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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_Os03g18310.2
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