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

GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaaccatggcacacttag

Basic information

species Oryza sativa
transcript LOC_Os02g50320.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G832989_T01 (Zea mays), 5'ss of exon 6
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaa-aagttgacccatgctaatctctaa------ccatggcacacttag-------------
||| ||||||||||| |||||| ||||||||| ||||||    |||||||||||||| ||||  || || |||||||| || |||||||||||||||||||||||      |||| |  |||||     ||||     | |||||  | |||  |||||     || | |||||||||        || | |   | |              
GCTGAGTCAAACTGTGAGAGAGTTGGAAGAGGATGTTCTGCAAGGTGGTGCAGCTGCCAATGTCGTTAGGGATTACCAACGAAAAGTTCAAGAAATGAATgtaac-----ctactat--ctttc-----atctcttagggtctgtttggaaaggaagttttatgatccaaatctctaagattctttatagaaagttgaactaaagcctaaaa

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G26540.1 (Glycine max), 5'ss of exon 6
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatccttta---ctgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctc----taaccatggcacacttag---------------
||| |  |||||||| |||||||| ||||||||||| ||||| ||||||||||| || ||||| || || ||||| ||||||||||||||||||||||||||||  |     |   ||   || |    | | ||     || | | | |   |      || | |  | |||  ||    | |   | ||||  ||                 
GCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAGGTGGTGCAGCCGCAAATGCAGTGAGGGATTATCAGCGGAAAGTTCAAGAAATGAATgtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G05100.1 (Glycine max), 5'ss of exon 6
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaa-----tctctaac--catggcacacttag-----------
|||||  ||||| || ||||| || ||||||||||| ||||| |||||||||||||| |||||||| |||||||| || |||||| ||||||||||||||||||  |     |||       |    |  |||    ||||   |     |  |  ||||||   |||||     ||| |     ||||      || |           
GCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAGGTGGTGCAGCTGCAAATGCTGTGAGAGATTATCAACGGAAATTTCAAGAAATGAATgtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA05G34560.1 (Glycine max), 5'ss of exon 6
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaat---ctctaaccatggcacacttag----------------
|||||  ||||| || ||||| || ||||||||||| ||||| |||||||||||||| |||||||| |||||||| || |||||||||||||||||||||||||  |  |  | |       |    |  |||    ||||   |     |  |   ||| |||    ||       |||   | |||   || |                
GCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAGGTGGTGCAGCTGCCAATGCTGTGAGAGATTATCAACGGAAAGTTCAAGAAATGAATgtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcatcttaattgttgcatgatttgttttgacactatatag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 6
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatccttta---ctgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctc----taaccatggcacacttag---------------
||| |  |||||||| ||||| || ||||||||||| ||||| |||||||||||||| ||||| || || ||||| ||||||||||||||||||||||||||||| |  |  |   ||   || |    | | ||     || | | | |   |  |  ||||| |  | |||  ||    | |   | |||   ||                 
GCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAGGTGGTGCAGCTGCAAATGCAGTGAGGGATTATCAGCGGAAAGTTCAAGAAATGAATgtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttatttgacattctttag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G01750.1 (Arabidopsis thaliana), 5'ss of exon 7
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcc----tttactgttgctttcggataatctt--cactgttct-gtacgcaaaaaagttgacccatgctaatctctaaccatggcacacttag-----------
| |||  || || ||| | ||||| ||||| |||||||||||||||||| ||||||| ||||| || |||||||||||| ||||| |||||||||||||||||| |       |  ||  ||  |  |  || | | |    ||   || ||||  ||||       ||  ||||||||  || | ||||| || | |            
GTTTACCCAGACCGTACGGGAGCTTGAAGAAGCTGTTCTTGCTGGTGGTACAGCTGCAAATGCAGTGAGAGATTACCAGAGGAAATTTCAAGAAATGAATgtaataattaaattacacgtttagtgcctcattagcctattgctacccttgtacttaaaattcaattcctgtgctaatca-tagctatggc-cattaatcctttcattag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 6
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgc-----taatctctaaccatggcacacttag
||||| ||| || ||| ||||||| ||||||||||||||||| |||||||| ||||| ||||| || || ||||||||||||||| ||||||| |||||||||||       |||       ||  | | |||  | | |  |||    | ||  |   ||  |||      ||||   |     || |    | ||
GCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAATTTCAAGAGATGAATgtaactaaacacact-------tcataaagtctctaatttcttgtcacaacaattgcctactgatgtaggaataattcttgtttttgtctt--tcag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 6
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaaccatggcacacttag
||||| ||| |||||| | || ||||||||||| ||||||||||||||||| ||||| ||||| || || ||||||||||||||  ||||||| ||||| ||||  |  |  | |   |      || | | |  | | ||   |   |  |  |    |    |  |  |||         |         
GCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaagttaatacatttccgaaaaaaga-agtatagaatctttactcaactgatgaaggaatatttcttgctctacttttgcag---------

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 5'ss of exon 6
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgta-acatcctttactgttgctttcggataatc-ttcactgttctgtacgcaaaaaagttgacc-catgctaatctctaaccatggcacacttag----------
|||||  || | |||  | ||  | ||||| ||||||||||||||||||||||| || || || || |||||||||||  ||||| | ||||||||||||||| |  || | | ||  |    |     |||   | |||||| |    |  |     |||  | | | || |||  |||   |||     |  |          
GCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTGGTGGTGCAGCCGCAAACGCAGTGAGAGATTACCAAAGGAAATTCCAAGAAATGAATgtatatttcatatgcttctatagtacctcaataacttactgtttttcttgttagtgttttggtctcgtactgatcg-taattgtggtgttttgtgttttccttag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 6
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatccttt------actgttgctttcggata------atcttcactgttctgtacgcaaaaa---agttgacccatgcta-atctctaaccatggcacacttag-------------------------
 || |  ||||||||||| ||||| |||||||||||||| ||||||||||||||||| |||||||||||||||||||| |||||||||||||| ||||||||||  | |  |      ||  |   | | | | |       || |  | |   | ||       |   ||||| |  |||| |  | |   | ||| |   | ||                           
ACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTGGTGGTGCAGCTGCAAATGCTGTCAGAGATTACCAACGGAAAGTTCAAGAGATGAATgtaatgtgccatttttaaacaataaatattgaacattgcaagtcatttcaggcttatatttttgcatctagttggcatatgccatgtgttctatcattgttgagttgtctttccttttcttttggaccttcag

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|25777864|gb|CA752614.1|CA752614
EST:     CAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAAT                         GAGGAAAGAAAAATTCTTGACCGTGAGCTTGCTCGGGCAAAAGTTACAGCA
genomic: CAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcct ... gcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCA
EST: gi|86495989|gb|CI138622.1|CI138622
EST:     CTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAAT                         GAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCA
genomic: CTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcct ... gcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaaccatggcacacttag

- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA