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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacttaattaattcattaattaattgccatttctagagctaagagcacctgcatctgcatgtggtgattaattactttggaattagtaattagttgctcatggtgattgattcctgaattgattgattgattgattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAGGTGAGGAAAATTCACCACTGTTT

Basic information

species Oryza sativa
transcript LOC_Os07g02800.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g02800.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G173882_T01 (Zea mays), 3'ss of exon 3
gtacacttaattaattcattaattaattgccatttctagagctaagagcacctgcatctgcatgtggtgattaattactttggaattagtaattagttgctcatggtgattgattcctgaattgattgat---tgattgattg---tgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAGGTGAGGAAAATTCACCACTGTTT
||   | |   |  ||||      ||||     ||   |   |  |    ||||||   || |||  | |   | |   |||      ||| |||| | |  |  ||     |||   || || ||| ||   ||||||  ||   |||||||||||| |||||||| ||||||||||||||||||||||| || || ||||| ||||| || |||||||| ||||||                       
gtgagccttgctc-ttcagatgcaaattatttcttgccggttttgggcggcctgca---gcgtgttcttacctacttgcttgcctgccgta-ttagatacgtagagttgg-aattaacgagttcattcatgtctgattgtctgcactgcagTTGCCACCCCAAAGCAGATCAGGGAGCTGATGAAGGTGGACGGCCTCACAAACGACGAAGTGAAAAGCCACCTTCAG-----------------------

upper sequence: LOC_Os07g02800.3 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S83_100V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacacttaattaattcattaattaattgccatttctagagctaagagcacct-gcatctgcatgtggtgattaattactttggaattagtaattagttgctcatggtgattgattcctgaattgattgattgattgattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAGGTGAGGAAAATTCACCACTGTTT
                                | |||    |      | ||| |||| |   | ||||| ||    |  ||||| |      | |     |||   | | |||       |  |  ||      || ||||||||||||||| |||||||||||  | |||||||||||||| || || || || || ||||| || || |||||||| |||                       
------------------------------tttctctgtgtcggcattctccttgcattttgttctggtgttt----atgttggattcgaacttcacaaattcaacttcactgac------acgggctg------tggttgtgcagTTGCCACGCCAAAGCAAATACGCGAGCTGATGAAGGTCGACGGCCTTACCAACGACGAAGTGAAGAGCCATCTGCAG-----------------------

upper sequence: LOC_Os07g02800.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ37607 (Selaginella moellendorffii), 3'ss of exon 3
gtacacttaattaattcattaattaattgccatttctagagctaagagcacctgcatctgcatgtggtgattaattactttggaattagtaattagttgctcatggtgattgattcctgaattgattgattgattgattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAGGTGAGGAAAATTCACCACTGTTT
                                                                                ||  |  |||||||    || |  | | |    ||| | ||    |    |  |||||    ||||||| ||||||||||||||| | ||||| |||||||| ||||| || ||||| || || || |||||||| || |||                       
-------------------------------------------------------------------------------gtgcgac-agtaattcaa-gcgctcgatcaaaagttcttaaaggtttcttcttcttgatc---cagTTGCAACTCCAAAGCAAATCCGAGAGCTCATGAAGGTAGATGGTCTTACAAACGATGAAGTAAAAAGCCACCTCCAG-----------------------

upper sequence: LOC_Os07g02800.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ15083 (Selaginella moellendorffii), 3'ss of exon 3
gtacacttaattaattcattaattaattgccatttctagagctaagagcacctgcatctgcatgtggtgattaattactttggaattagtaattagttgctcatggtgattgattcctgaattgattgattgattgattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAGGTGAGGAAAATTCACCACTGTTT
                                                               |||  ||  | ||| | || | | |          || |  | |      ||| | ||    |    |  |||||    ||||||||||||||||||||||| | || || |||||||| ||||| || ||||| || || || |||||||| || |||                       
---------------------------------------------------------------gtg-cgac-agttattctgaattcaa---------gcgctcgatcgaaagttcttaaaggtttcttcttcttgatc---cagTTGCCACTCCAAAGCAAATCCGAGAACTCATGAAGGTAGATGGTCTTACAAACGATGAAGTAAAAAGCCACCTCCAG-----------------------

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|29660199|gb|CB656474.1|CB656474
EST:     AGTTCGTCGCCGCC-TGCAGCAACTCGGTGGCCCTCAAG                         TTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
genomic: AGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattagttgctcatggtgattgattcctgaattgattgattgattgattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAGGTGAGGAAAATTCACCACTGTTT
                                         gattgat  putative branch site (score: 4)
                             aattgatt  TA-rich tract