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'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatacttgagcagaacaatagcaagatagtagcgtagggtgttggtactgtttcttctccatcctgtgactctgtgagcttcaaaaaaataaaaatgcctaatgaccctctaccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA

Basic information

species Oryza sativa
transcript LOC_Os03g52840.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
gtatatacttgagcagaacaatagcaagatagtagcgtagggtgttggtactgtttcttctccatcctgtgactctgtgagcttcaaaaaaataaaaatgcctaatgaccctctaccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA
||||   | |||  | ||| |||  || | | ||||    |||||||   ||| |||||   |||            | |    ||||    ||   ||        ||    ||   | |||||||||||||| ||||||||||| ||||||||||||||||| || |||||||||||||| || ||||| ||||||||||||||||| ||||||||||| |
gtatg-gcatgatgaaaacgataa-aaaaaactagca---ggtgttgaacctgcttctt--gcat------------taaaaaccaaaggtttagtgatat------acttaatattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatatacttgagcagaacaatagcaagatagtagcgtagggtgttggtactgtttcttctccatcctgtgactctgtgagcttcaaaaaaataaaaatgcctaatgaccctctaccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA
                   || |   | | || |||  |     || | ||       | |      | ||    | | | |||  |    ||  |  ||         | |  |      ||||| ||||||| ||||| |||||||||||    ||||||||||| ||||| |||||||| ||||| || || || || || ||  ||||||||||  | |
-----------------gtaaaaaagaaaaagaagcaaaa----tttgaaccaaaatgttttagatttatg----tataatctttcacgtcattcatttgtt-----gtcttgaa------agGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTTCAAGGTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGA

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------------------gtatatacttgagcagaacaata-gcaagatagtagcgtagggtgttggtactgtttcttctccatcctgtgactctgtgagcttcaaaaaaataaaaatgcctaatgaccctctac-cgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA
                                        |     ||||| |   | |     |   ||    |  |   ||||  |     ||| ||    | | || |  | | |    ||  |      |  ||    ||   ||  | ||   ||  ||||| ||||||||| ||| ||||| ||||||   |||||||| || || || |||||||| || || ||||| || ||| ||||||||||||||||  | |
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcctactccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattg--ttggacgtggaactaacatttat--actttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 9
gtatatacttgagcagaacaatagcaagatagtagcgtagggtgttggtactgtttcttctccatcctgtgactc-tgtgagcttcaaaaaaataaaaatgcctaatgacc---ctctaccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA
                             |     |    |||  ||||    ||   | |  |       | || |  | |  | |        | | |    ||||       || | | |  ||||  ||||||||| ||| ||||| ||||||   |||||||| || || || |||||||||||||| |||||||| ||| |||||||||| |||||  | |
---------------------------tttttccccaattggttatggtttctttcagttttgaaagcaaaattcataagtgaattatctggcacacatttttcaatggttgaattccatcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGA

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------gtatatacttgagcagaacaata-gcaagatagtagcgtagggtgttggta-ctgtttcttctccatcctgtgactctgtgagcttcaaaaaaataaaaatgcctaatg-accctctac-cgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA
                                        |     ||||| |   | |  |  |   ||       ||    |   ||  ||| ||||| |    |          || |  ||     |  |  || |  |   |  ||  | ||   ||  ||||| ||||||||| ||| ||||| ||||||   |||||||| || || || |||||||| || || ||||| || ||| ||||||||||||||||  | |
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

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|29674139|gb|CB670414.1|CB670414
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|58691302|gb|CK079989.1|CK079989
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|58691585|gb|CK080272.1|CK080272
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAG
EST: gi|38479794|gb|CF963883.1|CF963883
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAACTGCTGCTGTCTTCCCAGGTCT
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAA-TGCTGCTGTCTTCCCAGGTCT
EST: gi|29672938|gb|CB669213.1|CB669213
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|24468780|gb|CA305729.1|CA305729
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|38472528|gb|CF956660.1|CF956660
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCT
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCT
EST: gi|4716856|gb|AU057972.1|AU057972
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|38474897|gb|CF959030.1|CF959030
EST:     ATCTTGTTAGCAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATAGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCT
genomic: ATCTT-TTA-CAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTAT-GACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCT
EST: gi|13420583|gb|AU174673.1|AU174673
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|11442748|gb|BF430651.1|BF430651
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|29629705|gb|CB634714.1|CB634714
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|33663440|gb|CF294407.1|CF294407
EST:     GAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: GAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|58692040|gb|CK080727.1|CK080727
EST:     TGAAAGGAGT-AACAAGCAA-GCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|29681405|gb|CB677680.1|CB677680
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|29681406|gb|CB677681.1|CB677681
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|14571290|gb|BI118658.1|BI118658
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|55411163|gb|CV723539.1|CV723539
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|38478032|gb|CF962165.1|CF962165
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|29674038|gb|CB670313.1|CB670313
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
EST: gi|218505280|gb|FG952910.1|FG952910
EST:     TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAG                         GTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG
genomic: TGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatactt ... taccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgactctgtgagcttcaaaaaaataaaaatgcctaatgaccctctaccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA
                               gcctaat  putative branch site (score: 3)
                                        ccctctacc  putative PPT
                 aaaaaaataaaaatgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatacttgagcagaacaatagcaagatagtagcgtagggtgttggtactgtttcttctccatcctgtgactctgtgagcttcaaaaaaataaaaatgcctaatgaccctctaccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT