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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatctgctcctgaactgtcaagtctttagatagttacatatagaaacactcttgtttctcaagatctcctaacatttttcttctccatgtag

Basic information

species Oryza sativa
transcript LOC_Os11g08300.1
intron # 5
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 5
lower sequence: GRMZM2G060800_T02 (Zea mays), 5'ss of exon 4
CCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatctgctcctgaactgtcaagtctttagatagttacatatagaaacactcttgtttctcaagatctcctaacatttttcttctccatgtag
 || ||||||||||||||||| ||||||||||| ||||| || ||||| ||||||||||| |||| |||||  || || ||||| |||  |||||| ||||||||    |     |||||| ||| ||  ||| |||           |   ||  || |||    || | |   || |    | || ||  || ||
ACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGACCCCGGTAGCTCTGGAGCTTGGTGGGAAATCCCCTGTTATCGTGGATTCAAATGTTGATCTCCATgtaaatgcatctctatgaactatcatgttcttaaata----------aagttaccatttttt----agttattacaaaaccggtattttcattgcag

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G118800_T01 (Zea mays), 5'ss of exon 5
CCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaa--catctgctcctgaactgtcaagtctttagatagttacatatagaaacactcttgtttctcaagatctcctaacatttttcttctccatgtag
 ||||| |||||||||||||| ||||||||||| || || |||||||| ||||||||||| |||| |||||   |||| || || |||  ||| |||||||||||  |||||   |  ||||| ||| || |||  | |    |||        |   ||||||     | |  |  |||   | |||||  |      
ACGCATCGTGATGGCAGCAGCCGCAAAGCATCTAACTCCGGTGGCTCTGGAGCTTGGTGGGAAATCCCCTGTTGTTGTGGACTCAAATGTTGACCTTCATgtaaatgcatctctgcgcgaactatcatgtttttgaacaagatcat-------tatcattgttttagttgtttacagaaccggtgtcttcgtcgcag--

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv18s0001g02440.t01 (Vitis vinifera), 5'ss of exon 7
CCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatctgctcctgaactgtcaagtctttaga--tagttacatatagaaacactcttgtttct--caagatctcctaacatttttcttctccatgtag---------------------------------
 || || ||||||||||| ||||||||||| ||||| ||||| ||| | |||||||| || ||||| || |   | ||||||||  | | | || | | |||||| | |   || |   ||  ||    | | |   ||    ||| ||       |  |   | |  ||  ||   ||| | |||| | |||  |||                                    
ACGAATTGTGATGGCAGCTGCTGCAAAGCACCTTACACCTGTAGCTTTGGAGCTTGGGGGGAAATGTCCAGTTGTCGTTGATTCAGACATTAATTTACCTgtaaagaacctttcttagtcttgcatacttatggtgctatggtcatttaaccctgttgctacctgtggcataatgggctacccttttgcctctgtatggcttatgtgctgacatagtttttttgtgtttccaag

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:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|29660175|gb|CB656450.1|CB656450
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|29660180|gb|CB656455.1|CB656455
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|29645892|gb|CB650899.1|CB650899
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|33794991|gb|CF323375.1|CF323375
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAANNNNNNNATGTAACAACGGGCA
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGG-ATGTAACAACGGGCA
EST: gi|58591471|gb|CF989779.1|CF989779
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|29643971|gb|CB648978.1|CB648978
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|58689115|gb|CK077802.1|CK077802
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|29666336|gb|CB662611.1|CB662611
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|29665740|gb|CB662015.1|CB662015
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|58691193|gb|CK079880.1|CK079880
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|58691525|gb|CK080212.1|CK080212
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|58695788|gb|CK084475.1|CK084475
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|58690002|gb|CK078689.1|CK078689
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAAC
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAAC
EST: gi|25806016|gb|CA761977.1|CA761977
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|33675935|gb|CF304174.1|CF304174
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|29630144|gb|CB635153.1|CB635153
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|29681705|gb|CB677980.1|CB677980
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|33800254|gb|CF325992.1|CF325992
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|33675797|gb|CF304036.1|CF304036
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|58694731|gb|CK083418.1|CK083418
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
EST: gi|88199260|gb|CI199110.1|CI199110
EST:     AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCAT                         GTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG
genomic: AGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatct ... ctccatgtagGTTACCATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTCTAATACTGATCTTCATgtaaacatctgctcctgaactgtcaagtctttagatagttacatatagaaacactcttgtttctcaagatctcctaacatttttcttctccatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA