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

gtaagatatcctccgttgttctgtagattgatgtttggaattatgaacatttattcatatatttggtttgatacttttatgatgtgcagATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAATACCCCTCCGCTGTTCATTATAGGTGGTAAAAGCTCAGCGAAGTTCTTAT

Basic information

species Oryza sativa
transcript LOC_Os03g22430.1
intron # 9
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|29666271|gb|CB662546.1|CB662546
EST:     GTCAGACGCCCTGATATTATGTGATGTTGTACATTGAAATTTTAAATTAG                         ATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAAT
genomic: GTCAGACGCCCTGATATTATGTGATGTTGTACATTGAAATTTTAAATTAGgtaagatatc ... tgatgtgcagATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAAT
EST: gi|86431932|gb|CI085543.1|CI085543
EST:     GTGATGTTGTACATTGAAATTTTAAATTAG                         ATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAAT
genomic: GTGATGTTGTACATTGAAATTTTAAATTAGgtaagatatc ... tgatgtgcagATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAAT
EST: gi|8594770|gb|AU093308.1|AU093308
EST:     GTCAGACGCCCTGATATTATGTGATGTTGTACATTGAAATTTTAAATTAG                         ATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAAT
genomic: GTCAGACGCCCTGATATTATGTGATGTTGTACATTGAAATTTTAAATTAGgtaagatatc ... tgatgtgcagATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAAT
EST: gi|22307941|gb|BQ909163.1|BQ909163
EST:     AGACGCCCTGATATTATGTGATGTTGGTACACTTGAAATTGTTAAATTAG                         ATTA-GCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCC-ACAAGAA
genomic: AGACGCCCTGATATTATGTGATGTT-GTACA-TTGAAATT-TTAAATTAGgtaagatatc ... tgatgtgcagATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAA
EST: gi|58691504|gb|CK080191.1|CK080191
EST:     GTCAGACGCCCTGATATTATGTGATGTTGTACATTGAAATTTTAAATTAG                         ATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAAT
genomic: GTCAGACGCCCTGATATTATGTGATGTTGTACATTGAAATTTTAAATTAGgtaagatatc ... tgatgtgcagATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAAT
EST: gi|29666270|gb|CB662545.1|CB662545
EST:     GTCAGACGCCCTGATATTATGTGATGTTGTACATTGAAATTTTAAATTAG                         ATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAAT
genomic: GTCAGACGCCCTGATATTATGTGATGTTGTACATTGAAATTTTAAATTAGgtaagatatc ... tgatgtgcagATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAAT
EST: gi|58689717|gb|CK078404.1|CK078404
EST:     ATATTATGTGATGTTGTACATTGAAATTTTAAATTAG                         ATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCNACAAGAAT
genomic: ATATTATGTGATGTTGTACATTGAAATTTTAAATTAGgtaagatatc ... tgatgtgcagATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAAT

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: 68 (upstream exon), 61 (downstream exon)
Score: 7

AGTACATGGCTGACATGCTCTCCCCAGAGGAATGGGACAAAGTTGCTGGAGTCAGACGCCCTGATATTATGTGATGTTGTACATTGAAATTTTAAATTAGgtaagatatc ... tgatgtgcagATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAATACCCCTCCGCTGTTCATTATAGGTGGTAAAAGCTCAGCGAAGTTCTTAT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaattatgaacatttattcatatatttggtttgatacttttatgatgtgcagATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAATACCCCTCCGCTGTTCATTATAGGTGGTAAAAGCTCAGCGAAGTTCTTAT
                               gtttgat  putative branch site (score: 7)
                                       cttttat  CT-rich tract
     attatgaacatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatatcctccgttgttctgtagattgatgtttggaattatgaacatttattcatatatttggtttgatacttttatgatgtgcagATTAGGCGGTTAAGTTGTGGGATGTGAAAGCAGCTGTCATCCAACAAGAATACCCCTCCGCTGTTCATTATAGGTGGTAAAAGCTCAGCGAAGTTCTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA