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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttttgcttactgttacaatttacaaagctgtctgacttacacaaaatactgtcattctatactag

Basic information

species Oryza sativa
transcript LOC_Os04g59494.4
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 26
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacg-------cttttgcttactgttacaat-ttacaaagctgtctga-cttacac-aaaatactgtcattctatactag
|||  |||||||||||||||||||||| || || ||||| || |||||||||||| ||  |         ||  || |||  | | || | || |  | |||  ||| |||   |  ||||  | |     || || ||
GATCAGAGATGATTTTGAGAAAGAGGACGCGTTTCATGGACTGTGTGCAATGgtatatgtatatccagacctcctggttatggctgcattcttccttatctgggtgatcttgttctgaaatcttatttggttacaccag

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA20G24040.1 (Glycine max), 5'ss of exon 26
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttttgcttactgttacaatttacaaagctgtctgacttacacaaaatactgtcattctatactag-------
||||||||||||| |||||||||||||||| ||    ||||||||||| ||||||       |||  |  | |||  |  |||||      |     |||||  | |  |   ||| ||| || | | |       
GATACGAGATGATGTTGAGAAAGAGGATGCTTTTAGAGGTCTATGTGCTATGgtat------gctcctattcact-ctgtaattttttttacatgtagacttgtaaagtaatttgt-attttacatttgttttcag

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA10G42960.1 (Glycine max), 5'ss of exon 26
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttttgcttactgttacaatttacaaagctgtctgacttacacaaaatactgtcattctatactag-------
||||||||||||| |||||||||||||||| ||    ||||||||||| ||||||       |||  |  | ||||    |||||   |   |||  |||||  | |  |    |  ||| || | | |       
GATACGAGATGATGTTGAGAAAGAGGATGCTTTTAGAGGTCTATGTGCTATGgtat------gctcctattcactgggtaaattttttaca-tgta-gacttgtaaagtaattgggtattttacatttgttttcag

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 5'ss of exon 26
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttt------tgcttactgttacaatttacaaagctgtctgacttacacaaaatactgtcattctatactag
|||||| |||||| ||||||| || ||||| |||| ||||||||||||||  |||     |  ||||      | |||| |     |  | | | |  | | |   ||  |   |||   |   |   ||   ||
GATACGTGATGATATTGAGAAGGAAGATGCCTTCCGTGGTCTATGTGCAACTgtatgcaaattctttcttgattccttagtagatgagatcaaagaaatatatatattgtaattaatgaagcattggaattgcag

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: PP1S276_77V6.1 (Physcomitrella patens), 5'ss of exon 26
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatc---cacgcttttgcttactg---------ttacaatttacaaagctgtctgacttac--acaaaatactgtcattctatactag---------------------------------------------------
|||||||||||||||||||||||| ||||| || |  || || ||||| |||||| ||    ||        |  ||              || | |  |||||  | |     |   |||| || || ||||   ||   ||                                                   
GATACGAGATGATTTTGAGAAAGAAGATGCTTTTCGAGGCCTGTGTGCTATGgtatatttcgcagatcacaaccaaccaggaacatatccgcattatcgaaagccattttttagattgacaagatgctttcatagaattgaaggaaatttattaaaaagtgtcgactaattgatcgtgtggggtggtatattag

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: PP1S41_175V6.1 (Physcomitrella patens), 5'ss of exon 25
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttt-tgcttac--------tgttacaatttacaaagctgtctgacttacacaaaatactgtcattc--tatactag------------
||||||||||||||||||||| || ||||||||||  ||  | ||||| ||||||      |  ||| || ||||        | |  ||| || ||    |  |||  | |     | | | ||  | |  | |  |||            
GATACGAGATGATTTTGAGAAGGAAGATGCATTCCGGGGCTTGTGTGCCATGgtatgatggctttttgtggttacataagttttatggcaacttgcagctgttcctgtttgaattggagttcagtgctcccttgttttagaattcttctgat

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|29669949|gb|CB666224.1|CB666224
EST:     TACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG                         GTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
genomic: TACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccac ... tctatactagGTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
EST: gi|29624709|gb|CB629720.1|CB629720
EST:     TACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG                         GTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
genomic: TACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccac ... tctatactagGTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
EST: gi|29626308|gb|CB631319.1|CB631319
EST:     AGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG                         GTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
genomic: AGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccac ... tctatactagGTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
EST: gi|86437650|gb|CI119570.1|CI119570
EST:     TACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG                         GTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
genomic: TACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccac ... tctatactagGTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
EST: gi|29623087|gb|CB628098.1|CB628098
EST:     TACGAGATGA-TTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG                         GTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
genomic: TACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccac ... tctatactagGTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
EST: gi|66929408|gb|CX116256.1|CX116256
EST:     TACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG                         GTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
genomic: TACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccac ... tctatactagGTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
EST: gi|29624359|gb|CB629370.1|CB629370
EST:     TACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG                         GTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG
genomic: TACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccac ... tctatactagGTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAG

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: 52 (upstream exon), 69 (downstream exon)
Score: 20

GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccac ... tctatactagGTAGCAGCAAACCCAACTGGAGCTGTGGGTTCACTAACTTTTATCTGCCAGGCCTGTGCAAGTTGGAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttttgcttactgttacaatttacaaagctgtctgacttacacaaaatactgtcattctatactag

- -  GAGATG
- - - - - - - - - - AAGAGG
- - - - - - - - - -  AGAGGA
- - - - - - - - - - - GAGGAT
- - - - - - - - - - -  AGGATG