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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgttgttggtccagtttttcttatatattagatgttcaggcaaatccatcaagtactgactgctgcttcaccattttatggttacaatatgtgatgactctaaactaaagttgttattttcaaattcagTCCAGTGGCAGTGGAAGTGAAAGTGGCATTCAGACACAAAAGTGTGCCAAATCAAAAAGTGGGGATGAATCCAATAATAACAATGGCAGCAATGACGATG

Basic information

species Oryza sativa
transcript LOC_Os07g49460.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 3
gtaagttgttgttggtccagtttttcttatatattagatgttcaggcaaatccatcaagtactgactgctgcttcaccattttatggttacaatatgtgatgactctaaactaaagtt-gttattttcaaattcagTCCAGTGGCAGTGGAAGTGAAAGTGGCATTCAGACACAAAAGTGTGCCAAATCAAAAAGTGGGGATGAATCCAATAATAACAATGGCAGCAATGACGATG-----
                                         |  | | |||   | |    ||   |  |  | ||    |     | |    |  ||| |      |||  ||||||   |  |||  || |||||||||||| |||||||||||||||||||||||||| || |||||| |||| |||||| |||   ||||||||  ||| |||| ||| ||||| |||||||     
----------------------------------------attggtctaattt-ttagacccttcttcttaatacaatgatacgcagctctcctgcgtgttcgaaaaaaaaaaaagtttacttatttggaactcagtccagTGGTAGTGGAAGTGAAAGTGGCATTCAGACGCAGAAGTGTACCAAGTCAAAAGGTGCCAATGAATCCGGTAACAACAGTGGTAGCAACGACGATGAAGCT

upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G033962_T01 (Zea mays), 3'ss of exon 3
gtaagttgttgttggtccagtttttcttatatattagatgttcaggcaaatccatcaagtactgactgctgcttca-------------------------ccattttat-------------ggttacaatatgtgatgactctaaactaaagttgttattttcaaattcagTCCAGTGGCAGTGGAAGTGAAAGTGGCATTCAGACACAAAAGTGTGCCAAATCAAAAAGTGGGGATGAATCCAATAATAACAATGGCAGCAATGACGATG
||||||||||  |||||  ||||   |  |||| |   | |  |   ||| |  ||||||  | | || |||||||                           | |||||             ||| |   | |||  | |||||||    |  ||  |  |||  || |||||||||||| |||||||||||||||||||||||||| || |||||||||||||||||| |||   ||||||||  ||| |||| ||| ||||| || || |
gtaagttgttcatggtctggtttgaatattatactttct-tgaaaaaaaaactgtcaagtgataattgttgcttcagtttcaaggattactcaagttttttttactttattcatggttctctgggtaaatttgtgtatttactctaacaagagtttacttgtttggaactcagTCCAGTGGTAGTGGAAGTGAAAGTGGCATTCAGACCCAGAAGTGTGCCAAATCAAAAGGTGTCAATGAATCCGGTAACAACAGTGGTAGCAACGATGACG
















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|89172761|gb|CI022640.1|CI022640
EST:     AGAATGAACTTAAGAACCTATGGCAGCATGTGTGGAGACGGTGCCACAGC                         TCCAGTGGCAGTGGAAGTGAAAGTGGCATTCAGACACAAAAGTGTGCCAAA
genomic: AGAATGAACTTAAGAACCTATGGCAGCATGTGTGGAGACGGTGCCACAGCgtaagttgtt ... tcaaattcagTCCAGTGGCAGTGGAAGTGAAAGTGGCATTCAGACACAAAAGTGTGCCAAA
EST: gi|58611601|gb|CK039313.1|CK039313
EST:     TTAAGAACCTATGTGCAGCATGTGTGTGAGACGGTGCCACAGC                         TCCAGTGGCAGTGGAAGTGAAAGTGGCATTCAGACACAAAAGTGTGCCAAA
genomic: TTAAGAACCTATG-GCAGCATGTGTG-GAGACGGTGCCACAGCgtaagttgtt ... tcaaattcagTCCAGTGGCAGTGGAAGTGAAAGTGGCATTCAGACACAAAAGTGTGCCAAA
EST: gi|88978654|gb|CI384995.1|CI384995
EST:     AGAATGAACTTAAGAACCTATGGCAGCATGTTTGGAGACGGTGCCACAGC                         TCCAGTGGCAGTGGAAGTGAAAGTGGCATTCAGACACAAAAGTGTGCCAAA
genomic: AGAATGAACTTAAGAACCTATGGCAGCATGTGTGGAGACGGTGCCACAGCgtaagttgtt ... tcaaattcagTCCAGTGGCAGTGGAAGTGAAAGTGGCATTCAGACACAAAAGTGTGCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatggttacaatatgtgatgactctaaactaaagttgttattttcaaattcagTCCAGTGGCAGTGGAAGTGAAAGTGGCATTCAGACACAAAAGTGTGCCAAATCAAAAAGTGGGGATGAATCCAATAATAACAATGGCAGCAATGACGATG
                            aactaaa  putative branch site (score: 2)
                                       ttattttc  putative PPT
                               taaagttgttattttc  TA-rich tract