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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGCTCAACGCTGTTTACATCCCCCAGGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacattatttgtcattgttgttttgtaattatttgcaccaataatatagtcaactgtacgtgatatgcctcttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g23610.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 14
TTTGCTCAACGCTGTTTACATCCCCCAGGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat-tatttgtcattgt--tgttttgtaattatttgcaccaataatatagtcaactgtacgtgatatgcctcttttcag-------------------------------------------------
                            |||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| |||||||||||| ||     |||||| | || |  | | | |||  ||  |  |  | |  |   || ||   |||     |    | |   | |                                                 
----------------------------GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag

upper sequence: LOC_Os01g23610.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA07G37050.1 (Glycine max), 5'ss of exon 14
TTTGCTCAACGCTGTTTACATCCCCCAGGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgta---tatacattatttgtc--------attgttgttttgtaa--ttatttgcac--caataata-----tagtcaactgta-cgtgatatgcctcttttcag---------------------------------------------------------------------
                            ||||| || ||||| ||||||||||| ||||||||||| |||||||| ||||| || |||||| | || |||||    ||  | ||| || ||        | | || | || |||  |||||   ||   || ||||     ||   || || | |     |        |||||                                                                     
----------------------------GACATAAAATTTGCAGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAGgtgagctaatccttaattttcttccaataacttttctattctaaccttattaagacaataacaataaggaataaagaattgaaacaaagaacattcaccttcagacttgcacacacacagctagtttattgtcgcaggcgccttaacacatgtgtcttatattactgaggcag

upper sequence: LOC_Os01g23610.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 14
TTTGCTCAACGCTGTTTACATCCCCCAGGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtat----atacattatttgt---cattgttgttttgtaat-tatttgcaccaataatatagtcaactgtacgtgatatgcctcttttcag
                            ||||| || ||||| ||||||||||| ||||||||||| |||||||| ||||| || |||||| | || |||||      || | | ||||     ||      |||| || | ||   | |  || |  |||  |||      |  |   |         ||
----------------------------GACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAGgtgagctaatccttaatttacttccaaaaactttttctattctagccgtattaagacaataa-caataaggagaaaagagttgaaacatag

upper sequence: LOC_Os01g23610.2 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 5'ss of exon 6
TTTGCTCAACGCTGTTTACATCCCCCAGGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacattatttgtcattgttg--ttttgtaatt---------atttgcaccaataatatagtcaactgtacgtgatatgcctcttttcag-------
                            |||||  ||||||||||||||||||| ||||| ||||| ||||| || ||  | ||||||||| |||| |||||| ||   || |||  |  | | |     | | |||         |||      ||  || || |  | || |   |       | || |||        
----------------------------GACATAGAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACAAACTCTTCAAATCTGCTAAGgta-atctcttctttccctctatagacccctctgattgacctgttaattcattataaagatttaatagattggaaagggagaatatgttgtcatacatagc

upper sequence: LOC_Os01g23610.2 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 5'ss of exon 14
TTTGCTCAACGCTGTTTACATCCCCCAGGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacattatttgtcattgttg--ttttgtaatt---------atttgcaccaataatatagtcaactgtacgtgatatgcctcttttcag-------
                            ||||| |||||||||||||||||||| ||||| ||||| ||||| || || || ||||||||| |||| ||||||    | || |||  |  | | |     | | ||          |||      ||  || || |  | || |   |       | || |||        
----------------------------GACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAGgtaagctc-ttctttccctctatagacccctctgatcgacctgttaattcattataaagatttaatagattggaaagggagaatatgttgtcatacatagc

upper sequence: LOC_Os01g23610.2 (Oryza sativa), 5'ss of exon 13
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 14
TTTGCTCAACGCTGTTTACATCCCCCAGGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacatt--atttgtcattgttgttttgtaatt----atttgcaccaataatatagtcaactgtacgtgatatgcctcttttcag---------------------------------------------------------------
                            ||||||||||||||||||||||| || || || || ||||| ||| |||| ||||| ||||| || || ||||||| |   |   | |     | |||| | |   |||    ||   |  || |   ||     | ||| | | || ||  |||| |                                                                  
----------------------------GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttctttcgaactcaaagtagttggtgtagcattttgaatgaacctcagtggaattcaggattgtgcttcatgtgtttcttcttcatgggacgatttatcctgcttcatttttctgctttctaaagcttgttggtttgagggttggcag

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|218481788|gb|FG954747.1|FG954747
EST:     CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|88518587|gb|CI446241.1|CI446241
EST:     CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTGTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|88284358|gb|CI405804.1|CI405804
EST:     CACACCCAACTTTGTGTGAGTTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTNTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|88477276|gb|CI414547.1|CI414547
EST:     CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCNTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|22304992|gb|BQ906214.1|BQ906214
EST:     CACACCC-ACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|33678411|gb|CF306650.1|CF306650
EST:     CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|88556074|gb|CI486380.1|CI486380
EST:     GTCTGAGTTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCCCAGCCTAGAGA
genomic: GTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|88511777|gb|CI439283.1|CI439283
EST:     CACACCCCACTTTGTGTGAGGTTCTGGATGAGCTCTTCAAAGCTGCC-AG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|88851216|gb|CI373974.1|CI373974
EST:     CACACCCAACTTTGTCTGAGGGTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAAGGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGCTCAACGCTGTTTACATCCCCCAGGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacattatttgtcattgttgttttgtaattatttgcaccaataatatagtcaactgtacgtgatatgcctcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC