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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttataaatgaagtttttgtaattttgtccaattaggtacatacataatactacctttttgtcagttttgttttgacctatctgtattgtcttcaacagCTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCTCTGGACGGGTTGGTTCAGATACACCACTTATCTGCCAACAAAGTGGCAT

Basic information

species Oryza sativa
transcript LOC_Os07g45350.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G871572_T01 (Zea mays), 3'ss of exon 2
-----------ttttataaatgaagtttttgtaattttgtccaattaggtacatacataatactacctttttgtcagttttgttttgacctatctgtattgtcttcaacagCTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCTCTGGACGGGTTGGTTCAGATACACCACTTATCTGCCAACAAAGTGGCAT
           |||| || |  |  | |  || ||||||     ||  ||| ||  || ||| ||  | |||           |||||| || ||  | ||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| || ||||||||  | ||||||||||| ||||||||||| ||||||||||| |||||
ttaggtgtgttttttgtacagaatttatcggtcattttgattgtttgagtatatggatgatattatttattt-----------tttgacatacctacactgtcttcaacagCTGCTATCTTGGACACTGCAAGTAAAGTCCTACCACTTGTAGTTGCCGTCTCTGGGAGAGTTGGTTCAGACACACCACTTATATGCCAACAAAGCGGCAT

upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G020574_T08 (Zea mays), 3'ss of exon 2
---ttttataaatgaagtttttgtaattttgtccaattaggtacatacataatactacctttttgtcagttttgttttgacctatctgtattgtcttcaacagCTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCTCTGGACGGGTTGGTTCAGATACACCACTTATCTGCCAACAAAGTGGCAT
    ||||    |  | ||| || |   ||   |  | |  |   |   |||   || |  |  |  | || | |||| || | |||  | || ||  |||||||||||| ||||||||||||||||||||||| ||||||||||| ||  |||||||  | ||||||||||| ||||||||||| ||||||||||| |||||
ttagtttaggtgtatattttgtgcagaatttatcggtcatttgattgtttaagtgtatcaat--gata-ttattttttcacatgtctacactgcctcgaacagCTGCTATCTTGGACACTGCAAGTAAGGTCCTACCACTTGTAGTTGCCATCTCTGGGAGAGTTGGTTCAGACACACCACTTATATGCCAACAAAGCGGCAT
















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|58695660|gb|CK084347.1|CK084347
EST:     TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGG                         CTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT
genomic: TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGGgtgagcgagc ... tcttcaacagCTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT
EST: gi|29684518|gb|CB680793.1|CB680793
EST:     TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGG                         CTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT
genomic: TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGGgtgagcgagc ... tcttcaacagCTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT
EST: gi|58693123|gb|CK081810.1|CK081810
EST:     TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGG                         CTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT
genomic: TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGGgtgagcgagc ... tcttcaacagCTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT
EST: gi|29680615|gb|CB676890.1|CB676890
EST:     TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGG                         CTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT
genomic: TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGGgtgagcgagc ... tcttcaacagCTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT
EST: gi|88299031|gb|CI568034.1|CI568034
EST:     TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGG                         CTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT
genomic: TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGGgtgagcgagc ... tcttcaacagCTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT
EST: gi|66923542|gb|CX110390.1|CX110390
EST:     TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGG                         CTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT
genomic: TGCGGAGGTGCTGCGATCGGTGGCGAGGGCCGGAAGCACGAAGGATTTGGgtgagcgagc ... tcttcaacagCTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatactacctttttgtcagttttgttttgacctatctgtattgtcttcaacagCTGCTATATTGGACACTGCAAGTAAGGTCCTGCCACTTGTAGTGGCAGTCTCTGGACGGGTTGGTTCAGATACACCACTTATCTGCCAACAAAGTGGCAT
                          ttttgac  putative branch site (score: 3)
                                          ttgtcttc  putative PPT
                     ttttgtttt  TA-rich tract