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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA

Basic information

species Oryza sativa
transcript LOC_Os02g40830.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G064695_T03 (Zea mays), 3'ss of exon 7
gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA----------------------------------
             |||||||||        | ||   |||||    || ||   ||  || || |  |             |   | ||||||| ||||||| |||||||||||||| || |||||||| ||||| ||||||||||| ||||| ||||||||||| || ||||||||||| ||||| || ||||| || |                                  
-------------cttgcctctta------gctagtactttt----ttttggttatataatctcagcac-----------cagaaccaatacctgtacaggtcgctgctgccaaagcagatttgaactatattgGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTATAAAGTTGCATGGTGGTACGCCCGCCAATTTTCT

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------------------------------gaggatggcttgacttgcctctggagggatgttac----agcttttgttgttctgagaatggaaactgaagatatttatgagtttatctcta------atacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
                                                                     | |    ||||||| | | | |       || |    ||   |||    |  |  | |      |   | | | ||| |  | | | | |      |||||| ||||||| |||||||||||||| || |||||||| ||||| ||||||||||| ||||| ||||||||||| || ||||||||||| ||||| || ||||| || |
gtataaaattacctatctttccatttgttcattctctccttgtgtcaagttttcttctaatgtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggt-tatataatctcagcaccagaaccaatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 8
-gaggatggcttg-acttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
   |    | |||  ||||  | |  ||     ||| | | ||     ||||     |  |   |     ||    ||  | |  || | ||   |  ||||||| ||||||| || || || || || || |||||| | |||||||||||||||||||||||||| || ||||| || |||||||| |||||||| || |
catgatctgtttgtgcttgattattaag--cccttatatccttgaaccttctttctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 8
gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatgga--aactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
     ||  |   ||||  | |  ||     ||| | | ||   | ||||     |  |     ||    ||    |  || |  || | |    |  ||||||| ||||||| || || ||||| || || |||||| | ||||||||||| |||||||||||||| || ||||| || |||||||| |||||||| || |
ttatctgtttgtgcttgattattaag--cccttatatccttgaatcttctttttttttactgggtgtgtgtaacattatgtgtgccttttaactttgaacagGTGACTGCTGCAAAGGCAGACTTAAATTATATTGGGTTAGATGGAGAAATAGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 8
gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagttta-tctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
      | ||     |  |||| |       | |         ||||| ||  |||   |    | ||| || |   |  || | | |  |  ||  | ||||||||||||| |||| |||| |||||||||| ||  | |||||||| ||||| ||||||||||| ||||| |||||||| ||||| || ||||||||||
------gtctctgtctatctcttgta--tcatcaagaaagccattgttatgttaattcgat---aggatgttaaaaggaatagtgtgttgtgtctc-atagGTGGCTGCTGCTAAAGTTGACCTGAACTACATCGGTTTAGATGGAGAGATTGGTTGCATGGTGAATGGTGCTGGATTGGCCATGGCAACCATGGACATCA

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------------------------gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatg-gaaactgaaga----tatttatgagtttatctctaataccttt-----acagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
                                                    ||   | ||     |     |   |  |    | |  || |  |       | || |  ||||| ||||    ||| ||    | ||| | |  |  |  |     | ||||||||||||||||||| || ||||||||||| ||  | |||||||||||||| ||||||||||| ||||| || || ||||||||||| ||||| || |
gttgggttacttcttttaatttcttgaccctgttttatctgtgatgtaagtggaaagtagcacatgtacataccataaaggcaatccccctctcttcacaactacaaggtaaaactaaagaacaatatgtaatgttctatttgtggtttcactgtacaatagGTGGCTGCTGCCAAAGCAGATTTGAACTACATCGGCTTAGATGGAGAAATTGGTTGCATGGTGAATGGTGCTGGCTTAGCAATGGCTACCATGGATATAA

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
-------------------------------------gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatattt--atgagtttatctctaatacctttac---agGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
                                      |  ||   ||||  |||   | |    | |  | |   | || | |    | |||   || |      | ||  |||   ||  |  |       || |   |||| |||||||  || |  ||| |||| ||||| ||  | ||||| |||||||| ||||||||||| || || ||  | ||||||||||||||||| ||||
gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacga-agattatctgctttggaaacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ13492 (Selaginella moellendorffii), 3'ss of exon 8
gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
                                               | |||||       |   | |  || | |  || ||  ||  |      |||||| ||||||||    || || ||||||||||||||  | ||||| || ||||||||||||||||| || |||||| | || ||||| || ||||| ||||
----------------------------------------------gtttgagaccttgttc---atagtttcacgttttaatgcctgttcgaaaaacagGTCGCTGCTGCTGCCGCCGATTTGAACTACATTGGATTGGATGGCGAGATTGGCTGCATGGTGAATGGAGCAGGACTCGCGATGGCAACCATGGATATCA

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|58589675|gb|CF987983.1|CF987983
EST:     CAGGAAGATCCCAGAGAG                         GTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
genomic: CAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
EST: gi|218478127|gb|FG953382.1|FG953382
EST:     AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAG                         GTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
genomic: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
EST: gi|163921201|gb|EG714126.1|EG714126
EST:     AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAG                         GTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
genomic: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
EST: gi|163929534|gb|EG713477.1|EG713477
EST:     AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAG                         GTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
genomic: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
EST: gi|13420568|gb|AU174658.1|AU174658
EST:     AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAG                         GTGGCTGCTGCCAAAGCTGACTTGAACTAC
genomic: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
                                      ctctaat  putative branch site (score: 3)
                                            taccttt  CT-rich tract
                      atatttatgagtttat  TA-rich tract