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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g18310.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttca-------aattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
       ||   |||  ||| | || |||   |||| ||   ||  | |  |||        || ||    |||||||||| | | |    | |||||  ||||||||||||| | |||||||| ||||||||||||||||| ||||| |||||||| || || ||||||||||||||||||||||||||||||||||||||||||
-------agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 7
catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattct-----agGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
    ||   ||    | |||||  |   |  ||| |   |  ||| ||   ||    ||      | |  |  | | |||   || | ||    || |     |||| ||  |||||||  | ||||| || || || || ||||| |||||||| || ||||| |||||||||||| | || ||||||||||||||||| |||
---ctggcaaaaatgtcatttccatttgta-gttcatcaaagttagtaaatttggttttttaaaagtaaattatttttaatt-ttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGTTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
--catatgaagaatgaataatttctgtc---aatgtgttgaaat-actttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
   ||   || ||||    |||||  ||   | |   |  || | | |  || ||  || |||  |    |  | || ||   |||    | |  ||      ||||| ||  ||||||| || ||||| || || || || ||||| |||||||| || |||||||||||||||||| | || ||||||||||||||||| |||
ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaatttcttttatg------tagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
-----catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
        |  || ||||    ||| |  ||  |  ||| |  || |||| ||   |  ||| ||  |||| |  |      |  |  | ||          |||||  | ||||||||||| || ||||| |  || || ||||| || ||||| || |||||||||||||||||| | || ||||||||||||||||| |||
tacctggaaaaaaaaatgccacattcccatctgta-gttcatctaatttagtaaaat--aaaata--tttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagt---tcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
 |  || | ||  |||      |  |  | |||      |  |||||  |    | |  |  |||| | |   |  | | |||| |  ||       |  |||||  | ||||||||||| || ||||| |  || || ||||| |||||||| || |||||||||||||||||| | || ||||||||||||||||| |||
tacctggaaaaaaaatgccacattcccttctgt-acttcatcttatttagtaaaataaaatatttgaaatgaataatttctaacta--gtttctttttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
catatgaagaatgaataatttctgtc---aatgtgttgaaatactttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
    ||   ||    | |||||  |    | |   |  || |   | | | || ||      |  |      || ||   |    | |    |     | ||||| ||  |||||||  | ||||| || || || || ||||| |||||||| || ||||  |||||||||||| | || ||||||||||||||||| |||
---ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
--catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagttctt--ctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
   |  |  || |  |  |  ||   || || ||||| |       |||    | | ||||   ||   | |   |   |||||| | | |      |||  ||||||| ||||||||||| ||||| || ||||| || ||||| |||||||| || ||||| ||||| |||||||| || |||||||||||||||||||||
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaattta----tatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 3'ss of exon 7
---catatgaagaatgaataattt--ctgtcaatgtgttgaaatactttattatgct-tcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
     |   |  | || ||  ||   |    |||||| |      |    | | ||| | ||  |||  | | ||||       ||  | | |       ||  |||||||||| || |||||||| ||||| || || || ||||| || || || ||  | || |||||||||||||| || || |||||||||||||| |||
tgctttcctagtagtgtattgttgagcgtataatgtgattgtggccaaattcacgctgttaagctacgctgggagttg------aatgagtctctgatggtttcagGTTGGGTTACCGGCTCGTGGAAAGACATTCACTGCAGCTAAACTGACCAGATATTTGCGGTGGTTAGGTCATGACACCAAGCACTTCAATGTTGGCAAG

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|58689570|gb|CK078257.1|CK078257
EST:     CTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTG                         GTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGG
genomic: CTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTGgtacttttca ... gccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
                             ctgtaac  putative branch site (score: 3)
                                              ccattct  putative PPT
      ttcaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

- -atgaagaa
- - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - tgcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgtgc