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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATAGGGCTCCGGAGCTCATATTTGGTGCCACCGAATACACTACAGCTATTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggctggattttctttgcacattttggggaagtttgttgtttaccaccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacag

Basic information

species Oryza sativa
transcript LOC_Os01g14860.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G835235_T03 (Zea mays), 5'ss of exon 7
CTATAGGGCTCCGGAGCTCATATTTGGTGCCACCGAATACACTACAGCTATTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggctggattttctttgcacattttggggaagtttgttgttt---accaccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacag
|||||||||||| |||||||||||||||||||| || || || ||||| |||||||| ||||||||||| |||||||||||||| |||||| ||||||||||| |     |  | |||  |    |||   || | |||| || |||     || |    |   | || |  |  ||    |  |||||||    | |   ||| ||||
CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatg-----gtgtcttcgatatttatt---ggcatgtttattttttcaagtcaacaaaaaaagtcttttgaagttcacattttcttacaagaactat---ttcaacag

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G129482_T01 (Zea mays), 5'ss of exon 3
CTATAGGGCTCCGGAGCTCATATTTGGTGCCACCGAATACACTACAGCTATTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggctggattttctttgcacattttggggaagtttgttgtttaccaccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacag-----
|||||||||||| |||||||||||||||||||| || || || ||||| |||||||| ||||||||||| |||||||||||||| |||||| ||||||||||| |     |  | |||  |    |||   || | |||| || |||          |      | | ||  ||    |  |||||||    | |   ||| ||||     
CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatg-----gtgtcttcgatatttatt---ggcatgtttattttttcaagtaaaaaaaaagtcttttgagttcacattttcttacaagaactat---ttcaacagccttt

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 7
CTATAGGGCTCCGGAGCTCATATTTGGTGCCACCGAATACACTACAGCTATTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaag-cggctggattttctttgcacattttggggaagtttgttgtttaccaccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacag
|||||||||||| |||||||||||||||||||| || || || ||||| |||||||| |||||||||||||||||||||||||| |||||| |||||||||||||  | ||  | ||| | |   ||||||    ||| || |      ||| |  || |  |   ||  |        || |||||||    | | ||   |||||
CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtctcaaatttttattgccattttaaaaaaggttttcaa--gccaacaaggtcctttcagttcacac-----tgtcttacaagaactatttg---gacag

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 8
CTATAGGGCTCCGGAGCTCATATTTGGTGCCACCGAATACACTACAGCTATTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggctggattttctttgcacattttggggaagtttgttgtttaccaccctggactctattgtcgaagt-cggtatgccttacaattgttttctgttcgacag
 ||  | |||||||| || ||||||||||| || || ||||| ||||| || |||||||||||  ||||||| ||||| |||||  |  |  | || |||||    |  |   |  || |||||  | ||     | | ||    | |||  |         |||  |   || | |                              
TTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCTGGTCGACTGGATGCGTTCTGGCTGAGTTACTTCTTGGTCAGgt---tgtatacctcgtccttgcaactcttcc---attatgccactcaccgtctcatcaatcatttccactgtgcag------------------------------

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ07216 (Selaginella moellendorffii), 5'ss of exon 8
CTATAGGGCTCCGGAGCTCATATTTGGTGCCACCGAATACACTACAGCTATTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggctggattttctttgcacattttggggaagtttgttgtttaccaccctggactctattgtcgaagt-cggtatgccttacaattgttttctgttcgacag
|||  | |||||||| || ||||||||||| || || ||||| ||||| || |||||||||||  ||||||| ||||| |||||  |  |  | || |||||    |  |   |  || |||||  | ||     | | ||    | |||  |         |||  |   || | |                              
CTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCTGGTCGACTGGATGCGTTCTGGCTGAGTTACTTCTTGGTCAGgt---tgtatacctcgtccttgcaactcttcc---attatgccactcaccgtctcatcaatcatttccactgtgcag------------------------------

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|33381492|gb|CF196835.1|CF196835
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58686155|gb|CK074842.1|CK074842
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58606572|gb|CK034605.1|CK034605
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58687307|gb|CK075994.1|CK075994
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58679602|gb|CK068289.1|CK068289
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58590369|gb|CF988677.1|CF988677
EST:     TGGGCATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58673993|gb|CK062679.1|CK062679
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         GCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATC
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATC
EST: gi|218498670|gb|FG952679.1|FG952679
EST:     TGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58602991|gb|CK013519.1|CK013519
EST:     TTGAGATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58672614|gb|CK061300.1|CK061300
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|218486932|gb|FG950343.1|FG950343
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGTTGAAAGTGGTGTAGACCAACTTGTGGA
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGA
EST: gi|38469291|gb|CF953422.1|CF953422
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|29677190|gb|CB673465.1|CB673465
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58679239|gb|CK067926.1|CK067926
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|29677191|gb|CB673466.1|CB673466
EST:     GCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: GCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58682391|gb|CK071078.1|CK071078
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|66918477|gb|CX105325.1|CX105325
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|2317500|gb|C22554.1|C22554
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATAGGGCTCCGGAGCTCATATTTGGTGCCACCGAATACACTACAGCTATTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggctggattttctttgcacattttggggaagtttgttgtttaccaccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacag

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