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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaatctagtttcgtgcacatctactcttgcaagaatttgactcggttttcccttttgcacgctgcaattggcctctctgtgatgatgatgatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGAGAGGGCTAGTCAGGACTGAAGAGAGCAAAGCCAAGATTGGGGGCGCTGC

Basic information

species Oryza sativa
transcript LOC_Os05g01970.5
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01970.5 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G047219_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------gaaatctagtttcgtgcacatctactcttgcaagaat--ttgactcggttt----tcccttttgcacgctgcaattggcctctctgtgatgatgatgatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGAGAGGGCTAGTCAGGACTGAAGAGAGCAAAGCCAAGATTGGGGGCGCTGC
                                         | | || |   ||  |    |   || |||  |||    || ||   |||     | | | |       |||||    ||  | |       |  || |  | ||||||| ||||||||||||||| | |||||||||| ||  || ||||||||  | || ||||||||||| | ||||||||||| ||| ||||| |||| || 
gtaggtttcctgaagttccgctcatttggcatttctcatccgtagtcaaagctctcggcttttggctgttgatagagcggttcacattgttcatgattcatgtcaacgtttgcaaaaaaccaattttcatcatttgtggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGACGTGGCCTAGTCAGGACGGGAGAGAGCAAAGGCAAAATTGGAGGCGGTGA
















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|29637321|gb|CB642330.1|CB642330
EST:     CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAG                         GCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
genomic: CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAGgtgcaatgta ... gatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
EST: gi|58682453|gb|CK071140.1|CK071140
EST:     CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAG                         GCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCGGACCAATTTGTGGGGA
genomic: CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAGgtgcaatgta ... gatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
EST: gi|58667512|gb|CK056198.1|CK056198
EST:     CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAG                         GCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCGGACCAATTTGTGGGGA
genomic: CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAGgtgcaatgta ... gatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
EST: gi|88327982|gb|CI648387.1|CI648387
EST:     CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAG                         GCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
genomic: CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAGgtgcaatgta ... gatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
EST: gi|29637203|gb|CB642212.1|CB642212
EST:     CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAG                         GCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
genomic: CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAGgtgcaatgta ... gatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
EST: gi|701156|gb|D47447.1|D47447
EST:     CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAG                         GC-AGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
genomic: CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAGgtgcaatgta ... gatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
EST: gi|29614613|gb|CB619626.1|CB619626
EST:     CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAG                         GCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCGGACCAATTTGTGGGGA
genomic: CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAGgtgcaatgta ... gatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
EST: gi|88333296|gb|CI642333.1|CI642333
EST:     CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAG                         GCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
genomic: CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAGgtgcaatgta ... gatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA
EST: gi|29637365|gb|CB642374.1|CB642374
EST:     CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAG                         GCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAAACCAATTTGTGGGGA
genomic: CGGTGGCCCGCTTCCCACCGTGCTCGTCACCGGCGCAGGCGGCCGAACAGgtgcaatgta ... gatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttcccttttgcacgctgcaattggcctctctgtgatgatgatgatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGAGAGGGCTAGTCAGGACTGAAGAGAGCAAAGCCAAGATTGGGGGCGCTGC
                                               tctttc  CT-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaatctagtttcgtgcacatctactcttgcaagaatttgactcggttttcccttttgcacgctgcaattggcctctctgtgatgatgatgatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGAGAGGGCTAGTCAGGACTGAAGAGAGCAAAGCCAAGATTGGGGGCGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG