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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAACGTGTCCGGCTTAGTTGTTTGCGAGTGCTGCATCAGCTGGCTTCCAGCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAGgtattgaattgcaacccttgttttttctgttttaattttcttggtacttgcgtattgattttttttttacacactaatttctttgcttatccaacagtat...

Basic information

species Oryza sativa
transcript LOC_Os10g42439.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 12
AGAACGTGTCCGGCTTAGTTGTTTGCGAGTGCTGCATCAGCTGGCTTCCAGCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAGgtattgaattgcaacccttgttttttctgttttaattttcttggtacttgc--gtattgattttt----tttttacacactaatttctttgcttatccaacagtat
||||||||| || |||||||||||||| || ||||||||||| || || || || ||||||||||||||||||||||| ||||||||||||||||||||||||||  ||||     ||| ||||||  || || | ||   |     || |  || |  |   ||     |||| || |  | |   | | ||| |   |      
AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttattgtttgacttctttttttagtctttacttatataagttttcctggtttccaccattgtcacttttgcaaagaagtccttatacttttttta------

upper sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G049288_T01 (Zea mays), 5'ss of exon 18
AGAACGTGTCCGGCTTAGTTGTTTGCGAGTGCTGCATCAGCTGGCTTCCAGCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAGgtattgaattgcaacccttgtttttt------ctgttttaattt-----tcttggtacttgcgtattgattttttttttacacactaatttctttgcttatccaacagtat
|||||||||||| |||||||||||||| || ||||||||||| || || ||||| || |||||||||||||||||| | ||||||||||||||||||||||||||  |||      ||| ||||||      || |  ||| |      | | | ||  |  |   || |   | | || || | ||  || ||   ||            
AGAACGTGTCCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGCACAACCTGTGCAGAAGCTATGGCATCAACAAGTGCAGGAACTCCTCAGgtatttgattctttgacttcttttttaagttactatagtaagtagtaagtttagctaggtaaggcatggtcgatctcttgcataatatctttttattttg-----------

upper sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 18
AGAACGTGTCCGGCTTAGTTGTTTGCGAGTGCTGCATCAGCTGGCTTCCAGCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAGgtat-tgaattgcaacccttgttttttctgttttaattttcttggtacttgcgtattgatttttttt--ttacacactaatttctttgcttatccaacagtat
||||||||| || |||||||||||||| || || ||||| || ||  | |||||||| ||||| |||||||||||||| || ||||  ||||| ||||| |||| |  |   | | |  |  |||| |   |  ||||   |   || |       ||| | |  |   |||    | | ||| || |  |    ||      
AGAACGTGTACGCCTTAGTTGTTTGCGTGTTCTACATCAACTTGCAGCTAGCACTACATGTGCTGAAGCTATGGCAGCAACTAGTGTCGGAACACCTCAAgtatgttcagaactatctgttgttttccccatgaaattaattatatattcataacatgaatgtgctggattatcttcaagtttgttggaatgatgaattc---

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|33683077|gb|CF311316.1|CF311316
EST:     GCACTACTTGTGTAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAG                         GTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGGTGGAAGTATACT
genomic: GCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAGgtattgaatt ... ctgtttgcagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGG-TGGAAGTATACT
EST: gi|2428708|gb|C73171.1|C73171
EST:     GCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAG                         GTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAG-TGGAAGTAT
genomic: GCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAGgtattgaatt ... ctgtttgcagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAACGTGTCCGGCTTAGTTGTTTGCGAGTGCTGCATCAGCTGGCTTCCAGCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAGgtattgaattgcaacccttgttttttctgttttaattttcttggtacttgcgtattgattttttttttacacactaatttctttgcttatccaacagtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC