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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaatggtgcattcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgctattgagtagggattaattgcaatttttgg...

Basic information

species Oryza sativa
transcript LOC_Os11g08300.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g08300.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G118800_T01 (Zea mays), 5'ss of exon 3
GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaatggtgcattcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgctattgagtagg---gattaattgcaatttttgg
 ||||||| ||| | || || ||||| ||  |||| ||||| ||| | ||||| || ||||| || ||  |||||||||| ||||||||||||||| ||||||| | |      |  | |  |  |  | ||  ||   |    | | |       | || ||   || ||   |      ||||| | ||||    |  
ATACCTGCGGCCTTAACCACGTTCCCGTCCTCTGCTCAAATCGTGCCGGAGCCCCTCGGTGTGGTGCTCATCATCTCAGCCTGGAACTACCCTTTCAgtaagttgattccaaactgtacgagttctttttgtt-ttttttttctagcttgcccgtctggactatctctgttttttgaatttgattattagcaacagat--

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G060800_T02 (Zea mays), 5'ss of exon 2
GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagtt------aaatggtgca---ttcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgctattgagtagggattaattgcaatttttgg
|||||||| ||| | ||||||||||| ||  | || ||||| ||| | ||||| || || ||||| ||  |||||||||| ||||||||||||||| |||||||      |||  || ||   ||  | | |  | ||  ||  |   ||  |     |||  |      | |        | |||| |   | |           
GTACCTGCGGCCATAACTACATTCCCGTCCTCCGCCCAAATCGTGCCGGAGCCCCTCGGCGTCGTGCTCATCATCTCAGCCTGGAACTACCCTTTCAgtaagttcattctaaactgtacaatttttttttcttcttcttctagcttgctaggctggactatctctggtttttaattcgaaaaataggaacagaatct---------

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G26390.1 (Glycine max), 5'ss of exon 3
GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa---tggtgcat-tcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatg-ctattgagtagggattaattgcaatttttgg--------
||     |  |  || | || || || ||  | ||  |||| || || || || || || || ||  |||||||||| |||||||||||||| ||||||| |||||    | ||   | |  | |  ||||||  | |    | |     | || |||  |     |||  ||    | |    ||||  | |  | | |          
GTCAAAACTTCAATCGCAACTTTTCCTTCTTCAGCTGAAATAGTATCTGAACCACTGGGGGTTGTGTTAGTCATCTCTGCATGGAACTACCCATTCTgtatgttaatatttagttggtattgtttcacatacttttgagctgacatctcacctttttctttcctccaatctctgcaaaatctatattacattctctgtctatctttccag

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA14G24140.1 (Glycine max), 5'ss of exon 3
GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa---tggt--gcattcatgtttcatactcgtaattgcata----aacaccgttattccatagagtaatgctat-tgagtagggatta----attgcaatttttgg------------
||     |  |  || | || || || ||  | ||  |||| || || || || || || || ||  |||||||||| |||||||||||||| ||||||| |||||    | ||  |||||  | |  ||| ||  | |    | |    | |    |  ||||   |||   ||| |  |   ||  ||| |    ||| || | | |              
GTCAAAACTTCAATCGCAACTTTTCCTTCTTCAGCTGAAATAGTATCTGAACCACTGGGGGTTGTGTTAGTCATCTCTGCATGGAACTACCCATTCTgtatgttaatatttagtcagcatt-gtctcacatgcttttgagctgacatctcacctttttctttcctccgagctctgcaaaatctataaagatgataatattacattctctatctatctttgcag

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G44170.3 (Arabidopsis thaliana), 5'ss of exon 3
GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaatggtgcattcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgctattgagtagggattaattgcaatttttgg
| |    |  | || || || || ||  || | ||  | |||||||| |||||||||||||| || ||||| ||||| || |||||||| |||||  ||| |||           | | |||| | |||   | ||  ||    ||  ||  |    || || |  || ||   |     ||  ||||||       
GCAAAGACTTCTCTAACAACGTTTCCTGCATCCGCGGAGATTGTGTCTGAGCCTCTTGGTGTTGTGCTAGTGATCTCGGCTTGGAACTATCCTTTTCgtatgttccgatcactgattaagtttta-actataagttatat---tacattttgtatgaagtgtgacactttttttt-----ttttttgcaag------

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv07s0031g02630.t01 (Vitis vinifera), 5'ss of exon 5
GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaatggtgcattcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgcta-ttgagtagggattaattgca-atttttgg
|      |  |  | || ||||  |||||| | ||| ||||||||||||| ||||||||||||||  | ||||||||| ||||||| || ||||| |||| || |       |  |  | |  || |     |  |  |  || |||  |  |   |||  |  ||| |  |   |  | ||   |   | |  | || 
GCCAAAACTTCAATGACAACATATCCATCATCAGCAGAAATTGTGTCAGAACCTCTTGGTGTCGTGTTGGTCATCTCAACATGGAATTATCCTTTGTgtatgtaaggcaaccc--tggtatcacacaacttcatatctaggaaaaccaatcatatctagcatgttgcaagctatatttgaatagttcatatagctctga

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|29680879|gb|CB677154.1|CB677154
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|29660175|gb|CB656450.1|CB656450
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|88433183|gb|CI569852.1|CI569852
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGG
EST: gi|58695219|gb|CK083906.1|CK083906
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|58604207|gb|CK014735.1|CK014735
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|29645892|gb|CB650899.1|CB650899
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|58594363|gb|CF992671.1|CF992671
EST:     TAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATGGAGGCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: TAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|33794991|gb|CF323375.1|CF323375
EST:     GCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: GCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|58591471|gb|CF989779.1|CF989779
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTGCT                         GGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|29643971|gb|CB648978.1|CB648978
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|58689115|gb|CK077802.1|CK077802
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|58691193|gb|CK079880.1|CK079880
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|58691525|gb|CK080212.1|CK080212
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|58695788|gb|CK084475.1|CK084475
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|58690002|gb|CK078689.1|CK078689
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|33675935|gb|CF304174.1|CF304174
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|29630144|gb|CB635153.1|CB635153
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|29681705|gb|CB677980.1|CB677980
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|33800254|gb|CF325992.1|CF325992
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGTTTTTTCCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaatggtgcattcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgctattgagtagggattaattgcaatttttgg

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