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

gtatttcttttagggagagcttggatgtaggactgaacattagagctggtgcaatttgacgacttgtaattaacttgctcagaattttttttggttttacttcgaataatcataatttcacgtgcattactttatgtcgattgcttgatttccttttaacagGGGGAGAGCACTAAAATGTCGGCCAGTGACCCAAACTCTGCAATATATGTGACAGATAATTCTAAACAAATAAAGGCAAAG

Basic information

species Oryza sativa
transcript LOC_Os07g17770.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g17770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 6
gtatttcttttagggagagcttggatgtaggactgaacattagagctggtgcaatttgacgacttgtaattaacttgctcagaattttttttggttttactt-cgaataatcataatttcacgtgcattactttatgtcgattgcttgatttccttttaacagGGGGAGAGCACTAAAATGTCGGCCAGTGACCCAAACTCTGCAATATATGTGACAGATAATTCTAAACAAATAAAGGCAAAG
                      |  ||| |  ||  ||  ||   || ||  ||||| | |  ||  ||||  ||||       |||   ||  | |||  |   |||| |    | |||| | |||||  ||| |||   || |||  |||| |||| ||||||||||| ||| |||||||| || |||||| |||| || || ||||| |||||||||| | ||||| |||||||| |||||
----------------------gtttgttgaccttgac--tatttctagt-taatttaaag--tttaaatttgcttgtggtttctttacctttttattatatgtaaatagttcatagttcaagggcatttattt-tgtgtgtt-ctttctttctttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG

upper sequence: LOC_Os07g17770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 6
gtatttcttttagggagagcttggatgtaggactgaacattagagctggtgcaatttgacgacttgtaattaacttgctcagaattttttttggttttacttcgaataatcataatttcacgtgcattactttatgtcgattgcttgatttccttttaacagGGGGAGAGCACTAAAATGTCGGCCAGTGACCCAAACTCTGCAATATATGTGACAGATAATTCTAAACAAATAAAGGCAAAG
                                                  | ||  ||| |  ||  |  ||  ||  |   |||||| | ||       |   |||  | ||      |  ||   |     || |  ||    | | ||| |     |||||||| |     |||||||| |||||||| || || ||||||||||||||||| |||  | | ||| | ||||||   |||
--------------------------------------------------ggaaactgaag--ttacatataggtt--ttgaaattttctctgaaaaaggtctaaattcttatg----tagatgttatctcacatctttataatataaattctt----gcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG

upper sequence: LOC_Os07g17770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 6
gtatttcttttagggagagcttggatgtaggactgaacattagagctggtgcaatttgacgacttgtaattaacttgctcagaattttttttggttttacttcgaataatcataatttcacgtgcattactttatgtcgattgcttgatttccttttaacagGGGGAGAGCACTAAAATGTCGGCCAGTGACCCAAACTCTGCAATATATGTGACAGATAATTCTAAACAAATAAAGGCAAAG
                                                  | ||  ||   | ||  |  ||   |  |   |||||| | ||  |    | | |||  ||     ||        |||  | |  ||  |    |   |   || |  ||||| || |     |||||||| |||||||| || || ||||||||||||||||| |||  | | ||| | ||||||   |||
--------------------------------------------------ggaaactg--cagttacatatagact--ttgaaattttctctgaataaggtccaaat--tc----ctttgtagctgttatctcacatctttaaaata--taaattcttgcagGGAGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcataatttcacgtgcattactttatgtcgattgcttgatttccttttaacagGGGGAGAGCACTAAAATGTCGGCCAGTGACCCAAACTCTGCAATATATGTGACAGATAATTCTAAACAAATAAAGGCAAAG
                                   gcttgat  putative branch site (score: 5)
                                    cttgatttcctttt  CT-rich tract
                  attactttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcttttagggagagcttggatgtaggactgaacattagagctggtgcaatttgacgacttgtaattaacttgctcagaattttttttggttttacttcgaataatcataatttcacgtgcattactttatgtcgattgcttgatttccttttaacagGGGGAGAGCACTAAAATGTCGGCCAGTGACCCAAACTCTGCAATATATGTGACAGATAATTCTAAACAAATAAAGGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG