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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTCGGTTATTCAGGCATTCAGTTTGATGCGGACCAGCTTGATATTTCCCTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaaccttgacaacatagaattattttttttattgacgactttgaatgaattgtaatttgtgtagatcttacaatagaatttaaaatatctactgtttcttcatag

Basic information

species Oryza sativa
transcript LOC_Os03g17120.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G044237_T02 (Zea mays), 5'ss of exon 14
CTGTCGGTTATTCAGGCATTCAGTTTGATGCGGACCAGCTTGATATTTCCCTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaaccttg-acaacatag--aattattttttt----tattgacgactttgaatgaattgtaatttgtgtagatcttacaatagaatttaaaatatctactgtttcttcatag
| || ||||||||||||||||| ||||| ||  | |  ||||||||||| || |||| ||||||||||||||||||||| ||||||||||| ||||||||||||   ||  ||  |   |||||  |||   | ||||    | |||   ||  | |||  | |    ||| | ||| |||   | ||| || |||  |   || | | | |   |||
CAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaagttatattgcatagtcaatccatgttttgtcgtcttggtcaccgtaaatagactagggtttctttagttct---attaggatctaag-tgcttattctctttctttag
















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|58665134|gb|CK053820.1|CK053820
EST:     CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|88427802|gb|CI554310.1|CI554310
EST:     AATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: AATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|27546388|gb|CA767223.2|CA767223
EST:     CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|88907071|gb|CI376143.1|CI376143
EST:     C-TGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCACCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|86417804|gb|CI032013.1|CI032013
EST:     CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|86483772|gb|CI126405.1|CI126405
EST:     AGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: AGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|58675407|gb|CK064094.1|CK064094
EST:     CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|86494844|gb|CI137477.1|CI137477
EST:     CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|218488450|gb|FG961506.1|FG961506
EST:     GGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGTAAGATGCTGGAGACATCCATGGTACAGT
genomic: GGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|88385172|gb|CI561828.1|CI561828
EST:     TAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: TAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|88254735|gb|CI353559.1|CI353559
EST:     CCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|86600773|gb|CI356530.1|CI356530
EST:     ATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAAG
genomic: ATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTAC-AG
EST: gi|89162406|gb|CI099098.1|CI099098
EST:     CTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|87020790|gb|CI269507.1|CI269507
EST:     CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|86499008|gb|CI141641.1|CI141641
EST:     CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|89168167|gb|CI109371.1|CI109371
EST:     CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|86433912|gb|CI094255.1|CI094255
EST:     CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|88263131|gb|CI366905.1|CI366905
EST:     CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|88257574|gb|CI360160.1|CI360160
EST:     ACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: ACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|29613227|gb|CB618240.1|CB618240
EST:     CTTGGAGCTATTGCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|87012910|gb|CI297137.1|CI297137
EST:     CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
EST: gi|86490354|gb|CI132987.1|CI132987
EST:     CTGGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAG                         ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT
genomic: CTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaac ... ttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTCGGTTATTCAGGCATTCAGTTTGATGCGGACCAGCTTGATATTTCCCTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaaccttgacaacatagaattattttttttattgacgactttgaatgaattgtaatttgtgtagatcttacaatagaatttaaaatatctactgtttcttcatag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT