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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGTGATGAGGTGGAGTGACGGTTCCTATCTTGAAGACCAGGACCATTGGTGGCTATCTGGTATTCACAGGGATGTTCTACTAGTATCAAAGCCACAGgttacttctctagttttgctcatgcaatattgaacgaattctttcccttttgcaatgaagtgaatggttagctgagcttatgacattttcttcgtctcag...

Basic information

species Oryza sativa
transcript LOC_Os01g72340.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72340.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA13G26700.1 (Glycine max), 5'ss of exon 5
TCAAGTGATGAGGTGGAGTGACGGTTCCTATCTTGAAGACCAGGACCATTGGTGGCTATCTGGTATTCACAGGGATGTTCTACTAGTATCAAAGCCACAGgttacttctct----agttttgctcatgcaatattgaacgaattctttcccttttgcaatgaagtgaatggttagctgagcttatgacatttt-cttcgtctcag-----
||||||| | || ||| |||| ||||| || ||||||||||||||||| ||| || |||||||||| ||| | |||||||| ||  |  |||||||  |||||| || |||    | || | ||||   | |||||       | | |    ||| | | ||||   ||  |||   ||| |||||  | |   | || |   ||     
TCAAGTGTTTAGATGGTGTGATGGTTCTTACCTTGAAGACCAGGACCAATGGAGGTTATCTGGTATCCACCGTGATGTTCTTCTTATGGCAAAGCCGGAGgttagttttctccaaatttctcctcacctactattg------ctttatattgtttacga-gaagc--attcttattagag-ttatgttagtgcgcatcataaaaggtcaa

upper sequence: LOC_Os01g72340.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G54440.3 (Arabidopsis thaliana), 5'ss of exon 5
TCAAGTGATGAGGTGGAGTGACGGTTCCTATCTTGAAGACCAGGACCATTGGTGGCTATCTGGTATTCACAGGGATGTTCTACTAGTATCAAAGCCACAGgttacttctctagttttgctcatgcaatattgaacgaattctttcccttttgcaatgaagtgaatggttagctgagcttatgacattttcttcgtctcag
||||||  | || |||||||| ||||| || ||||||||||| || ||||||||| | |||||||||||  | ||||| ||  |  || |||||||  |||||  | ||||||||| | | |    |   |     |||| |    | | | |       |  | ||  |  |||  | || |  || | |  |      
TCAAGTCTTTAGATGGAGTGATGGTTCATACCTTGAAGACCAAGATCATTGGTGGTTGTCTGGTATTCATCGAGATGTGCTTTTGTTAGCAAAGCCCAAGgtttttcctctagtttcgttaaccagagtgtatgtcaattttaattcatcttctccactatatacggcca-ttgaattgattaacttctgtatgcag---

upper sequence: LOC_Os01g72340.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ11904 (Selaginella moellendorffii), 5'ss of exon 5
TCAAGTGATGAGGTGGAGTGACGGTTCCTATCTTGAAGACCAGGACCATTGGTGGCTATCTGGTATTCACAGGGATGTTCTACTAGTATCAAAGCCACAGgttacttctctagttttgctcatgc-aatattgaacgaattctttcccttttgcaatgaagtgaatggttagctgagcttatgacattttcttcgtctcag
|||||||||| |||||||||| || || |||||||||||||| ||||| |||||||||||||| |||||| | |||||  ||||  | |||||||| || || | | ||       || |  | | || || |  ||  || |      | ||  ||    |  || |                                 
TCAAGTGATGCGGTGGAGTGATGGATCGTATCTTGAAGACCAAGACCACTGGTGGCTATCTGGGATTCACCGAGATGTGATACTGTTTTCAAAGCCGCAAgtaagtacttggtcggtgtttgttctaacatgggccgtgttataa----tgtgggattgttttgatag---------------------------------

upper sequence: LOC_Os01g72340.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ13378 (Selaginella moellendorffii), 5'ss of exon 5
TCAAGTGATGAGGTGGAGTGACGGTTCCTATCTTGAAGACCAGGACCATTGGTGGCTATCTGGTATTCACAGGGATGTTCTACTAGTATCAAAGCCACAGgttacttctctagttttgctcatgc-aatattgaacgaattctttcccttttgcaatgaagtgaatggttagctgagcttatgacattttcttcgtctcag
|||||||||| | |||||||| || || |||||||||||||| ||||| |||||||||||||| |||||| | |||||  ||||  | |||||||| || || | | ||       || |  | | || || |  |  ||| |      | ||  ||    |  || |                                 
TCAAGTGATGCGATGGAGTGATGGATCGTATCTTGAAGACCAAGACCACTGGTGGCTATCTGGGATTCACCGAGATGTGATACTGTTTTCAAAGCCGCAAgtaagtacttggtcggtgtttgttctaacatgggccatattataa----tgtgggattgttttgatag---------------------------------

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|29622528|gb|CB627539.1|CB627539
EST:     GGTGGCTATCTGGTATTCACAGGGATGTTCTACTAGTATCAAAGCCACAG                         ATCTTTATTACAGATTATTTTTTCAAAGCAACCTTGGATGAAGGCTTCCGT
genomic: GGTGGCTATCTGGTATTCACAGGGATGTTCTACTAGTATCAAAGCCACAGgttacttctc ... ttgtttacagATCTTTATTACAGATTATTTTTTCAAAGCAACCTTGGATGAAGGCTTCCGT
EST: gi|29621652|gb|CB626663.1|CB626663
EST:     GGTGGCTATCTGGTATTCACAGGGATGTTCTACTAGTATCAAAGCCACAG                         ATCTTTATTACAGATTATTTTTTCAAAGCAACCTTGGATGAAGGCTTCCGT
genomic: GGTGGCTATCTGGTATTCACAGGGATGTTCTACTAGTATCAAAGCCACAGgttacttctc ... ttgtttacagATCTTTATTACAGATTATTTTTTCAAAGCAACCTTGGATGAAGGCTTCCGT