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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttcttaacactgcttctaccctttgtttaataaagaaagaattgatagtttctttgaagattatccattttcttcactcaacattgttctattgg...

Basic information

species Oryza sativa
transcript LOC_Os02g15870.3
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15870.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G135816_T02 (Zea mays), 5'ss of exon 1
---------------GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttcttaacactgcttctaccctttgtttaataaagaaagaattgatagtttctttgaagattatccattttcttcactcaacattgttctattgg---
               |||||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||| || || ||||||||||||||| ||||| ||     | |||  |||   ||   ||  |  |  | |||| || ||    ||     ||   |    | |  | || | | ||| |    
CCTCCCTATGTTCAGGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctcttatcaacatctgtacatttttactac--aatgactatgtaatagattgttcacggacatgacaagattgatatttgagat-gatttatcgcatg

upper sequence: LOC_Os02g15870.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G135816_T01 (Zea mays), 5'ss of exon 6
GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttcttaacactgcttctaccctttgtttaataaagaaagaattgatagtttctttgaagattatccattttcttcactcaacattgttctattgg---
|||||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||| || || ||||||||||||||| ||||| ||     | |||  |||   ||   ||  |  |  | |||| || ||    ||     ||   |    | |  | || | | ||| |    
GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctcttatcaacatctgtacatttttactac--aatgactatgtaatagattgttcacggacatgacaagattgatatttgagat-gatttatcgcatg

upper sequence: LOC_Os02g15870.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA15G42290.1 (Glycine max), 5'ss of exon 6
GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttcttaacactgcttctaccctt-----tgtttaataaagaaagaattgatagtttctttgaagattatccattttcttcactcaacattgttctattgg
|| || ||||||||||||  ||||||||| |||||||| || || ||||| |||||||| || ||||| || |||||||| | ||||  ||  | | |  | ||| ||||  |     | |||  ||||  |   |||      ||   ||| |   |  || |   ||  ||| |  |           
GTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAGgt--ctgttcatctttccttttaccaataaaggtttttcctaaaatatttattttacaatttactgagg--cacacaatgatttgtctctatttcag--------

upper sequence: LOC_Os02g15870.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA08G16780.1 (Glycine max), 5'ss of exon 6
GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttcttaacactgcttctaccctttgtt-taataaagaaagaattgatagtttctttgaagattatccattttcttcactcaacattgttctattgg
|| || ||||||||||||  ||||||||| ||||| || || || ||||| |||||||| |||||||| || |||||||| | ||||  ||  | | |  | |||||||   |     |  |    |||  ||| ||   ||     | |   || || |   ||  ||| |  |           
GTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAGgt--ctgttcatctttccttctactaataaaggtttttcctaaaatattcat--cttacaatagggggatacaatactttgtctctatttcag--------

upper sequence: LOC_Os02g15870.3 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G31955.1 (Arabidopsis thaliana), 5'ss of exon 6
GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttcttaacactgcttct---accctttgtttaataa---agaaagaattgatagtttct-----ttgaagattatc--cattttcttcactcaaca------ttgttctattgg---------------------------------------------------------------
|| || || |||||||||  ||| ||||| ||| |||| |||||||| || || |||||||| ||||| ||||||||||||| || |  |   | |||     ||||   | || |||||   |||   | ||| | | |||| ||| |     || |||  | |   || ||  |      ||||      ||| |  ||||                                                                
GTGAAGAGAAAGAAAGCTGCACACGCTGGAATGCTTGACATTGCTAAAACAGCTAATAGACCAATGATACACATTGGTGGCTAAGCT--CCGGTGAACgtaagttctttaatccattgttatgtaactcataaaaattggatactttgtgtcgattcaagggttttgacacttgatctcagtaacaaagtctttgatgcattgatccgtttagtgtaactctgcgttttgattcacgtgactcatcgcgtcatatttctctttacag

upper sequence: LOC_Os02g15870.3 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv13s0156g00170.t01 (Vitis vinifera), 5'ss of exon 8
GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatc-ttcttaacactgctt------ctaccctttgtttaataaagaaagaattgatagtt---tctttgaagattatccattttcttcactcaacattgttctattgg
|| || ||||||||||||   |||||||| |||||||| ||||| ||||| |||||||| || ||||| || |||||||||| |||| |  ||||   | |    |       |  |||   |  | ||||  |   ||  | |  |   |  || |||     || | |||||  | |  | ||          
GTCAAGAGGAAGAAAGCTTCTCATGCTGGAATGTTTGACATTGCAAAGACCGCAAATAGGCCCATGATACATATTGGTGGCTAAGgtttggttctctcctccaactagaaacttgtcctgcatccattaaatgagatatgtaaaactacattcttaaagggctgccttgttcttttccc--ctttaa--------

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|29664100|gb|CB660375.1|CB660375
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|29687345|gb|CB683620.1|CB683620
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|88540819|gb|CI468892.1|CI468892
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|29686873|gb|CB683148.1|CB683148
EST:     TGATATTGCTAAGACGGAAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGATTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|86597930|gb|CI276716.1|CI276716
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|25806204|gb|CA762165.1|CA762165
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|86493550|gb|CI136183.1|CI136183
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|88529807|gb|CI458153.1|CI458153
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|88483054|gb|CI420325.1|CI420325
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|29674321|gb|CB670596.1|CB670596
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|29631794|gb|CB636803.1|CB636803
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|86859612|gb|CI299827.1|CI299827
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|29675364|gb|CB671639.1|CB671639
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
EST: gi|88514136|gb|CI441642.1|CI441642
EST:     TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG                         ATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA
genomic: TGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttctt ... cttgtttcagATCAGTTTTACCAGCTGAAAGTACCTTGGCTCCTCCATACGATGACTGCGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttcttaacactgcttctaccctttgtttaataaagaaagaattgatagtttctttgaagattatccattttcttcactcaacattgttctattgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG