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

gtaagattctttttccactatcatgcgatgaaacaacattatctttcaccggaattaccgaagcccttatatatactttaaatgaacatcagagctgcaatggtattaacagatgctttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG

Basic information

species Oryza sativa
transcript LOC_Os09g32680.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G408242_T03 (Zea mays), 3'ss of exon 6
gtaagattctttttccactatcatg--cgatg-------aaacaacattatctttcaccggaattaccgaagcccttatatatactttaaatgaacatcagagctgcaatggtattaacagatgctttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
|||||| ||  |||||  | | ||    | ||           ||||||| ||||| |    ||  ||  |||  | || |||   ||        | | || || |||     || | |||||   |   |  ||||| ||||||||||||||||||||||| |||||||||||||||||
gtaagaatccgtttcctgtgtaatcgctggtgttttttcgtggaacattacctttctc--atatctccacagctttcatttatttgttc------tagcggaactccaa----gttgatagatgtcctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
















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|218486157|gb|FG964429.1|FG964429
EST:     GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACA                         GTTATTGCAGGATGCTGGCATAACA
genomic: GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACAgtaagattct ... ttgattttagGTTATTGCAGGATGCTGGCATAACA
EST: gi|38568817|gb|CD671032.1|CD671032
EST:     GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACA                         GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCCTG
genomic: GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACAgtaagattct ... ttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCC-TG
EST: gi|24468776|gb|CA305725.1|CA305725
EST:     GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACA                         GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
genomic: GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACAgtaagattct ... ttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
EST: gi|86493556|gb|CI136189.1|CI136189
EST:     GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACA                         GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
genomic: GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACAgtaagattct ... ttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
EST: gi|29660228|gb|CB656503.1|CB656503
EST:     GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACA                         GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
genomic: GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACAgtaagattct ... ttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
EST: gi|29660227|gb|CB656502.1|CB656502
EST:     GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACA                         GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
genomic: GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACAgtaagattct ... ttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
EST: gi|218483409|gb|FG950971.1|FG950971
EST:     GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTATACA                         GTTATTGCAGGATGCTGGCATAACAGATCTGACA
genomic: GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACAgtaagattct ... ttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACA
EST: gi|218503593|gb|FG957186.1|FG957186
EST:     GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACA                         GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
genomic: GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACAgtaagattct ... ttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
EST: gi|27547661|gb|CA765583.2|CA765583
EST:     GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACA                         GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
genomic: GCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACAgtaagattct ... ttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG

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: 70 (upstream exon), 45 (downstream exon)
Score: 39

ACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATATCGTCCTCTTTTACAgtaagattct ... ttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactttaaatgaacatcagagctgcaatggtattaacagatgctttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
                                            tttgatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattctttttccactatcatgcgatgaaacaacattatctttcaccggaattaccgaagcccttatatatactttaaatgaacatcagagctgcaatggtattaacagatgctttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG