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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtgttgtagtactctagcattggttacacattaacctataaaatgtaacattctgctagttctttttcctgcggcctttcaaatggttcttcctcatgacgctgccagctaggggaaagataaccgcagcaaagattgttttggttggtgttgtttacaatgtgaatatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGATGTTGTGAAGAGAGTAATTGATGTTGAACTGACTGAAGCTGAGCTGGAAG

Basic information

species Oryza sativa
transcript LOC_Os08g44530.1
intron # 12
splice site 3'
intron type U2

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|86413805|gb|CI068012.1|CI068012
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|58586955|gb|CF985263.1|CF985263
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGGTC-AATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGA
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGG-TCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGA
EST: gi|88830002|gb|CI074674.1|CI074674
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|8858265|gb|AU095583.1|AU095583
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|86255894|gb|CI068343.1|CI068343
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|88965683|gb|CI006589.1|CI006589
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|218478481|gb|FG953986.1|FG953986
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|88971557|gb|CI017871.1|CI017871
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|86823618|gb|CI258691.1|CI258691
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|86428510|gb|CI075191.1|CI075191
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|86537187|gb|CI177393.1|CI177393
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|89180557|gb|CI044836.1|CI044836
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|88848058|gb|CI086580.1|CI086580
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|88960472|gb|CI006433.1|CI006433
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|5038803|gb|AU070913.1|AU070913
EST:     CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
genomic: CTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGAT
EST: gi|86488131|gb|CI130764.1|CI130764
EST:     GGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCCTGAAGCCACAG                         GAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGA
genomic: GGAGGATCACATGGATTTGTTGTAGGCCACATTTGT-CCTGAAG-CACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGA

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: 75 (upstream exon), 60 (downstream exon)
Score: 27

GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtgtt ... tatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGATGTTGTGAAGAGAGTAATTGATGTTGAACTGACTGAAGCTGAGCTGGAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccgcagcaaagattgttttggttggtgttgtttacaatgtgaatatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGATGTTGTGAAGAGAGTAATTGATGTTGAACTGACTGAAGCTGAGCTGGAAG
 agataac  putative branch site (score: 27)
                                             tatttttc  putative PPT
                                     aatgtgaatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtgttgtagtactctagcattggttacacattaacctataaaatgtaacattctgctagttctttttcctgcggcctttcaaatggttcttcctcatgacgctgccagctaggggaaagataaccgcagcaaagattgttttggttggtgttgtttacaatgtgaatatttttcagGAGGGAGGTCCAATTGGTCTTGTTCAAAACGGTGACAAAATTACCATTGATGTTGTGAAGAGAGTAATTGATGTTGAACTGACTGAAGCTGAGCTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG