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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgatcttttctgctgttctaatatttctatttcacattttgaacttcaggatttaaaatgttcattttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAGTACTCAGATTCA

Basic information

species Oryza sativa
transcript LOC_Os08g33850.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33850.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G152457_T03 (Zea mays), 3'ss of exon 7
gtgcgatcttttctgctgttctaatatttctatttcacattttgaacttcaggatttaaaatgttcattttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAGTACTCAGATTCA
|||    |||||||        |  | |||||||     ||   ||| |    |||||  |      |||| | |||||||||||||||  || |||||    || |||||||||||||||||||||||||||||||||||||||| | ||   |||   ||||||||||||||||||
gtgaagccttttct--------ataagttctattctttgttg-aaacctggatatttatga-----gttttttctcagGATTGATGTTGTAAACCAAATCCATGGCGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGACGACGATGAACAGAACAGAGTACTCAGATTCA

upper sequence: LOC_Os08g33850.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G152457_T05 (Zea mays), 3'ss of exon 6
----------------gtgcgatcttttctgctgttctaatatttctatttcacattttgaacttca--ggatttaaaatgttcat----tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAGTACTCAGATTCA
                 ||| |     ||        | |    | |  |  |  || |   |||    | |      || || ||    ||| | |||||||||||||||  || |||||    || |||||||||||||||||||||||||||||||||||||||| | ||   |||   |||||             
gcatgatacgcttaaaatgccactggatcataaaaggtgaagccttttctataagttctattctttgttgaaacctggatatttatgagttttttctcagGATTGATGTTGTAAACCAAATCCATGGCGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGACGACGATGAACAGAACAGA-------------

upper sequence: LOC_Os08g33850.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G152457_T04 (Zea mays), 3'ss of exon 7
gtgcgatcttttctgctgttctaatatttctatttcacattttgaacttcaggatttaaaatgttcattttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAGTACTCAGATTCA
|||    |||||||        |  | |||||||     ||   ||| |    |||||  |      |||| | |||||||||||||||  || |||||    || |||||||||||||||||||||||||||||||||||||||| | ||   |||   |||||             
gtgaagccttttct--------ataagttctattctttgttg-aaacctggatatttatga-----gttttttctcagGATTGATGTTGTAAACCAAATCCATGGCGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGACGACGATGAACAGAACAGA-------------

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|38482258|gb|CF966306.1|CF966306
EST:     ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAT                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|29688929|gb|CB685204.1|CB685204
EST:     ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAG                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
EST: gi|86492773|gb|CI135406.1|CI135406
EST:     ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAG                         GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG
genomic: ATTGTTGCTTTGCTGCATGATACTCTAAAGGTCCCGCTGGATGATAAGAGgtgcgatctt ... tttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttctatttcacattttgaacttcaggatttaaaatgttcattttgtttcagGATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAGTACTCAGATTCA
 ttctaat  putative branch site (score: 2)
                                            ttttgtttc  putative PPT
                              atttaaaatgttcatt  TA-rich tract