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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaagcgaagcactagtcgttcgtcgccattgatgagatgagatgagctttgcattcgagttctgggctgcgattctgattcgggtatgagcgaacagGATGCAGGTGGAGGTGAGCAAGTACACGGAGGGGCTCAGCGACAAGCGGATGCGGCCGAACGAGTTGCCGGTGTCGCTCATCCGCTACGACG

Basic information

species Oryza sativa
transcript LOC_Os04g23890.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 1
gtaagtaagcgaagcactagtcgttcgtcgccattgatgagatgagatgagctttgcattcgagttctgggctgcgattctgattcgggtatgagcgaacagGATGCAGGTGGAGGTGAGCAAGTACACGGAGGGGCTCAGCGACAAGCGGATGCGGCCGAACGAGTTGCCGGTGTCGCTCATCCGCTACGACG
                  |  | | || | | ||  ||   ||    |  ||| | |  |  |  ||||   || |||||      ||   ||     |||||||||| || |||||||||||||||||||||||||||||||| ||||| |||||||| |||||| |||| ||||| ||||||| ||||||||
---------------gtaacccatgcgac-ctatctatcttatcctctt-gctgtactgttta-ctctgctttgtgattc----atggaactgccgtgacagGATGCAAGTCGAGGTGAGCAAGTACACGGAGGGGCTCAGCGAAAAGCGCATGCGGCCAAACGAGATGCCAGTGTCCCTCATCCACTACGACG

upper sequence: LOC_Os04g23890.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S179_27V6.3 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------gtaagtaagcgaagcactagtcgttcgtcgccattgatgagatgagatgagct-ttgcattcgagttctgggctgcgattctgattcgggtat-----gagcgaacagGATGCAGGTGGAGGTGAGCAAGTACACGGAGGGGCTCAGCGACAAGCGGATGCGGCCGAACGAGTTGCCGGTGTCGCTCATCCGCTACGACG
                                                       ||  ||       |  | ||  |       || ||| ||  | ||  |     ||| | |  | | ||||  |   |||  |||| |||        |   | |||||||||| ||||| |||||||||||||| |||||    |  | |  |      || || ||||   |||| | |||||||||||| |||||||
gtgaggactgaaagctttccacattgacgaccaattgatcacgtttttattattatatttatattgtacttttgttctcgaattgcagtgaagacctaagcagtttcgttgtaatgaattgctggttttgaatt--gatttgggagcttttggtttgtacagGATGCAAGTGGAAGTGAGCAAGTACACTGAGGGTGCTAAAGCCGTGGCTCGACGTCCCAACGGTCTGCCCGAGTCGCTCATCCGATACGACG

upper sequence: LOC_Os04g23890.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S174_62V6.2 (Physcomitrella patens), 3'ss of exon 1
gtaagtaagcgaa-gcactagtcgttcgtcgccattgatgagatgagatga--gctttgcattcgagttctg--ggctgc--gattctg-attcgggtatgagcgaacagGATGCAGGTGGAGGTGAGCAAGTACACGGAGGGGCTCAGCGACAAGCGGATGCGGCCGAACGAGTTGCCGGTGTCGCTCATCCGCTACGACG
||| ||      | ||| | || |||   |  | |  |  | ||         ||   |   || |  ||||  | || |   ||   |    ||| |  |    ||||| |||||||| || ||||||||||||||||||||    |  | |  |      || || ||||   |||| | |||||| ||||| |||||||
gtacgtttctttacgcaatggttgttgaac-tcttcaacaaaatatttcagcggccacgaggtccaaatctgctgcctacttaatgacgtgcacggttgcggtacaacagAATGCAGGTTGAAGTGAGCAAGTACACGGAGGGTGCTAAAGCCGTGGCTCGACGTCCCAACGGCCTGCCCGAGTCGCTGATCCGTTACGACG

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|66923581|gb|CX110429.1|CX110429
EST:     ACCGTCACCCCCATCCGCGACGACAACGGCAAGGTCATCAAGTTCATCGG                         GATGCAGGTGGAGGTGAGCAAGTACACGGAGGGGCTCAGCGACAAGCGGAT
genomic: ACCGTCACCCCCATCCGCGACGACAACGGCAAGGTCATCAAGTTCATCGGgtaagtaagc ... gagcgaacagGATGCAGGTGGAGGTGAGCAAGTACACGGAGGGGCTCAGCGACAAGCGGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagctttgcattcgagttctgggctgcgattctgattcgggtatgagcgaacagGATGCAGGTGGAGGTGAGCAAGTACACGGAGGGGCTCAGCGACAAGCGGATGCGGCCGAACGAGTTGCCGGTGTCGCTCATCCGCTACGACG
                              ttctgat  putative branch site (score: 3)