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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcgactttgaattatcagcaactatttgtgtttaccactggattatcttccacaaattagttcctcttaccttattttatcatggtctgtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGTATGGAGCATGGATGACAGAAAGATAGTCGCGTGGGGCGAAGGGCATAAT

Basic information

species Oryza sativa
transcript LOC_Os12g07450.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G096070_T01 (Zea mays), 3'ss of exon 8
atgcgactttgaattatcagcaactatttgtgt-ttaccactggattatcttccacaaattagttcctcttaccttattttatcatggtctgtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGTATGGAGCATGGATGACAGAAAGATAGTCGCGTGGGGCGAAGGGCATAAT
   |   | |  || |||||||| | |||      |   |   |    | |  |||||| ||     ||   |  ||   |||       | |   |||||||| ||||| |||||||| || || ||||||||||||||||||||||||                                                   
tcactgatctatat-atcagcaaatgttttctcactgttatatgggcttgtcacacaaaataacatttcagcctctaacctatttattcttctgactacagCTCAGATGGAAAATATCTATTAACAGGTGGTGAAGATGATCTTGTGCAG---------------------------------------------------

upper sequence: LOC_Os12g07450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G096070_T01 (Zea mays), 3'ss of exon 9
--atgcgactttgaattatcagcaactatttgtgtttaccactggat-tatcttccacaaattagttcctcttacctta--ttttatcatggtctgtttttacagCTCG---GATGGCAAATAT--------CTGTTGACTGGTGGTGAAGATGATCTTG-----TGCAGGT----ATGGAGCATGGATGACAGAAAGATAGTCGCGTGGGGCGAAGGGCATAAT------
  ||| | | | | || ||    |  || |||  |        |||  ||  |       | |||||   | | |||||  |||| |||  |||  || | | | || |     ||  ||||          || ||    |   ||| || || | |||     |   |||    |   ||    ||||  |       |   |  |   ||   ||   |  |      
gtatggggcat-ggatgatagaaagatagttgcttggggtgaaggacataattcatgggtaatagttttgcctgccttaaattttctcagtgtcccttgtcaaatcttgttcattgagaaatgagaatgaggctatttcagGTCAGTGGAGTTGCTTTTGATTCATATTGGTCCCCACCAAGTTCTGATGGAAATGGAGAAAATGTATATCGCTTTGGTTCTGTTGGGCAG

upper sequence: LOC_Os12g07450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv06s0004g03040.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------------------------------------------------------------------------atgcgactttgaattatcagcaactatttgtgtttaccactggattatcttccacaaattagttcctcttaccttatttta---tcatggtctgtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGTATGGAGCATGGATGACAGAAAGATAGTCGCGTGGGGCGAAGGGCATAAT
                                                                                          |   || |   |    || ||     | ||  || ||  |  ||   |    | ||  |          | | ||||| |   | |    |||||    ||||| |||||| |||||  | ||||||||||||||||||||||| || || || ||||| ||||| ||  ||||| |||| || |||||||| ||||| |  
gtaaataaaaaataaaaacttctaatgctttccctttaaatcaagtaccagatgataccggtttgtcaatatttattttctagaacattttatcacatctcacatacatcattccctagtcatttccctttaatggaccattaaaagctttgaaacaagatcatatttgacatttacatgctgttcccccagCTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGTTTGGAGTATGGAAGATCGAAAGGTAGTAGCATGGGGCGAGGGGCACAGC

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|29670875|gb|CB667150.1|CB667150
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|29665681|gb|CB661956.1|CB661956
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|4715313|gb|AU056430.1|AU056430
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|4715180|gb|AU056297.1|AU056297
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|218478110|gb|FG955323.1|FG955323
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|33822326|gb|CF336974.1|CF336974
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|58685449|gb|CK074136.1|CK074136
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttccacaaattagttcctcttaccttattttatcatggtctgtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGTATGGAGCATGGATGACAGAAAGATAGTCGCGTGGGGCGAAGGGCATAAT
                    ctcttac  putative branch site (score: 3)
                                          tctgttttt  putative PPT
                       ttaccttattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcgactttgaattatcagcaactatttgtgtttaccactggattatcttccacaaattagttcctcttaccttattttatcatggtctgtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGTATGGAGCATGGATGACAGAAAGATAGTCGCGTGGGGCGAAGGGCATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA