Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaaaccatatccccttttttcgctaagcag

Basic information

species Oryza sativa
transcript LOC_Os03g49150.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G832740_T01 (Zea mays), 5'ss of exon 4
GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcat----atattgc---------tttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgc----ttgcccttgtattactctggaattc----aaaaccatatcccctt--------ttttcgctaagcag
|| || |||||||||||| ||||||| ||||||||||| || |||||| | ||||||| ||   |  ||| |  |     | |||          |||| | | ||||   |||   |    | |      | |||  | |   ||     ||    | |  | |  ||||   ||  | ||      || || |  | ||         |||   || |||||
GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccgcaacattgtcatggttttgtcgccttggatttgttctttttcccaaagaaatgtcctctgttcaaacagatctgtaactcggtttgcagattggtgcatcgattatattgttaatctggtggaatcagactcactgcaacaagatttgtcctgagcag

upper sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G856436_T02 (Zea mays), 5'ss of exon 4
GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaa-accatatccccttttttcgctaagcag
|| ||||| ||||||||||||||||| ||||||||||| || |||||| | ||||||| ||   |  |||                || ||||  ||||  | ||   | |||   |  || ||    ||||  |           |  ||||| ||||||||| |   || | |     |||  |  ||||||||
GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacgcaac---------------actctgttcaaacagac-ctgtgacttagtttgcaaaagac-cgcattgaata--------tattattattctggaattgactcactagaggaaatttgatt-ctaagcag

upper sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G856436_T01 (Zea mays), 5'ss of exon 1
--------------------------------------------GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaa-accatatccccttttttcgctaagcag
                                            || ||||| ||||||||||||||||| ||||||||||| || |||||| | ||||||| ||   |  |||                || ||||  ||||  | ||   | |||   |  || ||    ||||  |           |  ||||| ||||||||| |   || | |     |||  |  ||||||||
CGTATATTGCCTTGCATCTATGTTTTTATGATGCTCTTCTCTAGGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacgcaac---------------actctgttcaaacagac-ctgtgacttagtttgcaaaagac-cgcattgaata--------tattattattctggaattgactcactagaggaaatttgatt-ctaagcag

upper sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ14674 (Selaginella moellendorffii), 5'ss of exon 4
GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaaaccatatccccttttttcgctaagcag
|||   || ||  | |||  ||||| ||||||||||||||| || |||||||||||||||    | | |    || | ||| | ||       ||||  | ||      |||      |                                                                            
GAATTCGCGCAGCACAAGGCCCAGAAGTACAAGGAAGGGAAGTTCATTTTAGAGAGgtaaatgccgtcattcaatgttttg-tatgtgaca--tcaaggatcttgctcgtttgtttgcag---------------------------------------------------------------------------

upper sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ26336 (Selaginella moellendorffii), 5'ss of exon 4
GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgc-tgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaaaccatatccccttttttcgctaagcag
|||   || ||  | |||  ||||| ||||||||||||||| || |||||||||||||||      |  | ||||  | || ||||  ||||  ||||  |  |||      |    ||  ||                                                                         
GAATTCGCGCAGCACAAGGCCCAGAAGTACAAGGAAGGGAAGTTCATTTTAGAGAGgtaaa-----tgccgtcattcaatgttttgtatgtgcatcaaggatttcttgctcgtttgcttgcag-------------------------------------------------------------------------

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|88255532|gb|CI354356.1|CI354356
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88376195|gb|CI533097.1|CI533097
EST:     GAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCAGTACTTTGTTACACATGATGC
genomic: GAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|86417196|gb|CI031405.1|CI031405
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88662659|gb|CI471762.1|CI471762
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88366932|gb|CI553822.1|CI553822
EST:     AGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: AGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88251691|gb|CI350119.1|CI350119
EST:     CACATGAGAAGAGCCAGAGGTACAAGGAAGGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: CACATGAGAAGAGCCAGAGGTACAAGGAA-GGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|86886993|gb|CI324414.1|CI324414
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88663907|gb|CI488106.1|CI488106
EST:     ATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: ATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88437358|gb|CI528717.1|CI528717
EST:     CCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: CCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88535486|gb|CI464290.1|CI464290
EST:     AGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: AGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|86825997|gb|CI362437.1|CI362437
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88208722|gb|CI208571.1|CI208571
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTGTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88526066|gb|CI453109.1|CI453109
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88661066|gb|CI449874.1|CI449874
EST:     TGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: TGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|58657770|gb|CK046450.1|CK046450
EST:     GGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88286375|gb|CI524874.1|CI524874
EST:     AGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: AGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88522677|gb|CI449508.1|CI449508
EST:     CATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: CATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaaaccatatccccttttttcgctaagcag

- - - - - - - - - - - - - - - AAGGAA