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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattattattgtgatacctgtcaaatgccttacaagctttttcatgtctagttaaagcaaataccttggcattgcacatgtttgcaaaatatgatcat...

Basic information

species Oryza sativa
transcript LOC_Os03g16700.4
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16700.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G110309_T01 (Zea mays), 5'ss of exon 9
ATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattattattgtgatacctgtcaaatgccttacaagctttttcatgtctagttaaagcaaa--taccttggcattgcacatgtttgcaaaatatgatcat----------
 ||||||||||| |||||||| || ||||| ||||| |||||||| || || ||||||||||||||||             | ||||||||||| | ||      ||  |        |||||||||  || ||| || ||||| ||  | |  |||| |||| |           
GTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTATGTTGATCTTAAGgtaag------------aactgtcaaatgcttgactttgacttcaactaaagactaaagcaaaaatatctttgctttgcatatactcgtcaaatctgataactagttttctt

upper sequence: LOC_Os03g16700.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G063151_T01 (Zea mays), 5'ss of exon 8
ATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattattattgtgatacctgtcaaatgccttacaagctttttcatgtctagttaaagcaaataccttggcattgcacatgtttgcaaaatatgatcat--
 ||||||||||| |||||||| || ||||| |||||||||||||| || |||||||| ||||||||||| | |      || ||||||     | | |       |     || |  |||  |    |  ||    |||| |    ||| |    | ||   |   
GTGGCGAGATGTTAAACTTCGCGCTTTTGACAATGCAAAGCACCGTACCTACGTTGACCTTAAGgtaataactgcca-aatgcctgtctttgacgtcaactctcataattagtttccttactgtccttttctgattattg-attgattttctttttttgccgaacc

upper sequence: LOC_Os03g16700.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G41210.1 (Glycine max), 5'ss of exon 12
ATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattattattgtgatacctgt-caaatgccttacaagctttttcatgtctagttaaagcaaatacct-tggcattgcacatgtttgcaaaatatgatcat
 ||||| ||||| |||||||| || ||||| ||||||||||| ||||| ||||| ||| | |||||||    | ||||||  | | | || | || |   |     | | || ||| |  |||| |  |  || |  ||   ||  |  |||      | | |   
GTGGCGCGATGTTAAACTTCGTGCATTTGACAATGCAAAGCATCGGACATACGTGGATTTGAAGgtaaaaccttttgtgacccatatgcataagcatagtattggatattat-tcttgcaaaagaacgtggctgtcacacctcaggttgttgggtggcacgcttg-

upper sequence: LOC_Os03g16700.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA15G04200.1 (Glycine max), 5'ss of exon 9
ATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattat-tattgtgatacctgt-caaatgccttacaagctttttcatgtctagttaaagcaaataccttggc--attgcacatgtttgcaaaatatgatcat
 ||||| ||||| |||||||  || ||||||||||||||||| ||||| ||||| ||| | |||||||  |  | ||||||  | | | || | || |   |     ||| ||   |  | |||  || |      |   |  | || ||  ||  | |  | |    
GTGGCGTGATGTTAAACTTCATGCTTTTGATAATGCAAAGCATCGGACATACGTCGATTTGAAGgtaaaaaccttttgtgacccttatacataggcatagtattggattttattcttgctcaaatgaattgttgaagagaagaggacgtggctgtcacacctca----

upper sequence: LOC_Os03g16700.4 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G07540.1 (Arabidopsis thaliana), 5'ss of exon 8
ATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattattattgtgatacctgtcaaatgccttacaagctttttcatgtctagttaaagcaaataccttggcattgcacatgtttgcaaaatatgatcat
 ||||| || || ||| | || || ||||||||||| |||||||| |||||||||||| | |||||||     | |   |  |    |  |      |  || | | |  | ||| ||  ||| || || ||     | | |    || |              
GTGGCGTGACGTAAAATTGCGAGCTTTTGATAATGCTAAGCACCGTACTTACGTTGATTTGAAGgtaa-----aataaaactctctccttacagtgaatgaggtctat-gtttcttgtgcaag-aagtaactaattttgggattgattag--------------

upper sequence: LOC_Os03g16700.4 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ13094 (Selaginella moellendorffii), 5'ss of exon 2
ATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattattattgtgatacctgtcaaatgccttacaagctttttcatgtctagttaaagcaaataccttggcattgcacatgtttgcaaaatatgatcat
 ||||| ||||||||||| | ||| ||||| || || |||||| |||| ||||| ||||||||||| | |  | |||   |  || |    |   || |   | | |    | |  |||    ||                                       
GTGGCGTGATGTCAAACTCCAGGCTTTTGAGAACGCCAAGCACAGGACATACGTGGATCTTAAGgtcagtgctgttggattgtctttttgttttttttcttccatctaacaggcctgttgttccag--------------------------------------

upper sequence: LOC_Os03g16700.4 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ14112 (Selaginella moellendorffii), 5'ss of exon 2
ATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattattattgtgatacctgtcaaatgccttacaagctttttcat-gtctagttaaagcaaataccttggcattgcacatgtttgcaaaatatgatcat
 ||||| ||||||||||| | ||| ||||| || || |||||| |||| ||||| ||||||||||| | |  | |||   |  || |    |   ||     |  | | |  | || |||    ||                                       
GTGGCGTGATGTCAAACTCCAGGCTTTTGAGAACGCCAAGCACAGGACATACGTGGATCTTAAGgtcagtgctgttggattttctttttgtttttttttcttccgtctaacaggcttgttgttccag--------------------------------------

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|89191999|gb|CI393356.1|CI393356
EST:     AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAG                         GACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
genomic: AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
EST: gi|29614153|gb|CB619166.1|CB619166
EST:     AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTCCGTTGATCTTAAG                         GACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
genomic: AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
EST: gi|38468421|gb|CF952552.1|CF952552
EST:     AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAG                         GACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
genomic: AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
EST: gi|88470021|gb|CI407292.1|CI407292
EST:     CGGACTTACGTTGATCTTAAG                         GACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
genomic: CGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
EST: gi|29617377|gb|CB622389.1|CB622389
EST:     AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAT                         GACAAATGGAAGACGCTCGTGCA
genomic: AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCA
EST: gi|86504415|gb|CI147048.1|CI147048
EST:     AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAG                         GACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
genomic: AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
EST: gi|33381803|gb|CF197146.1|CF197146
EST:     AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAG                         GACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
genomic: AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
EST: gi|88488940|gb|CI426211.1|CI426211
EST:     TGATAATGCAAAGCACCGGACTTACGTTGATCTTAAG                         GACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
genomic: TGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
EST: gi|88488306|gb|CI425577.1|CI425577
EST:     CTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAG                         GACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
genomic: CTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
EST: gi|88515625|gb|CI443279.1|CI443279
EST:     AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAG                         GACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
genomic: AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
EST: gi|29627496|gb|CB632507.1|CB632507
EST:     AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAG                         GACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG
genomic: AACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 64 (upstream exon), 45 (downstream exon)
Score: 21

ATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattatta ... atgccaacagGACAAATGGAAGACGCTCGTGCACACGGCGAGCATCTCGCCCCAGCAGCGGCGTGGCGAGCCGGTGCCACAGGAGCTGCTCGACAGGGTCCTGGCGGCTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAGgtaattattattgtgatacctgtcaaatgccttacaagctttttcatgtctagttaaagcaaataccttggcattgcacatgtttgcaaaatatgatcat

- - - - - - - - - - - - - - - - - GCAAAG