgcatgctatttaatctgatcctctaaacatcttggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA

upper sequence: LOC_Os12g40880.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G31550.1 (Glycine max), 3'ss of exon 6
------------------gtgttaccagtttcactgt-caagtattctattacacataac-attgtgttttgactgatcgctgaaacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAA-ATGACATATTTGTAAA-GCCGCA------------------------
                  | |     ||  ||  ||       ||      |  | || |   | |||| ||    ||    |  | || ||| | | ||||| ||||||||||  ||||||||||| ||||||||||| || |||||| | |  ||    | |  | |       |                        
agctggggtgcacagaaagagcagtaagcatccgtgcattgacatgacggaattcttatctgctttgttctgttgcattttggtgaaattttttttt-cagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTAAGATGTGGTCCACTCATCAGCATTTTATAAATTTCTGACACAAATTATGAT

upper sequence: LOC_Os12g40880.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G34390.1 (Glycine max), 3'ss of exon 7
---------------------gtgttaccagtttcactgtcaagtattctattacacata-acattgtgttttgactgatcgctgaaacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCA
                       || | ||  |   |  | |  |  |  | | |  ||   | ||||  | |  |   | | |||||||  ||   || ||||| ||||||||||  ||||||||||| ||||||||||| || ||||||||| |||| || ||||| || |  ||
agctgggatgcacagaaagaacagtaagcatctgtgcactgacatgatggagttcttatctgctttgttctgttgcattttggtgaaacaaatt---cttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA

upper sequence: LOC_Os12g40880.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G03030.1 (Arabidopsis thaliana), 3'ss of exon 7
--gtgttaccagtttcactgtcaagtattctattaca-cataacattgtg---ttttgactgatcgctgaaacatctttg---tctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCA
           ||| ||   ||  ||   |  |   | | | |  ||| |    ||  | |   | ||||    | ||     | | ||||| ||||||||||  ||||||||||||||||| ||||| |||||||||||| |||| || ||||| |  |  ||
gtaaagaggtggttacaaaatcttgttgaccttaggatcttgaagttgggagacttacaatagactctgattagttttcaagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCA

upper sequence: LOC_Os12g40880.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0141g00310.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------------------------------------------------------gtgttaccagtttcactgtcaagtattctattacacataa-cattgtgttttgactgatcgctga--aacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCA
                                                                                      | || | |   | |     ||  | | | |   |||| |  | | |  |   | ||     |||  | ||   || |||| |||| ||||||||||| ||||| ||||||||||||||||| |||||||||||| |||| |||||| | |  |  ||
gtgagtagctattgatgttggctgcgtcattttattcttgttgagactttagaactggttggtgcataaacttatctttttttttttttttcaaaaataaaaaataaaaaatttgtggtacatgagtacttttctcatattgcattatgatgagcaatattttctgtagGGGTCAGTTTATGCACCATCGTTTGATCATGGTGTTGGAGATCCAGTTGAAGATGATATATTTATCAGCCTCCA

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|33683185|gb|CF311424.1|CF311424
EST:     CCATCCCGGTTTTTGAAATGCCTACAGACCCTGAGAGAAGAG                         GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAA
genomic: CCATCCCGGTTTTTGAAATGCCTACAGACCCTGAGAGAAGAGgtgttaccag ... ttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAA
EST: gi|38481157|gb|CF965246.1|CF965246
EST:     CGGTTTTTGAAATGCCTACAGACCCTGAGAGAAGAG                         GGTTCAGTTTAGTGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGA
genomic: CGGTTTTTGAAATGCCTACAGACCCTGAGAGAAGAGgtgttaccag ... ttgtctgcagGGTTCAGTTTA-TGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattacacataacattgtgttttgactgatcgctgaaacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCA
                         gactgat  putative branch site (score: 3)
                                          tctttgtct  putative PPT
          ataacatt  TA-rich tract