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'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcttgtagcaatactcacgcagcttttgccaccaacaattgaacacttgaatccaatcggctcagtgacttatccaacacacactcatcggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG

Basic information

species Oryza sativa
transcript LOC_Os05g45960.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G090087_T03 (Zea mays), 3'ss of exon 13
-------------------------------------------------------------------------------------catcttgt-agcaatactcacgcagcttttgccaccaacaattgaacacttgaatccaatcggctcagtgacttatccaacacacactcatcggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG
                                                                                     |||  | | || |   | | |  |    | ||   ||  ||   |||||||||||      | ||     || | | |  |  |   |  |   ||||||||| ||||||||| |||| |||||||||||||| || ||||| || ||||| ||||| || || |||||||||||||||||
gcaagtcggttcaactctctgcaagtttgtttagccccgcatttctcacatggaacttagtttgataaagtcagggtttcttcagcatgatctcaggatcccccccaaaagcatcgctgtcagtaaccaaacacttgaat------gacttccgaacgttttc--cttatcttggtttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG
















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|87028745|gb|CI349464.1|CI349464
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAATTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|86496475|gb|CI139108.1|CI139108
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|86486168|gb|CI128801.1|CI128801
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACTCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|86436669|gb|CI118391.1|CI118391
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCT
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|44673853|gb|CR287287.1|CR287287
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|88251843|gb|CI349080.1|CI349080
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|8956651|gb|BE230326.1|BE230326
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|86487725|gb|CI130358.1|CI130358
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|88848173|gb|CI086695.1|CI086695
EST:     ACGCTCATCTGACGGCTGCAGCTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|9865361|gb|AU101111.1|AU101111
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGNATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|88962017|gb|CI097170.1|CI097170
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|89180443|gb|CI044722.1|CI044722
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|88907945|gb|CI090541.1|CI090541
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|88269212|gb|CI380510.1|CI380510
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|88282820|gb|CI402020.1|CI402020
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|89162486|gb|CI099178.1|CI099178
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|29632954|gb|CB637963.1|CB637963
EST:     ACGCTCATTTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|86851512|gb|CI314095.1|CI314095
EST:     ACGCTCATCTGACGGCTGCACTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|89161684|gb|CI100844.1|CI100844
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|58656949|gb|CK045629.1|CK045629
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|29617924|gb|CB622936.1|CB622936
EST:     ACGCTCATTTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|88968032|gb|CI098274.1|CI098274
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|218484591|gb|FG954366.1|FG954366
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|88277860|gb|CI398662.1|CI398662
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|88908314|gb|CI090907.1|CI090907
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|88976781|gb|CI257525.1|CI257525
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|88275300|gb|CI395904.1|CI395904
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
EST: gi|86493002|gb|CI135635.1|CI135635
EST:     ACGCTCATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAG                         GAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA
genomic: ACGCT-ATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCA

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: 67 (upstream exon), 74 (downstream exon)
Score: 27

AGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGTGAAAGGATGAACGCTATCTGACGGCTGCAGTTGTTTCAAACGACCCTTTATTCCTGCAGgtaagttggt ... cggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttgaatccaatcggctcagtgacttatccaacacacactcatcggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG
                                                ttttc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcttgtagcaatactcacgcagcttttgccaccaacaattgaacacttgaatccaatcggctcagtgacttatccaacacacactcatcggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - -tgtagca
- - - - - - - - -cacgcag
- - - - - - - - - - - - cttttgc
- - - - - - - - - - - - - - - - - caacaat
- - - - - - - - - - - - - - - - - - - - -tgaacac
- - - - - - - - - - - - - - - - - - - - - - - - -tgaatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacaca