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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTGgtaagttatcaattgatggtatgtattatgcttatatagcttgatggagaaatttcatgatttgtcgggttgcgcggaattgtctcttgtag

Basic information

species Oryza sativa
transcript LOC_Os03g16570.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16570.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G337425_T01 (Zea mays), 5'ss of exon 4
TTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTGgtaagttatcaa--ttgatggtatgtattatgcttatatagcttgat-ggagaaatttcatgatttgt-cgggttgcgcggaa-ttgtctcttgtag----------------------------------------
||||| | |||||||||||||||||||| |||||||| ||||| ||  || ||||||||| ||    |   ||||  ||   | |  |  |    |  || | ||    ||  | ||| || |       ||     |||     | ||                                         
TTCTTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttcgtgctcagtggtcagtgcgaggtgtccacgagtcaattgaagttggtttcttattcgtacaaagcatgcaactcttgaacagtttaataactacatatttgtcggatgatcctttcttctctcttag

upper sequence: LOC_Os03g16570.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G492252_T01 (Zea mays), 5'ss of exon 4
TTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTGgtaagttatca---------------attgatggtatg-------------tattatgcttatatagcttg-----atggagaaatttcatga-------tttgtcgggttgcgcggaattgtctcttgtag---
|| || | ||||||||||||||||||||||||||||||||||| ||  |||||||| ||| |||                |  ||| | ||             | |||| | |||| ||| ||      ||||  | ||| || |       ||||| || ||| |||   || ||| || |     
TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTTTGgtaggttttcatgctctgtgcaagctgtccatgatttggttaaaattgttttcttattcgtataaagcatgcaactgtggaacagtttaataaccacatttttgttggattgtgcgatcttttcttttcttttag

upper sequence: LOC_Os03g16570.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G34130.2 (Glycine max), 5'ss of exon 4
TTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTGgtaagttatc-----aattgatg-------gtatgtattatgcttat----atagcttgatggaga--aatttcatgatttgtcgggttgcg-cggaattgtctcttgtag---
||||| |||| |||||| |||||||||| ||||||||||| || |||||| ||||||| | |      || | | |       | | || || |  ||||    | | ||  ||  |    | | |  || ||| |  |||     | || || |||||  | |   
TTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCTGgtaaggtcttgtagtaagtaaagcagacatgaaagttttttttttatgaaaaaaactacatttaatttattctagtggtttataaggtcttatctgagttatctctatttgcag

upper sequence: LOC_Os03g16570.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G04160.1 (Glycine max), 5'ss of exon 5
-TTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTGgtaagttatca----attgatggtatgtat-tatgcttatatagcttgatggagaaatttcat--gatttgtcgggttgcgcggaattgtctcttgtag--
 ||||| |||| |||||| |||||||||| ||||||||||| || |||||| ||||||| | |      ||  |  | |   ||  | | || | ||     ||   || |||| ||    | |   || ||    ||  || |||||  | |  
GTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCTggtaaggtcttgtagtatgtaaagcagacatgcaagtttttttatgaaaataatgacatttaatttattctagtggtttataaggttttatctctatttgta

upper sequence: LOC_Os03g16570.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv13s0019g01960.t01 (Vitis vinifera), 5'ss of exon 3
TTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTGgtaagttatca-attgatggtatgtattatgcttatatagcttgatgg--agaaatttcatgatttgtcgggttgcgcggaattgtctcttgtag------------------------
||||| || |||||||| |||| ||||||||||||||||| || |||||| |||||  || |   |||||   | ||  |   |  ||| || | |  ||   || |||        ||     ||||| |     || |  ||  ||                        
TTCTTTTGCTGTTCATGATACTAAACTCACACCAGATGTCACCTAACTTTCTGgtattttctttcattgagtttgtgcttggggagtatctacccttgtgcttagcaatgcttcagcttaaattgttgcaca----tgccatttaaagggccttcttaaccaatgtttgtag

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|218484447|gb|FG955624.1|FG955624
EST:     TTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG                         GTTTGGCTGGTTTTGGGTGTGTTCCTAATGGCCACCAGCCTAAGGATGTAC
genomic: TTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTGgtaagttatc ... tctcttgtagGTTTGGCTGGTTTTGGGTGTGTTCCTAATGGCCACCAGCCTAAGGATGTAC
EST: gi|218498707|gb|FG952314.1|FG952314
EST:     TTATGTTG-TCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG                         GTTTGGCTGGTTTTGGGTGTGTTCCTAATGGCCACCAGCCTAAGGATGTAC
genomic: TTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTGgtaagttatc ... tctcttgtagGTTTGGCTGGTTTTGGGTGTGTTCCTAATGGCCACCAGCCTAAGGATGTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTGgtaagttatcaattgatggtatgtattatgcttatatagcttgatggagaaatttcatgatttgtcgggttgcgcggaattgtctcttgtag

- - - - - - - - - - - - - - - - CAGATG