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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGAACCTTGAAAAGTGCGAGTCCAGCATCTCTTCTAAAGGAAGCAATTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os07g24190.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g24190.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G025231_T02 (Zea mays), 5'ss of exon 12
TGGTGGAACCTTGAAAAGTGCGAGTCCAGCATCTCTTCTAAAGGAAGCAATTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctt-tgttgcag-----
||||||||||||||| ||||| ||||| || |||||| | || ||||| || |||||||| || ||||| || ||||| |||||||||||||| |||||||| | | || |||| ||     || | | || || ||   |  |||||| | |||  |||| ||| |||| |  | || |       
TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTTTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtctagagcttg-----tggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcatcttacttttcag

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G028353_T02 (Zea mays), 5'ss of exon 12
TGGTGGAACCTTGAAAAGTGCGAGTCCAGCATCTCTTCTAAAGGAAGCAATTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctttgttgcag------
||||||||||||||| ||||| ||||| || |||||||| || ||||| || |||||||| || ||||| || ||||| ||||| || ||||| |||||||||| | || |||||||     || | | ||||| ||   |  |||||| | |||  |||| ||| ||||  |  || |        
TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTCTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACTGATTGGGGAAAAGAGgtaaagtcttgagcctg-----tggttattggttgatgagtcaaaacatatgttacatagtgaatcatatgatattttccttttcag

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G025231_T01 (Zea mays), 5'ss of exon 12
TGGTGGAACCTTGAAAAGTGCGAGTCCAGCATCTCTTCTAAAGGAAGCAATTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctt-tgttgcag---------------------------
||||||||||||||| ||||| ||||| || |||||| | || ||||| || |||||||| || ||||| || ||||| |||||||||||||| |||||||| | | || |||| ||     || | | || || ||   |  |||||| | |||  |||| ||| |||| |  | || |                             
TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTTTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtctagagcttg-----tggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcatcttacttttcagattggctggatctatggatcag

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|29632757|gb|CB637766.1|CB637766
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACATACTGGGGGAAAGAG                         ATTGGCTGGATCTACTGATCAGCTACAGAAGATATTCTAACTGGT
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGT
EST: gi|15008337|gb|AU222725.1|AU222725
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|58607492|gb|CK035525.1|CK035525
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTAAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|86882518|gb|CI327259.1|CI327259
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGG-AAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAT
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|163928491|gb|EG711376.1|EG711376
EST:     CAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: CAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|29675228|gb|CB671503.1|CB671503
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|29628005|gb|CB633016.1|CB633016
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|86876412|gb|CI318407.1|CI318407
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGAACCTTGAAAAGTGCGAGTCCAGCATCTCTTCTAAAGGAAGCAATTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctttgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA