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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccagttcatcttgcacagagtagacctagaccatttgtacttatatttccttgtttatggtgattctgctttgcttttaattattttatttgcttacagCGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACACCGGATCATACTGTCTGGCCAGAGGGAATGAACCTGCCTCGTTCAAGCAGCTTTAAT

Basic information

species Oryza sativa
transcript LOC_Os03g63020.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G045241_T07 (Zea mays), 3'ss of exon 5
----cccagttcatcttgcacagagtagac-ctagaccatttgtact-tatattt-ccttgtttatggtgattctgctttgcttttaattattttatttgcttacagCGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACACCGGATCATACTGTCTGGCCAGAGGGAATGAACCTGCCTCGTTCAAGCAGCTTTAAT
       || | |  ||  |   |||   | ||  | |||||  ||  ||| ||| || |   ||| |||||| | | |||||| |      ||| |||  | |||| || ||||| ||||| |||||||||||  ||||||||||||| || |||   ||| | |||||||||||||||||||||||||||||| |||||||||| 
gtattagagcttaagtta-atgaagtgcgcactgaaacatttagacagtatttttaccattgatattgtgattttacattgcttct------tttgtttcttaacagTGAAACTGACCAGCTTTACAAAATATGCACTGTGCTTGGGACCCCTGATTGCACTATTTGGCCAGAGGGAATGAACCTGCCTCGTTCATGCAGCTTTAAG
















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|34996388|gb|CF569133.1|CF569133
EST:     GCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAG                         CGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACACCGGATCA
genomic: GCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAGgtatgtatga ... ttgcttacagCGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACACCGGATCA
EST: gi|58692426|gb|CK081113.1|CK081113
EST:     GCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAG                         CGAGACTGATCAGCTA
genomic: GCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAGgtatgtatga ... ttgcttacagCGAGACTGATCAGCTA
EST: gi|58675001|gb|CK063688.1|CK063688
EST:     GCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAG                         CGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACACCGGATCA
genomic: GCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAGgtatgtatga ... ttgcttacagCGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACACCGGATCA
EST: gi|86848584|gb|CI293908.1|CI293908
EST:     GCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAG                         CGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACAC
genomic: GCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAGgtatgtatga ... ttgcttacagCGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACAC
EST: gi|33381171|gb|CF196514.1|CF196514
EST:     GCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAG                         CGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACACCGGATCA
genomic: GCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAGgtatgtatga ... ttgcttacagCGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACACCGGATCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 50 (upstream exon), 62 (downstream exon)
Score: 34

ATATGTGGGCTGTTGGTGCAATTTTGGCTGAGCTTTTCACACTGTCTCCACTTTTCCCTGGTGGAAGgtatgtatga ... ttgcttacagCGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACACCGGATCATACTGTCTGGCCAGAGGGAATGAACCTGCCTCGTTCAAGCAGCTTTAAT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttccttgtttatggtgattctgctttgcttttaattattttatttgcttacagCGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACACCGGATCATACTGTCTGGCCAGAGGGAATGAACCTGCCTCGTTCAAGCAGCTTTAAT
                              ttttaat  putative branch site (score: 34)
                                       ttttattt  putative PPT
                         tttgcttttaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccagttcatcttgcacagagtagacctagaccatttgtacttatatttccttgtttatggtgattctgctttgcttttaattattttatttgcttacagCGAGACTGATCAGCTATACAAAATATGTGCTGTGCTTGGGACACCGGATCATACTGTCTGGCCAGAGGGAATGAACCTGCCTCGTTCAAGCAGCTTTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT