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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaattgagaatttagaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT

Basic information

species Oryza sativa
transcript LOC_Os11g33240.3
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 16
--------------------------------------------------------------------------------tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaattgagaattta---gaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
                                                                                 | ||    |  |||||| ||||   ||| | |    |||| |  |||   |||||      || ||   ||    ||  | || | |    ||   || |||||||||||||| || |||||||||||||| |||||||| || ||||| ||| ||||||| |||||||||||  ||||| | ||||| |||||||||||||
gtatatcgtttcactgaggtctagtgtttatgttcatgctcgaacacggttttgtttcccataggaaagctatatcagttcactgagatttgaatgatgtgca-gtagtctgatag-atttgtctttgtttatgaaagtgatatctatctgatgatctgtgttcgctgttgcttgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTT

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 1
tattggatctctaat-gatctg-catacagttttaccttattttttgttgaacatgaattgagaatttagaattactaaggtcacagc--gcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
     ||| |  | | | ||||  | | |||| |   | | | ||| | |||  |||  |     |   |  ||            ||   |||||| |  |||||||||||||| || |||||||||||||| ||||||||||| ||||| ||| ||||||| |||||||||||  ||||| | |||||  ||||||||||||
---atgatgtgcagtaggtctgatagagagttgtctttgactgtttatggaa-gtgacatttctctgatggtttgtgtgcactgttgcttacattcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTT

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 14
-------------------------------------------------------------tattggatctctaatgatctgcatacagttttaccttat---tttttgttgaacatgaattgagaatttag--aatta-ctaaggtcacagc-----gcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
                                                             ||    | || ||    |   |  |   ||  |   |||    | |  |||   |||||||  |  | | |   || | ||  | || | |      ||||||| |   ||||||||| ||| || |||||||||||||| |||| ||| || ||||| |||  ||| || |||||||||||  ||||||| ||||| |||||||| ||||
gtatatcatttcactgaggtctagtgttcatgatcatgctcgaacacggccttgtttcccgtaggaaagctataccagttcactgaggtttgaaagatatgagctgtctttgtttatgaatttggtgtctcgctgatgatctgtgttcgctgttgcttgcattcaatcacagGTTGTTCATGGATTTGGTCATGGAGTTCTGCGTAGGACGGACCCACGGTATCTATGCCAAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTT

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 15
tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatga-attgagaattt-----agaatt---actaaggtcacagcgcattc---atttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
            | | || ||||||    || |||  ||  | |   ||  ||   | ||  || ||     | |||     ||  |||    | || ||    ||||| ||||||| ||||| |  || ||||| ||| ||||  |||| |||||| |||| ||||||||||||||||||||||||||| | |||||| | ||||||  ||
------------attaatatgcatatctgttcaccaaatgatgtagagagaatatcactgccaacttctcagataatataagctttggttgttgtgctttttggatttgcagGTTGTGCCTGGATATGGACATGGGGTTTTACGCCAGACAGATCCAAGATACACATGTCAGAGGGAGTTTGCTTTGAAGCATTTGCCTAATGATCCATATT

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 15
tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaatt-gagaatttagaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
| |   ||   ||    |   |  |  | ||||       | ||  ||   |    |  || ||| |||  ||      ||  ||     |  ||||| ||||||| ||||| |  || ||||| ||| ||||  |||| |||||| |||| ||||||||||||||||||||||||||| | |||||| | ||||||  ||
tttaatatacatatcttttcaccaaatgatttagagggaatattactgccaacttctcagataatataggctt-tggctgttgcactttttggatttgcagGTTGTGCCTGGATATGGACATGGGGTTTTACGCCAGACAGATCCAAGATACACATGTCAGAGGGAGTTTGCTTTGAAGCATTTGCCTAATGATCCATATT

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 15
--tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaattgagaatttagaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
  |     || ||| |  |||| |||||     |     |  | ||   || |     |||| || ||      |          |  |   |  | || ||||||||||||| || || ||||||||| | ||||| || |||||| ||||||  ||||| ||||||||||| |||||| |||||||||| |||||||| |
tttccctaatatctcaccatct-catactaacgt-ttgaacctctttaggagccctttttgacaaattgtttccatctctaatttattgttattgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT

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|3758954|gb|C96653.1|C96653
EST:     CAACTGATCAACTCAAAGAGTATGTGTGGAAGACACTAAAAAGTGGAAAG                         GTTGTTCCTGGCT-CGGTCATGGAGTTCTACGTAAGACCGAT
genomic: CAACTGATCAACTCAAAGAGTATGTGTGGAAGACACTAAAAAGTGGAAAGgtagcttatc ... tcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaacatgaattgagaatttagaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
                                            ttcattt  CT-rich tract
                aatttagaattactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaattgagaatttagaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT