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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccattgttcttagaatatttgacattttcctgcaagtctgttcattgtacatgtttacactggaaaccagaatttgaattgtgctgctcttgtgtgcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTCATCATGGCGGTTCTCCTTGACAACACACTCGATGTCAGAGAGGCGGCAA

Basic information

species Oryza sativa
transcript LOC_Os09g15170.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g15170.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G100484_T03 (Zea mays), 3'ss of exon 12
------------------------------------------------------tccattgttcttag---aatatttgacattttcctgcaagtctg------ttcattgtacatgtttacactggaaaccagaatttgaattgtgctgctcttgtgt-gcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTCATCATGGCGGTTCTCCTTGACAACACACTCGATGTCAGAGAGGCGGCAA
                                                       |||  |     |    || || |  |||  |   | || ||        | ||||||| |   ||| |   ||      | | |      |  || |  | ||| |||||||||||||||||||||||    |||||| || |||||  | |||||||||||  | || || ||||||||||||||||| ||||| ||||| || ||||
gttcgtatttttctctatgtacttcaaaattcaaattccaacttaaacttagctcccagcgaaaagaagaaaacatctagcatgatatagtaactcgaagctgatgcattgtatactgttaaagctgagtttgaagtgttgtgcattttgtttgtttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTCATTGTAGCAGTACTCCTTGACAACACACTTGATGTGAGAGATGCAGCAA
















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|27577160|gb|CA999854.1|CA999854
EST:     CAGCGCACACTAAGGCTGGATGG                         TTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
genomic: CAGCGCACACTAAGGCTGGATGGgttcgtactt ... ttgtgtgcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
EST: gi|88991286|gb|CI108673.1|CI108673
EST:     GGACCAGCGCACACTAAGGCTGGATGG                         TTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
genomic: GGACCAGCGCACACTAAGGCTGGATGGgttcgtactt ... ttgtgtgcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
EST: gi|87019213|gb|CI277929.1|CI277929
EST:     GGTATACCACGAGCGCACAACAAGGACCAGCGCACACTAAGGCTGGATGG                         TTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
genomic: GGTATACCACGAGCGCACAACAAGGACCAGCGCACACTAAGGCTGGATGGgttcgtactt ... ttgtgtgcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
EST: gi|58676289|gb|CK064976.1|CK064976
EST:     GGTATACCACGAGCGCACAACAAGGACCAGCGCACACTAAGGCTGGATGG                         TTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
genomic: GGTATACCACGAGCGCACAACAAGGACCAGCGCACACTAAGGCTGGATGGgttcgtactt ... ttgtgtgcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
EST: gi|112785328|gb|EE590478.1|EE590478
EST:     GGTATACCACGAGCGCACAACAAGGACCAGCGCACACTAAGGCTGGATGG                         TTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
genomic: GGTATACCACGAGCGCACAACAAGGACCAGCGCACACTAAGGCTGGATGGgttcgtactt ... ttgtgtgcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
EST: gi|58679435|gb|CK068122.1|CK068122
EST:     GGTATACCACGAGCGCACAACAAGGACCAGCGCACACTAAGGCTGGATGG                         TTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
genomic: GGTATACCACGAGCGCACAACAAGGACCAGCGCACACTAAGGCTGGATGGgttcgtactt ... ttgtgtgcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
EST: gi|27577161|gb|CA999855.1|CA999855
EST:     CAGCGCACACTAAGGCTGGATGG                         TTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC
genomic: CAGCGCACACTAAGGCTGGATGGgttcgtactt ... ttgtgtgcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtacatgtttacactggaaaccagaatttgaattgtgctgctcttgtgtgcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTCATCATGGCGGTTCTCCTTGACAACACACTCGATGTCAGAGAGGCGGCAA
                                       ctgctctt  CT-rich tract
                          aatttgaatt  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccattgttcttagaatatttgacattttcctgcaagtctgttcattgtacatgtttacactggaaaccagaatttgaattgtgctgctcttgtgtgcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTCATCATGGCGGTTCTCCTTGACAACACACTCGATGTCAGAGAGGCGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - ttgttct
- - - - - - - - - - - - - - tcctgca
- - - - - - - - - - - - - - - - - - - - - - - -gtacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgct