Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattttacttactgatgcctgaatcaacaatttatctgaatcatgttcattgggacaattaaatttcatgtgtttgccatgtctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGATGGCTTCAACAAAACTGGCATACCGAACACACTTTGGGAGCTCGTTGAAC

Basic information

species Oryza sativa
transcript LOC_Os03g05390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G028521_T04 (Zea mays), 3'ss of exon 4
gtatgattttacttactgatgcctgaatcaacaatttatctgaatcatgttcattg-ggacaattaaatttcatgtgtt-tgccatgtctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGATGGCTTCAACAAAACTGGCATACCGAACACACTTTGGGAGCTCGTTGAAC
||||| |  |      | |      | |||| ||    |    ||  |  | | || |||| |  |   |     |||| | |  ||     |   |||||||||| ||| |||||||||| ||||||||||||||||| || || ||||||||||||||||| ||||||||||||||||| |||||| | || ||||
gtatgctcctcaaattttaattaacactcaataacgggtggatattttacttagtgcggacgacgatcatcatcctgttgtactttgatgacttgcagGTGTCATATTCACTGCTGATCTTTTTCTGCGGGATGTTTATCACTGTTGATGGCTTCAACAAAACGGGCATACCGAACACACTATGGGAGTTAGTGGAAC

upper sequence: LOC_Os03g05390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G02260.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgattttacttactgatgcctgaatcaacaatttatctgaatcatgttcattgggacaatt-aaatttcatgtgtttgccatgtctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGATGGCTTCAACAAAACTGGCATACCGAACACACTTTGGGAGCTCGTTGAAC
                       ||||  | ||| || ||| || | | || |  |  |||||| |||  || | |    |   |  ||  ||  |||| || || ||  |  ||||||| |||||||||||||| || || || ||||| |||||||||||||| || || | | | || ||||| ||  | || |
----------------------gtgaaa-accaaattttcttaaac-tctttagagatacaattcaaagatcttatcaaagttgtaacttttg-cagGTATCGTATTCGCTTTTGATCTTTTTCTGCGGGATGTTCATAACCGTTGATGGATTCAACAAAACTGGTATCCCTACCGCTCTATGGGACCTAATGGAGC

upper sequence: LOC_Os03g05390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv16s0050g00780.t01 (Vitis vinifera), 3'ss of exon 1
-------------------gtatgattttacttactgatgcctgaatcaacaa---tttatctgaatcatgttcattgggacaattaaa--tttca------tgtgtttgccatgtctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGATGGCTTCAACAAAACTGGCATACCGAACACACTTTGGGAGCTCGTTGAAC
                   |  | | |||  ||  | || |    ||  |  |    ||   |  |   | ||  ||||   ||  |||   |  |      | | |||  ||| | ||||   |||| || || ||  |  |||| ||||||||||| ||||| ||||| || ||||| |||||||||||||| || || | | || | |||||  |  | || |
gtaaaatcagcaatacaatgcttaacttttatt-ttcatacagagattgatgaatacttgattataatttatttgttggagaaagaaaaaactctaaaaagttctatttctcatctttgat--cagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGATGGTTTCAACAAAACTGGAATCCCTAGCGCAGTATGGGACTTAATGGAGC

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|29656826|gb|CB653101.1|CB653101
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|25798436|gb|CA754397.1|CA754397
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|313084033|gb|HO213816.1|HO213816
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|88985311|gb|CI002828.1|CI002828
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|29629817|gb|CB634826.1|CB634826
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|29644052|gb|CB649059.1|CB649059
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGC
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGC
EST: gi|33381166|gb|CF196509.1|CF196509
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTNNNNNNN                         NTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|428144|gb|D24292.1|D24292
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGNT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|14571450|gb|BI118818.1|BI118818
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACAGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|218490860|gb|FG966651.1|FG966651
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|33684354|gb|CF312593.1|CF312593
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCGGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|88974168|gb|CI002787.1|CI002787
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|38473979|gb|CF958111.1|CF958111
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|218481056|gb|FG966658.1|FG966658
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
EST: gi|58670085|gb|CK058771.1|CK058771
EST:     TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAG                         GTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT
genomic: TTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGAT

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), 8 (downstream exon)
Score: 26

TGCACTTCTCATGGGGCTTAACATGTCATGGACAGCCATCACTGCGGCTCTTGTTCTTCTGGCGCTTGATTTTACTGATGCACAGGCTTGTCTGGAGAAGgtatgatttt ... ctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGATGGCTTCAACAAAACTGGCATACCGAACACACTTTGGGAGCTCGTTGAAC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatcatgttcattgggacaattaaatttcatgtgtttgccatgtctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGATGGCTTCAACAAAACTGGCATACCGAACACACTTTGGGAGCTCGTTGAAC
                                           gtctgat  putative branch site (score: 26)
                 acaattaaatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattttacttactgatgcctgaatcaacaatttatctgaatcatgttcattgggacaattaaatttcatgtgtttgccatgtctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGATGGCTTCAACAAAACTGGCATACCGAACACACTTTGGGAGCTCGTTGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT