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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag

Basic information

species Oryza sativa
transcript LOC_Os05g51530.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G128995_T01 (Zea mays), 5'ss of exon 9
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag
||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| || ||||||||||||||||| |   ||   | |  || || |||||| || ||   | |||||   |  ||  ||| ||  |||||| | |  || |         
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATCCTTAGATATGGTCTCCCTCCATCATTCCTGgtaatttg--ctgaggct--gttgtttatgatggtaaatagtatacttccgtttcttgtctgat--catatgttttgcatatcag------

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 9
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag
|| ||||||||||||||||||||||| || |||||  | ||||||||||||||||||||||| ||||| || ||||| ||||||||||||   ||| ||  |   |      |  | || | | ||  ||| | ||      | |  | |  | || | | | | ||  ||||||
GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgctctgctagtctctgactctttgttgtgatactta-actct-atcttgtgtgtcttgttgtctgatctctctattg-catcag

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G144372_T01 (Zea mays), 5'ss of exon 9
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag
||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||| || |||||||||||||||||    ||     ||      | | |||| |  ||  || | |||   |  ||  ||| ||   || |  ||  |  |          
GTATTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTGTCTTTGTGGAGAGCATTCTTAGATATGGTCTGCCGCCATCATTCCTGgtaattctctcagacttttt----tttgtgatggcaaatattatgcttcagtttcttgtctgatcatatgttttgcatcag----------

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA16G05470.1 (Glycine max), 5'ss of exon 9
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag
|| |||||||||||||||||||| |||||||||||| | ||||  ||||||||||| ||||||||||| || ||||| ||| ||||||| || ||| ||   |      | |    |||| |||     ||  |||     | |    ||||     | ||     || ||    
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCACCATCTTTCTTGgtaatatactcttctaaaat----caaagtgcagtctaatgacccctgggattttcaaacactgatcactgagtattgggtattccag---

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA19G27360.1 (Glycine max), 5'ss of exon 9
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttat-gttttcatcag
|| |||||||||||||||||||| |||||||||||| | ||||  ||||||||||| ||||||||||| || ||||| ||| ||||||| || ||| ||   |      | |    |||| ||  ||  |  ||     |  || ||||   |   |||   || |  |    |||
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatactcttctaaaat----caaagttcagtctaa--tggcccctgggattt--tcaaatactgttcactgaccattgggtattccag

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA02G07260.1 (Glycine max), 5'ss of exon 9
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgta-atctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag
|| ||||| |||||||||||||| ||||| |||||||| |||   ||||||||||| |||||||||||||| ||||| ||| ||||| || ||  |  ||||    |||  | | |   |||  |||    |   ||   | ||||   | | | || |  || || |     |||
GTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACTGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTGgtagatatacccatctgtacaatagctt-tcaccttcattttttccttcaaatattttatctctgaccct-tgattcttgtggtcattccag

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA16G26220.1 (Glycine max), 5'ss of exon 9
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgta-atctattctactgttacgtagtatatga--tagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag
|| ||||| |||||||||||||| ||||| |||||||| |||   ||||||||||| |||||||||||||| ||||| ||| ||||| || ||  || ||||     ||  |      |  ||   |   |  |   ||   | |||   |||| | || |  || || |     |||
GTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTGgtagatatacccttctgtacaacagctttcagcttcatcttttccttcttcgaatattttatcacttatcct-tgattcttgtggtcattccag

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G12840.1 (Arabidopsis thaliana), 5'ss of exon 9
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag
|| ||||| ||||||||||| |||||||||||||||   || |  ||||||||| | ||||| ||| | || ||  | ||| ||||||  ||     |       |  ||| | | ||  |    | |||  |  |  ||    ||  |  |  | || | | |  | |   |||
GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattaggactccaagctatgctattttagaga-attcctctaccctactatctcccttacca--aattactttctcttgtctttccag

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 5'ss of exon 9
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaat----ctattctactgttacgtagtatatgatagtcaaatttgtac-----tttgatgcctgatctaatatcatatgctgtttatgttttcatcag
|| ||||| ||||||||||| || |||||||| |||||||||| |||||| || |||||||||||  | || ||||| ||| ||||||     | |||| |||   || |    | |   | ||        ||     ||   |   ||||  |  ||    || ||   ||| |||||    
GTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTGgtaaataaaccattcaactccaacattccttcttggaatccctccctcacgaattttcttttattgattgaggattggttgttgag-atgatttcag---

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv17s0000g00460.t01 (Vitis vinifera), 5'ss of exon 9
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag
|| ||||| |||||||||||||| |||||||| |||||||||| |||||||||||| ||||||||  | || ||||| ||| | ||||   ||  |    |  |     ||||  |   |  ||| || | |   |      |   || |   ||| ||  | || |||||    
GTCTTCAGCTCCTGGATGCACTTTTGTGCTGTACGTGTCTTTGCAGAGAGCATTCTGAGATATGGATTGCCACCATCTTTCTTAgtaagtaatctttgcatacc----catatttttagctcattagtccctctgttatcatttacattttcaatgttggat-tggtttcag---

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|86841855|gb|CI337494.1|CI337494
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|88833079|gb|CI369969.1|CI369969
EST:     CCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: CCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|29621004|gb|CB626015.1|CB626015
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|38476572|gb|CF960705.1|CF960705
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|44674895|gb|CR288329.1|CR288329
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|89169855|gb|CI110214.1|CI110214
EST:     CCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGCTGAAAAGAAAGTAAGGAGCATC
genomic: CCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|86412678|gb|CI067083.1|CI067083
EST:     GTGTCTTTGTAGAGAGCATTCTCAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|88993179|gb|CI108807.1|CI108807
EST:     CCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: CCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|88762888|gb|CI772444.1|CI772444
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|29674593|gb|CB670868.1|CB670868
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|25802832|gb|CA758793.1|CA758793
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCANAAGGGTGAANAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|29674594|gb|CB670869.1|CB670869
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTTTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|89184153|gb|CI046718.1|CI046718
EST:     CCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: CCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|86602685|gb|CI357049.1|CI357049
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|38565596|gb|CK085049.1|CK085049
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|29613963|gb|CB618976.1|CB618976
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|58654927|gb|CK043607.1|CK043607
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTGGGGCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|58666296|gb|CK054982.1|CK054982
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|58590593|gb|CF988901.1|CF988901
EST:     GTGTCTTTGTAGAGAGCATGGTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|29612870|gb|CB617883.1|CB617883
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
EST: gi|88270309|gb|CI385567.1|CI385567
EST:     GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTC                         TCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC
genomic: GTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctatt ... ttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag

- - - - - - - - - - - - - - - - - - - - - - - AGAGCA