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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC

Basic information

species Oryza sativa
transcript LOC_Os05g28180.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 15
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
                                                     | ||    |  || |||  |||| ||             |  |||| ||  ||||  ||       | |||  |||    | |   |  ||||| ||||| |||| ||| || ||||||||||||||| ||||||||||| |||||||||||||| |||||||| || || || || ||||| |||| ||| ||||||||||| |||||||| ||  
---------------------------------------------------aggcaacaccaccagcaaatggcataac------------cttttgcacttcagtttcttt-------attttgaaagatgatgttcctctttcaacctgttactttaaatcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 15
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
                                                                        | |||||   ||| || | | | | |        ||| || | |||   ||| ||  |  |||   ||  || ||  ||||        |||||| ||||||| ||||||||||| || || ||||| |||||| | ||  | || ||||| ||||||||||| |||||||| |||  ||| || |||||||| || |
------------------------------------------------------------------------gtatgacccttttttcaattgattac--------ttggttgtgaga---tttgtagtttgctaattttagttgaa--tgtt--------ttttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 16
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
                                                                                              ||   |     ||| |  || |  |  |  ||  |  | |   | ||  | | | |  |   ||   |||||| ||||||| ||||||||||| || || ||||| |||||| | ||  | || ||||| ||||||||||| |||||||| |||  ||| || |||||||| || |
----------------------------------------------------------------------------------------------gtatggcccttttttcaattgattacttggttgtgatatttgtagttgctaattttagtttattt--ttttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
                                                                                           || ||| ||  ||   ||| | ||  | |  | |      | |||  |||||    |  |  |   |   ||||  |||||||||||||| ||||| ||| | ||||||||||| |||||||| |||||||||||||| || || ||  ||||||||  | |||| || |||||||| |
------------------------------------------------------------------------------------------gtttgtggagactg-cctgcatgtattacatatgt------attattgtttctgttctaagaagacatttcttttgacagATTGGTCTGGCCATGTCACCACTGAGCAACAACTCTTTGTTTCTAGATTACCACCGGAACCCGTTTCCTGTGTTTTTCTTAAGAGGTCTCAATGTTTCTC

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 15
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatct--aattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
                                                                 ||||||||   ||      | | |  |||   |  |   ||  ||| || |   | | | | | | |  || | ||| | |      |||| || |         ||||||||||||| ||||| ||  | |||||||| ||||||||| | || || || ||||||||||| || ||||||||||  || ||||| ||||||||||
-----------------------------------------------------------------gtaaaaagggagatgatgctgttttgaatatatctacactgacttgattattccatagtatctgattggctgtgattgcat------gttggttac---------agATTGGTCTGGCTATGTCTCCTCTGAGCAACAATTCCTTGTTTTTGGACTATCATCGGAATCCTTTTCCTATGTTTTTCCTTCGGGGCCTCAATGTTTCCC

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 15
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
                      |   |||   ||  |  ||   | | |   ||   |||  |          ||    ||||  |||  || || |     |     | |      ||  | | |   |||| |     || |   | | |   | || ||||   ||||||||  |||| ||||| || ||||||||||||||| | || || || ||||| || ||||||||||| ||||| ||    ||||| || || || ||  
---------------------gtgtggcactcttcctctaagattat-tgcttgatctttactctccgtctctcagatgagatccatcatat-agggtgacataaccgggt----gaaagatatatctatcacga----ctcatatgtttctcattatcgattta--cagATTGGATTGGCCATGTCTCCTTTAAGCAACAACTCCCTTTTCCTAGACTACCATCGCAATCCTTTCCCCATGTTCTTTTCTCGAGGTCTCAACGTATCGT

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|33796571|gb|CF324153.1|CF324153
EST:     TCAACTTAAGGAAATCTCCTGTGCTTCAATATCTATACTATCTTGGCCAG                         ATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTAC
genomic: TCAACTTAAGGAAATCTCCTGTGCTTCAATATCTATACTATCTTGGCCAGgtaattcttc ... attttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTAC
EST: gi|27548799|gb|CA767547.2|CA767547
EST:     TCAACTTAAGGAAATCTCCCGTGCTTCAATATCTATACTATCTTGGCCAG                         ATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTAC
genomic: TCAACTTAAGGAAATCTCCTGTGCTTCAATATCTATACTATCTTGGCCAGgtaattcttc ... attttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
                                              ttttatc  CT-rich tract
                                        tttcaattttatca  TA-rich tract