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

gtacgcatgaactcatacacatactatcatgctctactctatgcagaacgcaaagtaatctcatgatgcctaaatttcatctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGATGATCCCAGATGATGAG

Basic information

species Oryza sativa
transcript LOC_Os01g07090.1
intron # 10
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|88521753|gb|CI448420.1|CI448420
EST:     GAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|13420769|gb|AU174859.1|AU174859
EST:     TTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: TTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|55413992|gb|CV726368.1|CV726368
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|88470794|gb|CI408065.1|CI408065
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|24468854|gb|CA305803.1|CA305803
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTCGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|86851837|gb|CI316406.1|CI316406
EST:     GGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|117230125|gb|CT846221.1|CT846221
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTCGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|86541345|gb|CI181551.1|CI181551
EST:     GGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|88487810|gb|CI425081.1|CI425081
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|88487832|gb|CI425103.1|CI425103
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|29641054|gb|CB646061.1|CB646061
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTCCGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|88844338|gb|CI005711.1|CI005711
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|29685959|gb|CB682234.1|CB682234
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|29685960|gb|CB682235.1|CB682235
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|86259009|gb|CI004553.1|CI004553
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|86903280|gb|CI313643.1|CI313643
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAGTAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
EST: gi|88283322|gb|CI404768.1|CI404768
EST:     GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG                         GTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA
genomic: GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGA

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), 52 (downstream exon)
Score: 23

GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAGgtacgcatga ... atctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGATGATCCCAGATGATGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactctatgcagaacgcaaagtaatctcatgatgcctaaatttcatctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGATGATCCCAGATGATGAG
                                  gcctaaa  putative branch site (score: 23)
                                         tttcatct  CT-rich tract
                                     taaatttcatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcatgaactcatacacatactatcatgctctactctatgcagaacgcaaagtaatctcatgatgcctaaatttcatctatgcagGTGGTAAGATGGATGACATTACGGTTATTGTTGCACAGGTGAAGGCAGTGATGATCCCAGATGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG