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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCTCTTCGGCGCTGTTCTTCAGCTACAACACAGCGCTCGGGCCGCCATACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAGgtttgttctttgaggcttcgaattaggtgctcttctgtttatccactgaatgatttcgtgaagcctagcttaatctcaattgtgtcgagtatgtaactgt...

Basic information

species Oryza sativa
transcript LOC_Os06g06410.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g06410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G174312_T02 (Zea mays), 5'ss of exon 3
GGTCTCTTCGGCGCTGTTCTTCAGCTACAACACAGCGCTCGGGCCGCCATACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAGgtttgttctttgaggcttcgaattaggtgctcttctgtttatccactgaatgatttcgtgaagcctagcttaatctcaattgtgtcgagtatgtaactgt-------
||| || |||||| ||||||||||||||||||||||  | |||||||| || ||||| ||||||||||| ||||||||||||||||| || ||||| |||||| ||  ||| |   ||   || || |||||| || |||  |   |  ||  |||  || | |  || || |   |     || | | |   | |||         
GGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtttaa---tt---atcagctgctctcctatttcactgatatatt-ttttatgcaacagaggttcaatacttgcatgcccactgcttcactcagttaata

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G017761_T01 (Zea mays), 5'ss of exon 3
GGTCTCTTCGGCGCTGTTCTTCAGCTACAACACAGCGCTCGGGCCGCCATACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAGgtttgttctttgaggcttcgaattaggtgctcttctgtttatccactgaatgatttcgtgaagcctagcttaatctcaattgtgtcgagtatgtaactgt-------
||| || |||||| ||||||||||||||||||||||  | |||||||| || ||||| ||||||||||| ||||||||||||||||| || ||||| |||||| ||  ||| |   ||   ||  | |||||| || |||  |   |  ||  |||  || | |  ||  | |   |     || | | |   | |||         
GGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtttaa---tt---atctgctgctctcctatttcactgatatatt-ttttatgcaacagagggtcaatacttgcatgcccactgcttcactcagttaata

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G016330_T02 (Zea mays), 5'ss of exon 3
GGTCTCTTCGGCGCTGTTCTTCAGCTACAACACAGCGCTCGGGCCGCCATACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAGgtttgttctttgaggcttcgaattaggtgctcttctgtttatccactgaatgatttcgtgaagcctagcttaatctcaattgtgtcgagtatgtaactgt------
||| || |||||| ||||||||||||||||||||||  | ||||| || || ||||| ||||||||||| ||||||||||||||||| || ||||| |||||||  || || |        ||  | |||||| || |||  |   |  ||  |||  || | |  || || |   |     || | | |   | |||        
GGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCACCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgtttagtcgtttaatt-----atctgctgctctcctatttcactgatatatt-ttttatgcaacagaggttcaatacttgcatgcccactgcttcactcagttaat

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G140689_T01 (Zea mays), 5'ss of exon 3
GGTCTCTTCGGCGCTGTTCTTCAGCTACAACACAGCGCTCGGGCCGCCATACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAGgtttgttctttgaggcttcgaattaggtgctcttctgtttatccactgaatgatttcgtgaagcctagcttaatctcaattgtgtcgagtatgtaactgt-------
||| || |||||| ||||||||||||||||||||||  | |||||||| || ||||| ||||||||||| ||||||||||||||||| || ||||| |||||| ||  ||| |   ||   ||  | |||||| || |||  |   |  ||  |||  || | |  || || |   |     || | | |   | |||         
GGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtttaa---tt---atctgctgctctcctatttcactgatatatt-ttttatgcaacagaggttcaatacttgcatgcccactgcttcactcagttaata

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA03G41500.1 (Glycine max), 5'ss of exon 2
GGTCTCTTCGGCGCTGTTCTTCA-GCTACAACACAGCGCTCGGGCCGCCATACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAGgtttgttctttgaggcttcgaattaggtgctcttctgtttatccactgaatgatttcgtgaagcctagcttaatctcaattgtgtcgagtatgtaactgt-------
    || ||||| || || ||     ||||| || ||  | || || || |||||  || | |||||||| |||||||||||||| ||||||||||| || ||  || |      |||| |   |   | || || | ||| |  |    || || | ||| |     | |    ||    |   ||   ||  |||           
-CATTCATCGGCACTTTTTTTTTCAATACAATACTGCATTGGGACCCCCTTACCGTATTTTGGTGGATACCAACTTCATCAATTTTTCCATCCAGAATAAAgtgagtgc------gctttgttgtgctttctattttttttttttataacat-atgttgtggacttgtggtagtacttgtgtccctcttataaataaacaaatgaact

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA19G44090.1 (Glycine max), 5'ss of exon 3
GGTC--TCTTCGGCGCTGTTCTTCAGCTACAACACAGCGCTCGGGCCGCCATACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAGgtt--tgttctttgaggcttcgaattaggtgctcttctgtttatccactgaatgatttcgtgaagcctagcttaatctcaattgtgtcgagtatgtaactgt-
 |||  || ||||| || || ||||  ||||| || ||  | || || || |||||  || | |||||||| |||||||||||||| ||||||||||| || ||   ||| |||||    || |  ||||| | | |  ||  |    | |    ||     |   | | |    |||||  |   | |  |     ||  ||  
-GTCATTCCTCGGCCCTTTTTTTCAA-TACAATACTGCATTGGGACCCCCTTACCGTATTTTAGTGGATACCAACTTCATCAATTTTTCCATCCAGAATAAAgtgagtgtgctttg---ttttgctttagggggtgtattggattgagattttgagagaatattttgacaaaaacaatcttgaagattttaaaagattatgtggg

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT2G46230.2 (Arabidopsis thaliana), 5'ss of exon 3
GGTCTCTTCGGCGCTGTTCTTCAGCTACAACACAGCGCTCGGGCCGCCATACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAGgtttgttctttgaggcttcgaattaggtgctcttctgtt-tatccac----tgaat-gat-ttcgtgaagccta--gcttaatctcaattgtgtcgagtatgtaactgt-------------------------------------------
 ||  || | | ||| |||||    |||||| |  |  | |  || || ||||| ||| | |||||||| ||||||||||| ||||| |||||||| |||||  |||| |      ||  | ||   |        | | ||  ||     || || ||| || ||  ||  ||  |  |      |  ||  | || | | | | |||                                           
TGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCCTCCTTACCGTGTTTTGGTGGATACTAACTTCATCAACTTCTCTATCCAGAATAAGgtcggttcatcttcaattgcatttctctatcacagagctataatcagaatgtgtatcgatctttgtagagtttatagtcttggtgaacctgattggaatctctcattgtttgaaatcctttttgacttattttgctctggtgtatctaatag

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EDP01317 (Chlamydomonas reinhardtii), 5'ss of exon 3
GGTCTCTTCGGCGCTGTTCTTCAGCTACAACACAGCGCTCGGGCCGCCATACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAGgtttgttct--ttgaggcttcgaattaggtgctcttctgtttatccactgaatgatttcgtgaagcctagcttaatctcaatt--gtgtcgagtatgtaactgt--
 || || ||||||||||||||| ||||||||||   ||| |||||||| || | |||  | ||||| || ||||| ||||| ||||||||| ||||||||||  | |     || |||     |  | | |    |||    | | |||     | |  | |  |||  | | || |        | | || |   |   | ||  
-GTGTCGTCGGCGCTGTTCTTCCGCTACAACACGCAGCTGGGGCCGCCGTATCAGGTGCTGGTGGACACCAACTTTATCAACTTCTCCATCAAGAACAAGgtgcgctggggctggggcagaacaccaaggg----tctagcgagc-actatgctagtctgcgt-gcccggttgaagcgttggcaggggccgggcgagggccggtcg

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|86502684|gb|CI145317.1|CI145317
EST:     ACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAG                         TTGGATTTGGAGAAAGGAATGATGGACTGCCTTTATGCAAAAT
genomic: ACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAGgtttgttctt ... acctatgcagTTGGATTTGGAGAAAGGAATGATGGACTGCCTTTATGCAAAAT
EST: gi|86828506|gb|CI278611.1|CI278611
EST:     ACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAG                         TTGGATTTGGAGAAAGGAATGATGGACTGCCTTTATGCAAAAT
genomic: ACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAGAACAAGgtttgttctt ... acctatgcagTTGGATTTGGAGAAAGGAATGATGGACTGCCTTTATGCAAAAT