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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgtttccatgatggcgaataggtggttgacctatgcactagggaatagggatatattcatcatctctggctgacacattctgtaactattctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGAGGAGGCTGACGAAGAG

Basic information

species Oryza sativa
transcript LOC_Os12g25710.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 5
---cctgtttccat-gatggcgaataggtggttgacctatgcactagggaatagggatatattcatcatctctggctgacacattctgtaactattctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGAGGAGGCTGACGAAGAG
     ||| ||| | | |   |   |  ||| ||   ||  || |        ||  |       |  | ||    ||| ||||||||||  |||||||  |||||||||||| || || |||||||| |||||||| |||||||| |||||||| ||||| || ||||||
tttaatgtatcctttgtttatgtgcatatggctg---tacccagtcctcccctggtgtgcgcgtgttttttccttgtga-acattctgtagttattctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG

upper sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 6
cctgtttccatgatggcgaatag-gtggttgacctatgcactagggaata----gggatatattcatcatctctggc-tgacacattctgtaactattctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGAGGAGGCTGACGAAGAG
    ||   ||| |   | |||  || | |  | | |  | |||   |||    || |  |  || |  ||  | |  ||   | || |  || | ||    ||||||| |||||||| ||||||||||||||||| || ||||||||  | || ||||| || || | ||||
----ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaactttgtcctagtccattgtgtggtgc-ttatagaagt-ttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG

upper sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G40930.1 (Glycine max), 3'ss of exon 6
cctgtttccatgatggcgaatag-gtggttgacctatgcactagggaata----gggatatattcatcatctctggctgacacattctgtaactattctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGAGGAGGCTGACGAAGAG
    ||   ||| |   | |||  || | ||   | |  ||||    |||    || |  |  ||     |  ||  ||   | |  |  || | ||     |||||| || ||||| ||||||||||||||||| || ||||||||||| || || || || || | ||||
----ttaatatggttttggatactgttgctgttatgtaaactaatttatattatggaactttgtctagtccattgtgtggtgc-tcatagaagttttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGATGAAGCAGATGCAGAG

upper sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G62120.2 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------------cctgtttccatgatggcgaataggtggttgacctatgcactagggaatagggatatattcatcatctctggctgacacattctgtaactattct--ccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGAGGAGGCTGACGAAGAG
                                                                             ||||||     |    | | ||   || || | || | | |  |     || | |   ||   ||        | || |   ||||   | |    ||||||||||||||||||||||||| ||||| || || || || || || ||||  || || || ||||||
gtattttattatcatatactcctttctactttttctgttcattatcatgttagtactttttttcttgagctagtcattgtttctgctgtaaatattcggc--ttaacgtttggatt-gaaaccttcgacacagaaatttgcttgccacagcccactgcctaacctatttaattgcagGAGCCGTGAGTTCCTTTGGCAGGAAGGTCACACTGCATTCGCCACAAAAGCAGAAGCAGATGAAGAG

upper sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G10880.1 (Arabidopsis thaliana), 3'ss of exon 2
cctgtttccatgatggcgaataggtggttgacctatgcactagggaatagggatatattcatcatctctggctgacacattctgtaactattctccg-----cagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGAGGAGGCTGACGAAGAG-----------------------------------------------------------------------------------------------------------------------------
                                        ||   | | ||   || ||   | |   | | ||  |  ||  |  ||  | | ||      |||||||||||||||||||||||||||||| || || | |||||| || ||||| |||||||| || |||                                                                                                                             
--------------------------------------gttaaccagtgggctaatgtta--cgttgttagatggga-gtttagcgaccctaccccatttatcaggagccgtgagttcctttggcaagaaggacacactgattttgctaccaaagaagaggctgatgaggaggtgcttgatgtttgaacatctacagCCGCGTGTATGACTCATGGAGATGACAAAGGTTTAGTATTCCCTCCTAAAGTGGCACCTGTTCAAGTTGTTGTAATCCATGTTCCCATCAAAGGCGCTGC

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|33794258|gb|CF323019.1|CF323019
EST:     TGGTGTAACGTCGTGCGATGGGAGTTTAGCAATCCAACTCCATTCATAAG                         GAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGA
genomic: TGGTGTAACGTCGTGCGATGGGAGTTTAGCAATCCAACTCCATTCATAAGgtagtcaatt ... ttctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGA
EST: gi|58690340|gb|CK079027.1|CK079027
EST:     TGGTGTAACGTCGTGCGATGGGAGTTTAGCAATCCAACTCCATTCATAAG                         GAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGA
genomic: TGGTGTAACGTCGTGCGATGGGAGTTTAGCAATCCAACTCCATTCATAAGgtagtcaatt ... ttctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGA
EST: gi|88312613|gb|CI587521.1|CI587521
EST:     TGGTGTAACGTCGTGCGATGGGAGTTTAGCAATCCAACTCCATTCATAAT                         GAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTTGCAACTAAAG
genomic: TGGTGTAACGTCGTGCGATGGGAGTTTAGCAATCCAACTCCATTCATAAGgtagtcaatt ... ttctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTT-GCAACTAAAG
EST: gi|12404672|gb|AU166273.1|AU166273
EST:     TGGTGTAACGTCGTGCGATGGGAGTTTAGCAATCCAACTCCATTCATAAG                         GAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGA
genomic: TGGTGTAACGTCGTGCGATGGGAGTTTAGCAATCCAACTCCATTCATAAGgtagtcaatt ... ttctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGA
EST: gi|33811197|gb|CF331488.1|CF331488
EST:     GATGGGAGTTTAGCAATCCAACTCCATTCATAAG                         GAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGA
genomic: GATGGGAGTTTAGCAATCCAACTCCATTCATAAGgtagtcaatt ... ttctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGA
EST: gi|58674015|gb|CK062701.1|CK062701
EST:     TGGTGTAACGTCGTGCGATGGGAGTTTAGCAATCCAACTCCATTCATAAG                         GAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGA
genomic: TGGTGTAACGTCGTGCGATGGGAGTTTAGCAATCCAACTCCATTCATAAGgtagtcaatt ... ttctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagggatatattcatcatctctggctgacacattctgtaactattctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGAGGAGGCTGACGAAGAG
                                    ctgtaac  putative branch site (score: 3)
                                          ctattctcc  CT-rich tract
       atatattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgtttccatgatggcgaataggtggttgacctatgcactagggaatagggatatattcatcatctctggctgacacattctgtaactattctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGAGGAGGCTGACGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA