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

TATGGAGCTTTTTGTCATGATCGACGCATGTCGGCGGGCGTCGGCGAGGTCTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataaactcttaattgatggctgttgcggtatgccaagtgtgtttgtactgatcatcatgcaatttcatttttactggatatcttcttcccttat...

Basic information

species Oryza sativa
transcript LOC_Os06g41360.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g41360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G180863_T02 (Zea mays), 5'ss of exon 2
TATGGAGCTTTTTGTCATGATCGACGCATGTCGGCGGGCGTCGGCGAGGTCTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgta-tgtataaactcttaattgatggctgttgcggtatgccaagtgtgtttgtactgatcatcatgcaatttcatttttactggatatcttcttcccttat-
 |||||||| ||  ||||||| || ||||| |||||||| || ||  |||||||||| ||||| |||||||||||||| ||||||||||| |||||||||||| |   |  | | ||| ||  | |  | | |  ||   ||  | ||    ||   | | |||   ||    |  |     |||    |   |   | || 
CATGGAGCTCTTCATCATGATTGATGCATGCCGGCGGGCTTCAGCACGGTCTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctccatttttatttatttgacgct-caatagttcagatttgcac-taacaaacgtcaaataaaaaaaaatcggagggagtattagctaaatgata

upper sequence: LOC_Os06g41360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S212_43V6.1 (Physcomitrella patens), 5'ss of exon 2
TATGGAGCTTTTTGTCATGATCGACGCATGTCGGCGGGCGTCGGCGAGGTCTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataaactcttaattgatggctgttgcggtatgccaagtgtgtttgtactgatcatcatgcaatttcatt--tttactggatatcttcttcccttat-------------------------------------
|||||||||||| |||||||| |||||||| ||||| || || || | | | ||||| | ||| || |||||||||||||| ||||| || ||  | |||||  | |  |    |||| |||    | |||||      |    |    |||    | | |    ||  ||  |   |  | |||  ||| ||    |  ||                                     
TATGGAGCTTTTGGTCATGATTGACGCATGCCGGCGAGCATCAGCAAAGACCATTACCGCTGTGATCCCATACTTTGGGTACGCCAGGGCAGATCGTAAGgtgag-aagactggttaaatgaattttcttgcgactcagctctagaagatgttaccagcttggaacatatttgtcagtcaaatggtgatcatcgaaacagatatttctgctgtgtttaaatttggcagtgttttgacag

upper sequence: LOC_Os06g41360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ35181 (Selaginella moellendorffii), 5'ss of exon 3
TATGGAGCTTTTTGTCATGATCGACGCATGTCGGCGGGCGTCGGCGAGGTCTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataaactcttaattgatggctgttgcggtatgccaa-gtgtgtttgtactgatcatcatgcaatttcatttttactggatatcttcttcccttat
 |||||||| ||||| |||||||| || ||  | || |||   || |   | || ||||  || ||||||||||| || ||||| |||||||||||||||||| |   |   ||| |  | |    | ||  | | | | || |   |    | ||   ||                                        
AATGGAGCTGTTTGTGATGATCGATGCTTGCAGACGCGCGCATGCTAAAACGATCACTGCCGTGATTCCATACTTCGGATATGCTAGAGCTGACAGAAAGgta-gcgaagtttctcatcttagttttcttcggatgttctaacgctggcgaattctttccag---------------------------------------

upper sequence: LOC_Os06g41360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ24123 (Selaginella moellendorffii), 5'ss of exon 3
TATGGAGCTTTTTGTCATGATCGACGCATGTCGGCGGGCGTCGGCGAGGTCTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataaactcttaattgatggctgttgcggtatgccaagtgtgtttgtactgatcatcatgcaatttcatttttactggatatcttcttcccttat
 |||||||| ||||| |||||||| || ||  | || |||   || |   | || ||||  || ||||||||||| || ||||| |||||||||||||||||| |   |   ||| |  | |    | ||  | | | | ||    | | |   |     ||  |                                   
AATGGAGCTGTTTGTGATGATCGATGCTTGCAGACGCGCGCATGCTAAAACGATCACTGCCGTGATTCCATACTTCGGATATGCTAGAGCTGACAGAAAGgta-gcgaagtttctcatcttagttttcttcggatgttctaa---cgctggcgatttctttccag-----------------------------------

upper sequence: LOC_Os06g41360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ12994 (Selaginella moellendorffii), 5'ss of exon 2
TATGGAGCTTTTTGTCATGATCGACGCATGTCGGCGGGCGTCGGCGAGGTCTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataaactcttaattgatggctgttgcggtatgccaagtgtgtttgtactgatcatcatgcaatttcatttttactggatatcttcttcccttat
 ||||||||  | |||||||| |||||||| ||||| || || || | | | || || |  || |||||||||||||| || |||||||||||||||||||||   |         |  |  |  || |     ||  |   ||||| |  |  | |                                           
GATGGAGCTACTGGTCATGATAGACGCATGCCGGCGTGCATCCGCCAAGACCATCACAGCAGTAATTCCATACTTTGGATACGCCAGAGCTGACAGAAAGgtagtcactgtgatccagcttttt-ctttcaatctacacgtcgtgtgatgtttttcag------------------------------------------

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|218499483|gb|FG945822.1|FG945822
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88444674|gb|CI694909.1|CI694909
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88589479|gb|CI707362.1|CI707362
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88591333|gb|CI708261.1|CI708261
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88321686|gb|CI672827.1|CI672827
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88585810|gb|CI701401.1|CI701401
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88588268|gb|CI706074.1|CI706074
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88412811|gb|CI576075.1|CI576075
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88463487|gb|CI695951.1|CI695951
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88436551|gb|CI691275.1|CI691275
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88589127|gb|CI706983.1|CI706983
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88579250|gb|CI688230.1|CI688230
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88588958|gb|CI706805.1|CI706805
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88588009|gb|CI705799.1|CI705799
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88300135|gb|CI582369.1|CI582369
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|88444729|gb|CI694967.1|CI694967
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA
EST: gi|218783510|gb|GE329562.1|GE329562
EST:     CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAG                         GCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGATAATTTACTTACA
genomic: CTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataa ... tgtagtgtagGCTCAAGGACGTGAGGCCATTACTGCCAAACTTTCTGCTAATTTACTTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGAGCTTTTTGTCATGATCGACGCATGTCGGCGGGCGTCGGCGAGGTCTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgtatgtataaactcttaattgatggctgttgcggtatgccaagtgtgtttgtactgatcatcatgcaatttcatttttactggatatcttcttcccttat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA