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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAAGTTTTGACTGATTTGGTCGAGGGCCTTGAGGAGGCTTCTGTGACAGTGGAGATAAGATTGAAGATTGATCAGAATCATGCAGATTTGAAAGGGGGgtatgtccctttccaagagaagctatattaccagttatctaacactacacaattatcattgaaacaatgtcatttttgccatttctagttgagaaaatta...

Basic information

species Oryza sativa
transcript LOC_Os07g26610.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26610.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G069676_T03 (Zea mays), 5'ss of exon 15
GTAAAGTTTTGACTGATTTGGTCGAGGGCCTTGAGGAGGCTTCTGTGACAGTGGAGATAAGATTGAAGATTGATCAGAATCATGCAGATTTGAAAGGGGGgtatgtccctttccaagagaagctatattaccagttatctaacactacacaattatcattgaaacaatgtcatttttgccatttctagttgagaaaatta----
|||||||||||||||||||||| |||||||||||||| |||  ||||||||| |||||||| || |||||||||||||||||||||||||||||||| |||||||   ||  |   || | | | | |    | ||  | |  |     ||  | |    |||    | |  | ||   || ||  |   || |  | ||    
GTAAAGTTTTGACTGATTTGGTTGAGGGCCTTGAGGAAGCTGATGTGACAGTTGAGATAAGGTTAAAGATTGATCAGAATCATGCAGATTTGAAAGGAGGgtatg---ctaactctgaaatgttctttggttatttcacaaggagatagcatcttttgcagaagttttctagtattgtgcactta-aacagaaacgagtatgtg
















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|218504169|gb|FG954519.1|FG954519
EST:     GTGGAGATAAGATTGAAGATTGATCAGAAT-ATGCAGATTTGAAAGGGGG                         GTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAAT
genomic: GTGGAGATAAGATTGAAGATTGATCAGAATCATGCAGATTTGAAAGGGGGgtatgtccct ... gtctttacagGTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAAT
EST: gi|29660679|gb|CB656954.1|CB656954
EST:     GTGGAGATAAGATTGAAGATTGATCAGAATCATGCAGATTTGAAAGGGGG                         GTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAAT
genomic: GTGGAGATAAGATTGAAGATTGATCAGAATCATGCAGATTTGAAAGGGGGgtatgtccct ... gtctttacagGTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAAT
EST: gi|89186475|gb|CI048147.1|CI048147
EST:     GTGGAGATAAGATTGAAGATTGATCAGAATCATGCAGATTTGAAAGGGGG                         GTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAAT
genomic: GTGGAGATAAGATTGAAGATTGATCAGAATCATGCAGATTTGAAAGGGGGgtatgtccct ... gtctttacagGTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAAT
EST: gi|86892585|gb|CI312008.1|CI312008
EST:     TGGAGATAAGATTGAAGATTGATCAGAATCATGCAGATTTTGAAAGGGGG                         GTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAAT
genomic: TGGAGATAAGATTGAAGATTGATCAGAATCATGCAGA-TTTGAAAGGGGGgtatgtccct ... gtctttacagGTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAAT
EST: gi|86258642|gb|CI064995.1|CI064995
EST:     GAGATAAGATTGAAGATTGATCAGAATCATGCAGATTTGAAAGGGGG                         GTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAAT
genomic: GAGATAAGATTGAAGATTGATCAGAATCATGCAGATTTGAAAGGGGGgtatgtccct ... gtctttacagGTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAAGTTTTGACTGATTTGGTCGAGGGCCTTGAGGAGGCTTCTGTGACAGTGGAGATAAGATTGAAGATTGATCAGAATCATGCAGATTTGAAAGGGGGgtatgtccctttccaagagaagctatattaccagttatctaacactacacaattatcattgaaacaatgtcatttttgccatttctagttgagaaaatta

- - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctttcc