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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgagcatagttgatcattaccatttattttatttcaccatttgtttactttctaggttactgctattcagtgtttattcaattactgtgtgctctgctgttcatattattcatcacttgggttgaccattgtcagGTTCTTCACCACTTGCTGTCAATTATTTCTTTAGTCTATGCTATTTATTCTGAAGAAGGACAGTTGTACACATACATGGTTCTCATCTCTGAAACAACCA

Basic information

species Oryza sativa
transcript LOC_Os01g56230.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56230.5 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G825226_T03 (Zea mays), 3'ss of exon 5
gtaagtgagcatagttgatcattaccatttattttatttcaccatttgtttactttctaggt-tactgctattcagtgtttattcaattactgtgtgctctgctgttcatattattcatcac--ttgggttgaccattgtcagGTTCTTCACCACTTGCTGTCAATTATTTCTTTAGTCTATGCTATTTATTCTGAAGAAGGACAGTTGTACACATACATGGTTCTCATCTCTGAAACAACCA
                                        ||  ||   ||| | |  || | |||   | || |    | || | | ||||    | |      ||   | |   | | ||  |         ||||  ||||| ||||||||  |||||||  |||||||| ||||||||||||| |||||||  ||||||||||||||||||||||||||||||||||||||||||||||
---------------------------------------tact-ttcacttaatctagagatatacacttgttgaa---tcatactactactacaagttggcacattttgactgcaccttacggtaacaacatacatttccagGTCCTTCACCATATGCTGTCGCTTATTTCTATAGTCTATGCTATGTATTCTGGGGAAGGACAGTTGTACACATACATGGTTCTCATCTCTGAAACAACCA
















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|29660431|gb|CB656706.1|CB656706
EST:     ACCTTGCTATGTTATCCTGGGCTTATCCTTCCCTTGGCGGAATGGAGTAT                         GTTCTTCACCACTTGCTGTCAATTATTTCTTTAGTCTATGCTATTTATTCT
genomic: ACCTTGCTATGTTATCCTGGGCTTATCCTTCCCTTGGCGGAATGGAGTATgtaagtgagc ... ccattgtcagGTTCTTCACCACTTGCTGTCAATTATTTCTTTAGTCTATGCTATTTATTCT
EST: gi|300215972|gb|HO088598.1|HO088598
EST:     ACCTTGCTATGTTATCCTGGGCTTATCCTTCCCTTGGCGGAATGGAGTAT                         GTTCTTCACCACTTGCTGTCAATTATTTCTTTAGTCTATGCTATTTATTCT
genomic: ACCTTGCTATGTTATCCTGGGCTTATCCTTCCCTTGGCGGAATGGAGTATgtaagtgagc ... ccattgtcagGTTCTTCACCACTTGCTGTCAATTATTTCTTTAGTCTATGCTATTTATTCT
EST: gi|24208073|gb|AU225100.1|AU225100
EST:     ACCTTGCTATGTTATCCTGGGCTTATCCTTCCCTTGGCGGAATGGAGTAT                         GTTCTTCACCACTTGCTGTCAATTATTTCTTTAGTCTATGCTATTTATTCT
genomic: ACCTTGCTATGTTATCCTGGGCTTATCCTTCCCTTGGCGGAATGGAGTATgtaagtgagc ... ccattgtcagGTTCTTCACCACTTGCTGTCAATTATTTCTTTAGTCTATGCTATTTATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attactgtgtgctctgctgttcatattattcatcacttgggttgaccattgtcagGTTCTTCACCACTTGCTGTCAATTATTTCTTTAGTCTATGCTATTTATTCTGAAGAAGGACAGTTGTACACATACATGGTTCTCATCTCTGAAACAACCA
                                       ggttgac  putative branch site (score: 4)
                   ttcatattattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgagcatagttgatcattaccatttattttatttcaccatttgtttactttctaggttactgctattcagtgtttattcaattactgtgtgctctgctgttcatattattcatcacttgggttgaccattgtcagGTTCTTCACCACTTGCTGTCAATTATTTCTTTAGTCTATGCTATTTATTCTGAAGAAGGACAGTTGTACACATACATGGTTCTCATCTCTGAAACAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG