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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctttcttccatcagactgtcactgtaggctttcaatatcatcaccaatcttctgtaacttaaactgaacaactttctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATAAACATGGACGCCGATGTGATCACCATCGAGAACTCCCGGTCCGACG

Basic information

species Oryza sativa
transcript LOC_Os12g42884.3
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G149751_T06 (Zea mays), 3'ss of exon 10
---------gtaatctttcttccatcagac---tgtcactgtaggctttcaatatcatcaccaatcttctgtaacttaaactgaacaactttctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATAAACATGGACGCCGATGTGATCACCATCGAGAACTCCCGGTCCGACG
          | | || |   |  |    |   || || ||| ||       |  || || || |  | ||  |||  ||    |   | |||| | | ||||| |||||||||||||||||||| ||||||||||||||||||||||| |||||  |||||||||| || ||||||||||| |||||||| ||||||||||
gtcattctcttgaactgtgcgctgtggagcccttgccagtgtgggagag-gttcacaccaacatttctttggcactccaaactgatttccttctgttggcagATCCACACCCACATGTGCTACTCCAACTTCAACGACATCATCCACTCGATCATCGACATGGACGCGGACGTGATCACCATTGAGAACTCGCGGTCCGACG

upper sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ05611 (Selaginella moellendorffii), 3'ss of exon 11
gtaatctttcttccatcagactgtcactgtaggctttcaatatcatcaccaatcttctgtaacttaaactga-acaactttctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATAAACATGGACGCCGATGTGATCACCATCGAGAACTCCCGGTCCGACG
                            |||              |  | |    |  || | | | ||||       ||    || |||||| |||||||| |||||||||||  |||||||||||||||||    |||||||  |||||||||||||||||||||| ||||| ||||| || || || |
----------------------------gtaaaagacgcgacgagtttctatagcttcgtgaatgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG

upper sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
gtaatctttcttccatcagactgtcactgtaggctttcaatatcatcaccaatcttctgtaacttaaactga-acaactttctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATAAACATGGACGCCGATGTGATCACCATCGAGAACTCCCGGTCCGACG
                            |||              |  | |    |  || ||| | ||||       ||    || |||||| |||||||| |||||||||||  |||| ||||||||||||    |||||||  |||||||||||||||||||||| ||||| ||||| || || || |
----------------------------gtaaaagacgcgacgagtttctatagcttcgtgactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG

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|29623205|gb|CB628216.1|CB628216
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|29637651|gb|CB642660.1|CB642660
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|29623204|gb|CB628215.1|CB628215
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|58680942|gb|CK069629.1|CK069629
EST:     CACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|218486860|gb|FG950334.1|FG950334
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|428194|gb|D24342.1|D24342
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|29675800|gb|CB672075.1|CB672075
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|11025872|gb|AU162473.1|AU162473
EST:     CTGTTCACTCTTTCAGAATCACAAAATGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|29615680|gb|CB620692.1|CB620692
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|11564886|gb|AU165522.1|AU165522
EST:     AGAATCACAAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: AGAATCAC-AAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|58587657|gb|CF985965.1|CF985965
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|29620903|gb|CB625914.1|CB625914
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|58689121|gb|CK077808.1|CK077808
EST:     TCAGGACACCACCCAG                         ATTCACACCCACATGTGTTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: TCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|396941330|gb|HO188539.1|HO188539
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|86594958|gb|CI258212.1|CI258212
EST:     GCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: GCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|58585708|gb|CF984016.1|CF984016
EST:     CACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAAGCTTCAACGACATCATCCACTCCAT
genomic: CACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAA-CTTCAACGACATCATCCACTCCAT
EST: gi|29657688|gb|CB653963.1|CB653963
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|10930997|gb|AU161271.1|AU161271
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|218501245|gb|FG948195.1|FG948195
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGT
genomic: CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAGgtaatctttc ... ctctcgacagATTCACACCCACATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaatatcatcaccaatcttctgtaacttaaactgaacaactttctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATAAACATGGACGCCGATGTGATCACCATCGAGAACTCCCGGTCCGACG
                     ctgtaac  putative branch site (score: 3)
                                         ctttctctc  putative PPT
                        taacttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctttcttccatcagactgtcactgtaggctttcaatatcatcaccaatcttctgtaacttaaactgaacaactttctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATAAACATGGACGCCGATGTGATCACCATCGAGAACTCCCGGTCCGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA