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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttagatgcaaacttttttagttttctagctcaagattgtgatggcttctctaaattgtcccatgctccattgttctttctaatgctgcag

Basic information

species Oryza sativa
transcript LOC_Os12g30540.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 20
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttagatgcaaacttttttagttttctagctcaagattgtgatggcttctctaaattgtcccatgctccattgttctttctaatgctgcag
||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| |||||||||||  | |  ||     |||||||||| || |  ||| |   ||  | | |||| |  |  ||   || | ||  || |   ||      |||||  |||| |||||  ||
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAGgtttgcgaaatttc----tctttttagatacacatgtttcttagttattcggtcaacaaaggaat---ttgtttatttttttggat------ttgtt--ttcttatgctttag

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 10
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttagatgcaaactttt--ttagt------tttctagctcaagattgtgatggcttctctaaattgtcccatgctccattgttctttctaatgctgcag
||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||| || |||||||||||  | |  ||    ||||||||||||||   || |  || |       ||| ||      ||      | |   ||   ||  |  ||| ||      ||                 
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGCTCTAGTCAGgtttgtgaaatttc----cctttttagatgcagtgttatggttggcaacgtgtttttatggagggagcagactcgtggctgagaaccgagccacgccgtgacgt-----------------

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA13G16040.1 (Glycine max), 5'ss of exon 1
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttagatgcaaactttttt--agttttctagctcaagattgtgatggcttctctaaattgtcccatgctccattgttctttctaatgctgcag
|||||||||||||| |||||||| ||||| ||||  |||||||||||| |||| || ||  | || |||||        | |  |  || |  | |||||| | ||||||    ||||  |  | || |||     || |  |   ||| ||   |   |  | |  |  ||  |||       
GAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAGgt-------gagttatatccataattgatgcacatttttttcagattttgaaaataaatattcctggggatcttggtaatggtattac-ttggaataatgattgcaat-------

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA20G11330.1 (Glycine max), 5'ss of exon 12
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttagatgcaaacttttttagttttctagctcaagattgtgatggcttctctaaattgtcccatgctccattgttctttctaatgctgcag
|||||||||||||| |||||||| ||||| ||||  |||||||||||| |||| || ||  | || |||||  ||   | |||   |    || |    |||  || || || |||  |    || |||     || |  |   |||  |   |      | |  |  ||  |||| |    
GAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAGgt--gagttatatccataa---ttgatgcacaattttgttcagattttaaa---aatattcctggggatcttgggaatgatattac-tgggaataatgattgcaatgtt----

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 20
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttagatgcaaacttttttagttttctagctcaagattgtgatggcttctctaaattgtcccatgctccattgttctttctaatgctgcag
||||||||||||||||||||||| ||||| ||||  ||||| |||||| |||| || ||  | || |||||       ||||  | | |    | ||||||      ||||  || ||   ||    || || ||| ||      ||||           |||  | |||||||   |||||
GAAATTAAGTTTGAGCCAAATGTTATGTGTGAACCTATTGATAAGAAAGTAACATTTCGAGCAAGCCAGgt-------aaattataaacaccattgatgca-----ctttaagttactgcatc----ttttgttggttt------attg-----------atttgtttttctaaatttgcag

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 20
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttagatgcaaactttttta--gttttctagctcaagattgtgatg-gcttctctaaattgtcccatgctccattgttctttctaatgctgcag
||||||||||||||||||||||| ||||| |||| |||||| ||||||||||| || ||  | || |||||       ||||  | | |    | ||||||   |   |||  || |  | | |     |  ||||  | || |||| |||  |                               
GAAATTAAGTTTGAGCCAAATGTTATGTGTGAACCCATTGATAAGAAACTAACATTTCGAGCAAGCCAGgt-------aaattataaacaccattgatgcactttgagttactgtatctttgtttggtttattgatctgtttttctatatttgcag-----------------------------

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 20
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 5'ss of exon 20
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttag---atgcaaacttttttagttttctagctcaagattgtgatg----gcttctctaaattgtcccatgctccattgttctttctaatgctgcag
||||| ||||||||||| ||||| |||||||| |||||||| |||||    ||||||    | || |||||| |        | |  |  || | |   ||| |  ||  | |    | || | |    ||  |  |       |  | ||    |     ||  |||       |    ||  |||||
GAAATCAAGTTTGAGCCGAATGTCATGTGCGAGCACATTGAAAAGAAGTCCACTTTCAAGGCTAGCCAGgttagctcccctccattcctgttgtggtccatgaaggctagtattaaatgcttgttacgaatattagtacttaattattttaggaagctttttgacccagacggggtgactattttgcag

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 20
lower sequence: EFJ18164 (Selaginella moellendorffii), 5'ss of exon 17
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttagatgcaaacttttttagttttctagctcaagattgtgatggcttctctaaattgtcccatgctccattgttctttctaatgctgcag
|||||||| ||||| || ||||||||||||||||  |||||||||||||| || || ||   |||||||||  |     ||   |     | || ||  |  |  || |  ||||   ||                                                              
GAAATTAAATTTGACCCGAATGTGATGTGCGAACCAATTGACAAGAAACTTACGTTTCGAGACAGTCAGgtacgggtagaactatttttatatttgaccctga--ttgtacgtttctcag--------------------------------------------------------------

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 20
lower sequence: EFJ13603 (Selaginella moellendorffii), 5'ss of exon 17
-------------------------------GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttagatgcaaacttttttagttttctagctcaagattgtgatggcttctctaaattgtcccatgctccattgttctttctaatgctgcag
                               ||||| |||||||| ||||||||||||||||||| | | ||||| ||||| ||||||    | ||||||||  |   |   | || |  ||  |||   | || |   ||   ||  |  |                                                             
CGCGGCAAACACTGAGGTTCAAATATTTGAAGAAATAAAGTTTGAACCAAATGTGATGTGCGAACCCGTGGACAAAAAACTTACTTTCAAGGCGAGTCAGgta-ggctgtgtttgttagtttcctagtcactaattcacttccgttcttcacag-----------------------------------------------------------

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 20
lower sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 17
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttagatgcaaacttttttagttttctagctcaagattgtgatggcttctctaaattgtcccatgctccattgttctttctaatgctgcag
|||||||| ||||| || ||||||||||||||||  |||||||||||||| || || ||   |||||||||  |     ||   |     ||||| ||   | |    || ||    | |||||                                                          
GAAATTAAATTTGACCCGAATGTGATGTGCGAACCAATTGACAAGAAACTTACGTTTCGAGACAGTCAGgtacgggtagaactat-----ttttatatttgaccccgatt-gtacgtttgctcag---------------------------------------------------------

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|29625340|gb|CB630351.1|CB630351
EST:     ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAG                         CTTGAAGATGGGGACATAATATGTTTCCAAAAGTCACCTGTGTCAGATGGG
genomic: ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaaga ... aatgctgcagCTTGAAGATGGGGACATAATATGTTTCCAAAAGTCACCTGTGTCAGATGGG
EST: gi|58678676|gb|CK067363.1|CK067363
EST:     ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAG                         CTTGAAGATGGGGACATAATATGTTTCCAAAAGTCACCTGTGTCAGATGGG
genomic: ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaaga ... aatgctgcagCTTGAAGATGGGGACATAATATGTTTCCAAAAGTCACCTGTGTCAGATGGG
EST: gi|29637181|gb|CB642190.1|CB642190
EST:     ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAG                         CTTGAAGATGGGGACATAATATGTTTCCAAAAGTCACCTGTGTCAGATGGG
genomic: ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaaga ... aatgctgcagCTTGAAGATGGGGACATAATATGTTTCCAAAAGTCACCTGTGTCAGATGGG
EST: gi|29614412|gb|CB619425.1|CB619425
EST:     ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAG                         CTTGAAGATGGGGACATAATATGTTTCCAAAAGTCACCTGTGTTAGATGGG
genomic: ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaaga ... aatgctgcagCTTGAAGATGGGGACATAATATGTTTCCAAAAGTCACCTGTGTCAGATGGG
EST: gi|2309706|gb|C25861.1|C25861
EST:     ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAG                         CTTGAAGATGGGGACATAATATGTTTCCAAAAGTCACCTGTGTCAGATGGG
genomic: ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaaga ... aatgctgcagCTTGAAGATGGGGACATAATATGTTTCCAAAAGTCACCTGTGTCAGATGGG
EST: gi|88690794|gb|CI734873.1|CI734873
EST:     ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAG                         CTTGAAGATGGGGA
genomic: ATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaaga ... aatgctgcagCTTGAAGATGGGGA

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: 66 (upstream exon), 74 (downstream exon)
Score: 36

GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaaga ... aatgctgcagCTTGAAGATGGGGACATAATATGTTTCCAAAAGTCACCTGTGTCAGATGGGGAGACTCAAGTGCGGTATCCAGACGTTCCTTCATTTTTGGAGTATGTGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAGgtttgaaagaaatcgtcacctttttagatgcaaacttttttagttttctagctcaagattgtgatggcttctctaaattgtcccatgctccattgttctttctaatgctgcag

- - - - - - - - - - - - - - - - - - - - - AAGAAA