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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTTTATGCTATCCAGAGCAATGAACGTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCGgtgggtatataatttggaccgacctaaaattggttttctacatgacatatcaacacttcagtcactggcacagatttcataaaacattctggatttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g02020.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02020.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G860137_T01 (Zea mays), 5'ss of exon 6
GATCTTTATGCTATCCAGAGCAATGAACGTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCGgtgggtatataatttggaccgacctaaaattggttttctacatgacatatcaacacttcagtcactggcacagatttcataaaacattctggatttttcag
|||   ||||||||||  |||||||||||||  ||||||||||  || |||||  ||||||||||||| |||| ||| ||| ||  |  |||| ||  ||||  | ||   |  | |   ||  |  |  | ||||||||   ||| || ||| |||   |||||  ||  |||  |||
GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCTgtgcgtgcaagattttgattgacc--acataactcatttgtgtgttactttgatacttcagtacatggtaccgatctca---aacatgttg--tttcccag
















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|58609247|gb|CK037280.1|CK037280
EST:     CATTTTCTTGGGAAATTGCTCCG                         GTTGAAATTTCTTCCGGTAGAGGGAAAGCAGCACTTATTGTTGACAAGGAT
genomic: CATTTTCTTGGGAAATTGCTCCGgtgggtatat ... gatttttcagGTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGAT
EST: gi|29675317|gb|CB671592.1|CB671592
EST:     ATTTT-TTGGGAATTTGCTCCG                         GTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGAT
genomic: ATTTTCTTGGGAAATTGCTCCGgtgggtatat ... gatttttcagGTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGAT
EST: gi|218504789|gb|FG958555.1|FG958555
EST:     GTGC-ATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCG                         GTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGAT
genomic: GTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCGgtgggtatat ... gatttttcagGTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGAT
EST: gi|29641199|gb|CB646206.1|CB646206
EST:     GTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCG                         GTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGAT
genomic: GTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCGgtgggtatat ... gatttttcagGTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGAT
EST: gi|29675316|gb|CB671591.1|CB671591
EST:     GTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCG                         GTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGAT
genomic: GTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCGgtgggtatat ... gatttttcagGTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGAT
EST: gi|29640750|gb|CB645757.1|CB645757
EST:     GTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCG                         GATGAAATTTCTTCCGGTAGAGGGAAACCACCACTTA
genomic: GTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCGgtgggtatat ... gatttttcagGTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTA
EST: gi|218480326|gb|FG963594.1|FG963594
EST:     GTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCG                         GTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGAT
genomic: GTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCGgtgggtatat ... gatttttcagGTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCTTTATGCTATCCAGAGCAATGAACGTGCAATAGCAGCTCGTGATAGCGGCACATTTTCTTGGGAAATTGCTCCGgtgggtatataatttggaccgacctaaaattggttttctacatgacatatcaacacttcagtcactggcacagatttcataaaacattctggatttttcag

- - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - -  CAGCTC