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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGATGGTCATGGTTCAGTAGAAAGCACTGCTGCATACATAATTCGTGGGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagcaatatatccgatttgttgcagatgaaatgattgctactgtgctgcttgtatatagctaatatattgatacatgtttcttatatttttcag

Basic information

species Oryza sativa
transcript LOC_Os11g42420.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g42420.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G348675_T02 (Zea mays), 5'ss of exon 22
TTCTGATGGTCATGGTTCAGTAGAAAGCACTGCTGCATACATAATTCGTGGGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgt-----agcaa--------tatatccgatttgttgcagatgaaat-----gattgctactgtgctgcttgt--atatagctaat-atattgatacatgtttcttatatttttcag
||||||  |   |||||| || || ||||| ||||| ||||||||||| ||||| ||||| || |||||||| || ||||| |||||| ||||||||||||||| |      |||||        |  |  ||  |||||| | |  | |      | ||  |   ||||  ||      | |||   || | ||| ||   |||| ||| |||||  |||
TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgatcgagcaaatgatctgtgcaatcgtattgttgtacaaaatacatgtagtttcttggcgtgcccctcaccagtgtagacgattacattaatttttgttgcttttatttggcag
















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|88256554|gb|CI358942.1|CI358942
EST:     GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAG                         GCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
genomic: GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagc ... tatttttcagGCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
EST: gi|218496980|gb|FG962464.1|FG962464
EST:     GGCTTTGTCGTAGATGCTGCCTGCCAGGAACTATTCTACGATCTATGCAG                         GCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
genomic: GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagc ... tatttttcagGCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
EST: gi|58679628|gb|CK068315.1|CK068315
EST:     GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAG                         GCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
genomic: GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagc ... tatttttcagGCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
EST: gi|88269323|gb|CI380621.1|CI380621
EST:     GTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAG                         GCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
genomic: GTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagc ... tatttttcagGCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
EST: gi|8527388|gb|AU092203.1|AU092203
EST:     GGCTTTGTCGTAGATGCTNCCTGCCAGAAACTATTCTACGATCTATGCAG                         GCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
genomic: GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagc ... tatttttcagGCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
EST: gi|58665324|gb|CK054010.1|CK054010
EST:     GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAG                         GCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
genomic: GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagc ... tatttttcagGCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
EST: gi|58693556|gb|CK082243.1|CK082243
EST:     GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAG                         GCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
genomic: GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagc ... tatttttcagGCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
EST: gi|29629130|gb|CB634141.1|CB634141
EST:     GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAG                         GCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
genomic: GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagc ... tatttttcagGCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
EST: gi|38468516|gb|CF952647.1|CF952647
EST:     GCTGCCTGCCAGAAACTATTCTACGATCTATGCAT                         GCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
genomic: GCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagc ... tatttttcagGCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
EST: gi|29627724|gb|CB632735.1|CB632735
EST:     GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAG                         GCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
genomic: GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagc ... tatttttcagGCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
EST: gi|218482307|gb|FG954939.1|FG954939
EST:     GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAG                         GCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG
genomic: GGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagc ... tatttttcagGCATCCATCGCTCTATCTGAAGCAGGTGATTCTCTAGATCATTGTGATAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTGATGGTCATGGTTCAGTAGAAAGCACTGCTGCATACATAATTCGTGGGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgtagcaatatatccgatttgttgcagatgaaatgattgctactgtgctgcttgtatatagctaatatattgatacatgtttcttatatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC