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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaatagaaagtttattacgatgcctatcattttgcacattactttattgatgcgctcttcctgtttgtctgctactgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC

Basic information

species Oryza sativa
transcript LOC_Os01g10150.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
gtttgaatagaaagtttattacgatgcctatcattttgcacattactttattga-tgcgctcttcctgtttgtctgctactgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC
||| |  | | ||  ||| || |||     | |     ||| ||| || ||||| | |  |   | | | ||| |||| |  |||||||||| |||||||| |||||||| ||||||||||||||||||||||||||  | ||||||||||| ||||||||||| |||||||| |||||||| ||||||
gttcggttgggaatattagtatgatatgctttaccactcacgttatttcattgaatacttttgacatttgtgtttgcttc-ataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 8
gtttgaatagaaagtttattacgatgcctatcattttgcacattactttattgatgcgctcttcctgtttgtctgc-tactgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC
       || |   |||  ||  ||  |||| |  | | |    || |    | |  |       |  |   |||  | ||    ||||||| || ||||||||||||||||||||||| ||  | ||  |||| ||  |||||||||||||| | ||||| ||||| ||||| ||| | || ||||| 
------gtaaattatttgcta-aatatctataaact-gtagtcaacgtccaggttttgaatgattttgtaaactgtattcttgccacagGGGCACAGTTCGTTATGCTAGTGTGCATGCTCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 8
-------------------gtttgaatagaaagtttattacgatgcctatcattttgcacattactttattgatgcgctcttcctgtttgtctgctactgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC
                   | |    |||||| | | |||  ||| ||||  || | ||  ||  | |||||||    |   | ||| ||     || | |   ||||||||| || || ||||||||||||||||| || || || ||||||| | ||||||| |||||| | ||||| |||||||| ||||| ||||| ||||| 
gtgtttataattgaatttggatcatgtagaaaatgt-ttat-atgtctat--ttatacagttttttgtattgata---ttaacttgtatggaaaatatttt---cagGGGTACAGTCCGCTATGCTAGTGTGCATGCACATTTAGGGAGAACTGCAAGCAGGAGGGATGACTTGGAATCTCTTGCATATACACTGATTTTTCTTCTT

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 8
---------------gtttgaatagaaagtttattacgatgcctatcattttgcacattactttattgatgcgctcttcctgtttgtctgctactgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC
                |  || ||   ||   ||   ||| |   |  || ||||  ||  | |||||||    |   ||||| ||     || | |   |||||| || || || ||||||||||||||||| || || || ||||||| | ||||||| |||||| | ||||| |||||||| ||||| ||||| ||||| 
gtatttataattgaaatcggattatgtagaaaatgttgatacaactatttatgcagttttttgtattgata---ttaacctgtatggaaaatatttt---cagGGGCACAGTCCGCTATGCTAGTGTGCATGCACATTTAGGGAGAACTGCAAGCAGGAGGGATGACTTGGAATCTCTTGCATATACACTGATTTTTCTTCTT

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 8
gtttgaatagaaagtttattacgatgcctatcattt-tgcacattactttattgatgcgctcttcctgtttgtctgctactgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC
       || |   |||  ||  ||  |||| |  | |   || |       | ||| |   ||        | |  |  ||  | |||||| || |||||||||||||| |||||||||||  | || ||||| ||  |||||||||||||| | ||||| ||||| ||||| ||| | || ||||| 
------gtaaattatttgcta-aatatctataaactgtagtcaatgtccaggttatgagtgattttataaactatattcttgcca-cagGGGCACAGTTCGTTATGCTAGCGTGCATGCCCATCTTGGTAGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 8
-----------gtttgaatagaaagtttattacgatgcctatcattttg-cacattactttattgatgcgctctt---cctgtttgtctgctactgtaa---acagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC
             |||| ||   |  |   | |  |     |||||||        | ||| |  || |  |  |   | || | ||    ||   ||    ||||||| || || |||||||||||||||||||| ||| | ||||| |||||| |||| ||||||||  | ||||| ||||| ||||| || ||||| ||||||
gtaaaatcagaacttgagtattcaactgccttcagttagcttcattttaatgtgggattttgtatatccttttgtttacttgctggtacaatatgttatgctacagGGGAACAGTACGTTATGCTAGTGTGCATGCTCACCTTGGAAGGACTGGAAGCAGAAGAGATGATTTGGAATCTCTTGCTTACACCCTCATTTTTCTTCTC

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------------gtttgaatagaaagtttattacgatgcctatcattttgcacattactttattgatgcgctcttcctgtttgtctgctactgtaa-------acagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC
                                |   ||   | |||  | | |  |   |  |||   | |||    |||| |  | ||| | ||  |       ||   |||       | ||||| ||||| || |||||||||||||| || || ||||| ||||||||  | |||||||||||  | ||||| ||||| ||||| ||||||||||| |||
gtacaatcattgacaatttcttgttttataaatatttatgtactttccttctaccctgtttctttattatatttgcatattaaaac-ctcctacttctgactcattagaataatggtcttatagGGGAACTGTGCGATATGCTAGTGTGCACGCTCATTTGGGGAGAACTGGCAGTAGGAGAGATGATTTGGAATCTCTTGCTTACACTCTTATTTTCCTCCTC

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|88573975|gb|CI665744.1|CI665744
EST:     GCTGGTACAGGAAAGCATGTTGAATATGACCAGAGACCTGATATCTTTAG                         GGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATG
genomic: GCTGGTACAGGAAAGCATGTTGAATATGACCAGAGACCTGATATCTTTAGgtttgaatag ... ctgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATG
EST: gi|29645031|gb|CB650038.1|CB650038
EST:     GCTGGTACAGGAAAGCATGTTGAATATGACCAGAGACCTGATATCTTTAG                         GGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATG
genomic: GCTGGTACAGGAAAGCATGTTGAATATGACCAGAGACCTGATATCTTTAGgtttgaatag ... ctgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATG
EST: gi|29670785|gb|CB667060.1|CB667060
EST:     GCATGTTGAATATGACCAGAGACCTGATATCTTTAG                         GGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATG
genomic: GCATGTTGAATATGACCAGAGACCTGATATCTTTAGgtttgaatag ... ctgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcacattactttattgatgcgctcttcctgtttgtctgctactgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC
               tattgat  putative branch site (score: 3)
        attactttattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaatagaaagtttattacgatgcctatcattttgcacattactttattgatgcgctcttcctgtttgtctgctactgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG