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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTAGTGATATATCATACATATTTTCTGGATACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATGgtaagtttattgtcctaatcttcctttttcattgagaaagcttttttcttgtgtcttcaacagttccatgtagagaaatgaaaaacggtgacttgggctc...

Basic information

species Oryza sativa
transcript LOC_Os04g14654.2
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g14654.3 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G003734_T01 (Zea mays), 5'ss of exon 19
CCCTAGTGATATATCATACATATTTTCTGGATACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATGgtaagtttattgtcctaatcttcctttttcattgagaaagcttttttcttgtgtcttcaacagttccatgtagagaaatgaaaaacggtgacttgggctc---
||||| ||||||||| ||||| |||||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||||||| |||| |  | ||| | |   | | ||  |    |   |    |     || ||    ||   ||||||       || ||| | |   ||    ||   
CCCTACTGATATATCCTACATCTTTTCTGGATACGCACCTCTTAGTATTCGCCTTGTTCAGCATGCAGTGAGATCTGGATGgtatgtttctcatgctagtttctatgtgtccctttacattttacgatgacaagtgttgcttag---catgtaatctgtggagaaaggattgtttcacttccta
















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|163929156|gb|EG710989.1|EG710989
EST:     TACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATG                         GCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTT
genomic: TACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATGgtaagtttat ... tgccatgcagGCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTT
EST: gi|58603195|gb|CK013723.1|CK013723
EST:     TACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATG                         GCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTT
genomic: TACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATGgtaagtttat ... tgccatgcagGCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTT
EST: gi|163917728|gb|EG711274.1|EG711274
EST:     TACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATG                         GCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTT
genomic: TACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATGgtaagtttat ... tgccatgcagGCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTT
EST: gi|28298184|gb|CB238414.1|CB238414
EST:     TACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGACG                         GCGATCTATTGGAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTT
genomic: TACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATGgtaagtttat ... tgccatgcagGCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTT
EST: gi|86432914|gb|CI093257.1|CI093257
EST:     TACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATG                         GCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTTATCTGGATTT
genomic: TACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATGgtaagtttat ... tgccatgcagGCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTAGTGATATATCATACATATTTTCTGGATACGCCCCTCTCAGTATTCGCCTTGTTCAGCATGCTGTGAGATCTGGATGgtaagtttattgtcctaatcttcctttttcattgagaaagcttttttcttgtgtcttcaacagttccatgtagagaaatgaaaaacggtgacttgggctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC