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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacctttcgactatattctgttgaagttataggctgtctatataccctagaagttaattagccttctctctttcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGGCAAGAGAAGTATCTTCCAGTCCTCCTTATACTGACTATGTTTCCACCAG

Basic information

species Oryza sativa
transcript LOC_Os03g63020.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G045241_T07 (Zea mays), 3'ss of exon 2
gta-tacctttcgactatattctgttgaagttataggctgtctatataccctagaagttaattagccttctctctttcctcttt--agAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGGCAAGAGAAGTATCTTCCAGTCCTCCTTATACTGACTATGTTTCCACCAG
||| |   | | |   |||||   ||| | ||||    | ||| | |  |    ||  |||||||  || |  |||   | | |  ||| ||| ||||||||||| |||| | | |||||||||||||||||||||||||||||||| ||||||||| ||||||||| ||||| ||||||||||||||
gtaatgtgtcttgttgatattacattggaattatc--ttatctttctttctgtcaaaataattagtttttttccttctatttgtgcagAGAATTTGTTGGTGACAAATGGTATTATTAAAATTGCTGACTTTGGGTTGGCAAGAGAAATATCTTCCAATCCTCCTTACACTGATTATGTTTCCACCAG

upper sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G13020.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatacctttcgactatattctgttgaagttataggctgtctatataccctagaagttaattagcc---ttctctctttcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGGCAAGAGAAGTATCTTCCAGTCCTCCTTATACTGACTATGTTTCCACCAG
||||   ||   ||| | |  |||   | ||  |    || |     |  |  | ||    ||  |   || | |  |   |||  ||| ||| || |||||||  |    |   | ||||||||||||||||||||||| ||||||||  | || |  |||||||| ||||| ||||| |||||  |
gtatgttttggtactttgtattgtattaattg-aaatggttttcgctctttgaatgtcttataaacaagttttgttctgtttctgaagAGAATTTGCTGGTGACCAACAATATCCTGAAAATTGCTGACTTTGGGTTGGCTAGAGAAGTTGCATCTATGCCTCCTTACACTGAATATGTGTCCACACG

upper sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0151g00350.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------gtatacctttcgactatattctgttgaagttataggctgtctatataccctagaagttaattagccttctctctttcctcttt--agAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGGCAAGAGAAGTATCTTCCAGTCCTCCTTATACTGACTATGTTTCCACCAG
                                               |     |||    |  ||  |  |||||   |  |  | || |||    |||  ||  |||| |   | |  ||||    ||  ||| ||| || |||||||| |        |||||||||||||||| ||  |||| ||||||||||| || |  |||||||||||||||||||| |||||  |
gtatgaagttgacttctacaaaattatgcacttgtgcagtctatgatttggaattttatttgcatcttcatgaagaattgtgtaggctttatctaatagt-gtatattatcaaacaccatttctgtcttcaagAGAATTTGCTGGTGACAAACAATGTGATTAAAATTGCTGACTTCGGACTGGCTAGAGAAGTATCATCTATGCCTCCTTATACTGACTATGTGTCCACACG

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|25798660|gb|CA754621.1|CA754621
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGC
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGC
EST: gi|58675001|gb|CK063688.1|CK063688
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
EST: gi|86848584|gb|CI293908.1|CI293908
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
EST: gi|33381171|gb|CF196514.1|CF196514
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataggctgtctatataccctagaagttaattagccttctctctttcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGGCAAGAGAAGTATCTTCCAGTCCTCCTTATACTGACTATGTTTCCACCAG
                        agttaat  putative branch site (score: 4)
                          ttaattagccttctct  CT-rich tract
                       aagttaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacctttcgactatattctgttgaagttataggctgtctatataccctagaagttaattagccttctctctttcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGGCAAGAGAAGTATCTTCCAGTCCTCCTTATACTGACTATGTTTCCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT