Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTATTACATCGATGACAGAGCATTTTTGTGCTGGTTGCAATAGATTACGACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaaccagacactttgtgaaaccttgacttgtatttctgcaaattttcctatcatattttgggccaatatgtcaattttctactttggattccat...

Basic information

species Oryza sativa
transcript LOC_Os02g15870.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15870.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G135816_T01 (Zea mays), 5'ss of exon 4
GTTTATTACATCGATGACAGAGCATTTTTGTGCTGGTTGCAATAGATTACGACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaaccagacactttgtgaaaccttgacttgtatttctgcaaattttcctatcatattttgggccaatatgtca-attttctactttggattccat--------
 ||||||||||| ||||||||||||||||||||||| ||||||||||||||  ||||||||||||| ||| | || ||||||||||||||||||||||||||||||    | |  |          | |||| |  | ||||||  | |||   | |||| |  |  || ||  ||| | | |||||    |   |   ||        
ATTTATTACATCAATGACAGAGCATTTTTGTGCTGGCTGCAATAGATTACGGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgtactgctat-------ggcattgattcatgtttctg--attttctttctcatgtaatttgctaacgtgttacactttctgggctcattaatataaaagtat

upper sequence: LOC_Os02g15870.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G16780.1 (Glycine max), 5'ss of exon 4
GTTTATTACATCGATGACAGAGCATTTTTGTGCTGGTTGCAATAGATTACGACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaaccagacactttgtgaaaccttgacttgt-----atttctgcaaattttcctatcatattttgggccaatatgt-caattttctactttggattccat
 ||||| ||||||||||| ||||||||||||||||||||||||||||| |||||| | |||||||| ||||| ||||| || |||||||| || ||||||||| | ||  ||  ||  |  | |||  |     | |     ||| |    || |||  |        |||||| |  || |   || ||  |   |  |||    
ATTTATCACATCGATGACTGAGCATTTTTGTGCTGGTTGCAATAGATTGCGACTACTAGCTGATGGAAACTTTAAAGTCTGTTTATTTGGTCCTTCAGAGgtaagtta--cactcaaatcatcaaagttcagtatattatgcattccacttaaatttggtgatggcaattgggctagaatctgtgatgttgca---taaatttgg-

upper sequence: LOC_Os02g15870.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G42290.1 (Glycine max), 5'ss of exon 4
GTTTATTACATCGATGACAGAGCATTTTTGTGCTGGTTGCAATAGATTACGACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaaccagacactttgtgaaaccttgacttgt-atttctg-----caaattttcctatcatattttgggccaatatgtcaattttctactttggattccat
 ||||| ||||||||||| ||||||||||||||||||||||||||||| |||||| | |||||||| ||||| ||||| || |||||||| || ||||||||| | ||   |  ||  |  | |||  |     | | ||   ||      ||||||    ||   | || |||| |  || |    |   ||  || |||     
ATTTATCACATCGATGACTGAGCATTTTTGTGCTGGTTGCAATAGATTGCGACTACTAGCTGATGGAAACTTTAAAGTCTGTTTATTTGGTCCTTCAGAGgtaagtta--tattcaaatcatcaaagttcagtatattatgcatggcacttaaatttggtgatggcaatt-gggctagaatctgtgatgcatatatttgataa---

upper sequence: LOC_Os02g15870.4 (Oryza sativa), 5'ss of exon 5
lower sequence: AT2G31955.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTTATTACATCGATGACAGAGCATTTTTGTGCTGGTTGCAATAGATTACGACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaa----ccagacacttt----gtgaaaccttgacttgtatttctgcaaatt-ttcctatcatattttgggc--caatatgtcaattttct----actttggattccat-----------------------------------------------------------
 || || ||||| |||||||| || || |||||||| |||||||||||  ||||  | || ||||| ||||| ||||| ||||| ||||| || |||||||||   ||     ||| |   ||     |  |||  |       | ||  | ||| |   | | | ||| |    |    |||||  |  | |  |     || |  |  | | |                                                           
TTTCATCACATCCATGACAGAACACTTCTGTGCTGGCTGCAATAGATTGAGACTTCTTGCAGATGGGAACTTCAAAGTTTGCTTGTTTGGTCCTTCAGAGgtaaagtacatttccaaatttttccatggctaaaagtcagtaactgttgattcaagtggctgcgaacatgtacaagtgtgcaataacttgagtaccggtaaacatgagtattcgtggttgcttctcaataatgtgacgatcattttgtttcgcccgatgatttcttgtgaacag

upper sequence: LOC_Os02g15870.4 (Oryza sativa), 5'ss of exon 5
lower sequence: AT2G31955.3 (Arabidopsis thaliana), 5'ss of exon 4
------------------------GTTTATTACATCGATGACAGAGCATTTTTGTGCTGGTTGCAATAGATTACGACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaa----ccagacacttt----gtgaaaccttgacttgtatttctgcaaatt-ttcctatcatattttgggc--caatatgtcaattttct----actttggattccat-----------------------------------------------------------
                         || || ||||| |||||||| || || |||||||| |||||||||||  ||||  | || ||||| ||||| ||||| ||||| ||||| || |||||||||   ||     ||| |   ||     |  |||  |       | ||  | ||| |   | | | ||| |    |    |||||  |  | |  |     || |  |  | | |                                                           
CGATGGGCATTGCGGTTCTGTTTCTTTCATCACATCCATGACAGAACACTTCTGTGCTGGCTGCAATAGATTGAGACTTCTTGCAGATGGGAACTTCAAAgtttgcttgtttggtccttcagaggtaaagtacatttccaaatttttccatggctaaaagtcagtaactgttgattcaagtggctgcgaacatgtacaagtgtgcaataacttgagtaccggtaaacatgagtattcgtggttgcttctcaataatgtgacgatcattttgtttcgcccgatgatttcttgtgaacag

upper sequence: LOC_Os02g15870.4 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0156g00170.t01 (Vitis vinifera), 5'ss of exon 6
GTTTATTACATCGATGACAGAGCATTTTTGTGCTGGTTGCAATAGATTACGACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaaccagacactttgtgaaaccttgacttgtatttctgcaaattttcctatcatattttgggccaatatgtcaattttctactttggattccat-
 ||||||||||| |||||  || ||||||||||||||||||||||||| ||||| || |||||||| ||||| ||||| ||| | ||||| || ||||||||    || |      |  | |   || |  | |  |  |    |     |    |   |||||||     || | |   | ||     |||| |   |  
TTTTATTACATCAATGACTAAGAATTTTTGTGCTGGTTGCAATAGATTGCGACTTTTAGCTGATGGGAACTTCAAAGTATGCCTGTTTGGTCCGTCAGAGgtgaattatcttctt-cactattgtacttcaattcatgctagaacttgaatatgcaatttattttgacttgattttttgttgtttccaattgggtgaaacc

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|29664100|gb|CB660375.1|CB660375
EST:     GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAG                         GTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
genomic: GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaac ... gtttgtacagGTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
EST: gi|33654217|gb|CF276831.1|CF276831
EST:     GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAG                         GTGAGCCTGAGAGAGCCTATTCGAGTTGGTGTTGATGATGCTGGACTCAGA
genomic: GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaac ... gtttgtacagGTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
EST: gi|29687345|gb|CB683620.1|CB683620
EST:     GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAG                         GTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
genomic: GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaac ... gtttgtacagGTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
EST: gi|86597930|gb|CI276716.1|CI276716
EST:     GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAG                         GTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
genomic: GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaac ... gtttgtacagGTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
EST: gi|25806204|gb|CA762165.1|CA762165
EST:     GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAG                         GTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
genomic: GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaac ... gtttgtacagGTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
EST: gi|86493550|gb|CI136183.1|CI136183
EST:     GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAG                         GTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
genomic: GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaac ... gtttgtacagGTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
EST: gi|29674321|gb|CB670596.1|CB670596
EST:     GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAG                         GTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
genomic: GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaac ... gtttgtacagGTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
EST: gi|29675364|gb|CB671639.1|CB671639
EST:     GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAG                         GTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA
genomic: GACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaac ... gtttgtacagGTGAGCCTGAGAGAGCCTATTCGAGCTGGTGTTGATGATGCTGGACTCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTATTACATCGATGACAGAGCATTTTTGTGCTGGTTGCAATAGATTACGACTATTGGCTGATGGCAACTTGAAAGTGTGCTTATTTGGCCCCTCAGAGgtatgctaaccagacactttgtgaaaccttgacttgtatttctgcaaattttcctatcatattttgggccaatatgtcaattttctactttggattccat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT