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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcacagatatcttaaatcctttctgcttgtttttctcatgtccagacaaacatttcttactaggtctgtcttgaactttctgcagATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTCTTGGTATAAACTTCCGTGTGGAAGCCCTGCTCCAAAACTGTGCTACTGA

Basic information

species Oryza sativa
transcript LOC_Os01g40620.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40620.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G086052_T03 (Zea mays), 3'ss of exon 9
gtttgcacagatatcttaaatc--ctttctgcttgtttttctcat-gtccagacaaacatttcttactaggtctgtcttgaactttctgcagATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTCTTGGTATAAACTTCCGTGTGGAAGCCCTGCTCCAAAACTGTGCTACTGA
|| ||||| |   |  | | ||  |||| |||| || |      |     | || |  |||| ||        | ||| | |  ||  ||||| ||||| || || |||||||||||||| || ||||||||| |||| ||||| || || |||||| | || ||||| || || || |||||  |    ||
gtatgcactggcgttattactctactttttgctggtatcaacagttacttacacgagaatttttt-------ttttctcgtaacttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTCTCGGCATCAACTTCAGGGTAGAAGCTCTCCTGCAGAACTGCACCGAGGA

upper sequence: LOC_Os01g40620.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G28700.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgcacagatatcttaaatcctttctgct-tgtttttctcatgtccagacaaacatttcttactaggtctgtcttgaactttctgcagATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTCTTGGTATAAACTTCCGTGTGGAAGCCCTGCTCCAAAACTGTGCTACTGA
|||| |     |||  |   | ||      | || | |    | |   ||   |   || |||   |   |     ||    |||||||||  || | || || ||||| || |||||||| |||||||||||||| || ||||| ||||||||| | || || ||  |||| || || |||      ||
gttt-cgttcctatactggctactagtcattgtgatgtaggtagggttagctta--cttacttgacaaagcaaatgtgtgtgttctgcagAAAATGTCTCAGTCCATGGACCTATGACTCAGTCCCAGTTCTTGGGTTCGCTTGGAATAAACTTCAGAGTTGATGCATTGCTACAGAATTGTAACGACGA
















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|29661500|gb|CB657775.1|CB657775
EST:     TGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGGAAGCTTCAG                         ATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTC
genomic: TGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGGAAGCTTCAGgtttgcacag ... ctttctgcagATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTC
EST: gi|109712390|gb|CI104998.1|CI104998
EST:     TGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGGAAGCTTCAG                         ATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTC
genomic: TGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGGAAGCTTCAGgtttgcacag ... ctttctgcagATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTC
EST: gi|29644656|gb|CB649663.1|CB649663
EST:     TGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGGAAGCTTCAG                         ATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTC
genomic: TGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGGAAGCTTCAGgtttgcacag ... ctttctgcagATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTC
EST: gi|29643066|gb|CB648073.1|CB648073
EST:     TGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGGAAGCTTCAG                         ATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTC
genomic: TGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGGAAGCTTCAGgtttgcacag ... ctttctgcagATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTC

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: 64 (upstream exon), 74 (downstream exon)
Score: 14

AAGCACAAGTTTGTACACATATTGGATAACCCTGGTTCAGCCGATCTGAGTGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGGAAGCTTCAGgtttgcacag ... ctttctgcagATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTCTTGGTATAAACTTCCGTGTGGAAGCCCTGCTCCAAAACTGTGCTACTGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctcatgtccagacaaacatttcttactaggtctgtcttgaactttctgcagATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTCTTGGTATAAACTTCCGTGTGGAAGCCCTGCTCCAAAACTGTGCTACTGA
                       ttcttac  putative branch site (score: 14)
                                             ctttctgc  putative PPT
                 aaacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcacagatatcttaaatcctttctgcttgtttttctcatgtccagacaaacatttcttactaggtctgtcttgaactttctgcagATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTCTTGGTATAAACTTCCGTGTGGAAGCCCTGCTCCAAAACTGTGCTACTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG