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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaaaatatggaaatgaaaatgtgtaataatagggagagaaatgagcgatgtattaattcactgtacattgtattgtggctttgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTGGGGACATACTCATCCCTCTCCAAGATTATCCAGAACTACACCTGACCTG

Basic information

species Oryza sativa
transcript LOC_Os02g01100.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01100.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G134888_T01 (Zea mays), 3'ss of exon 11
----gtacaaaaatatggaaatgaaaatgtgtaataatagggagagaaatgagcgatgtattaattcactgtacattgtattgtggct--ttgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTGGGGACATACTCATCCCTCTCCAAGATTATCCAGAACTACACCTGACCTG
     || | | | |||  | ||    |  || |  |   |       | ||    |  | |  | || | || | || |  |   ||  ||||||  ||||| ||||||||||| |||||||| || || ||||||||||| || | |||||| |||||||| ||||| || ||||| |||||||||||| | |  |   
ttatataaatagacatgctattgtttttaagtgaacactagacacactacgaaatgtagaattgtgcattctatactg-accgcatctgtttgattcgcagATAGCAGCTTGCTCGTTCATCATAGTTGTCGGGGTTTGCTGTGCCTACGTGGGAACATACTCGTCCCTGTCGAAGATAATCCAGAACTACGCATAGCACA

upper sequence: LOC_Os02g01100.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G105192_T03 (Zea mays), 3'ss of exon 10
--------------------------------------------------------------------gtacaaaaatatggaaatgaaaatgtgtaataatagggagaga--aatgagcgatgtattaattcactgtacattg-------tattgtggcttt----gatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTGGGGACATACTCATCCCTCTCCAAGATTATCCAGAACTACACCTGACCTG
                                                                    |||    |     ||     |  ||  |   || | ||    |  ||||  |  |   | | ||  |   |   |        || || | |||     |||   ||| | ||||  ||||| |||||||||||||| ||||||||||||||||| ||||| |||||||| || || || ||||| |||||||||||||| |||    
gtatgtatatttgcaattaatacttaccagagttgcattgtttcgttaacaaataagcagagatgtcagtatcctacctaagatgctgatttgctttgaaacatggtagaactaatgctctgtccctcactttgcgtcatgctaatgctattaatgggacttctttcgatcggcagGTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTGGGAACATACTCGTCTCTGTCAAAGATAATCCAGAACTACACATGATACA
















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|89168324|gb|CI109528.1|CI109528
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88266546|gb|CI377448.1|CI377448
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|89167449|gb|CI038956.1|CI038956
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88484073|gb|CI421344.1|CI421344
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88544177|gb|CI474251.1|CI474251
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88516600|gb|CI444254.1|CI444254
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88991353|gb|CI034688.1|CI034688
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88489526|gb|CI426798.1|CI426798
EST:     CATGCGCCTGTTTCTTGNCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|29678444|gb|CB674719.1|CB674719
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|58686741|gb|CK075428.1|CK075428
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88515198|gb|CI442852.1|CI442852
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88284203|gb|CI405649.1|CI405649
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88470483|gb|CI407754.1|CI407754
EST:     CATGCCCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88543000|gb|CI472364.1|CI472364
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|27548100|gb|CA766182.2|CA766182
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88272468|gb|CI386323.1|CI386323
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|86498766|gb|CI141399.1|CI141399
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88275672|gb|CI396276.1|CI396276
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|40494256|gb|BX901140.1|BX901140
EST:     CATGCGCCTGTTTCTTGCCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATGATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|18386237|gb|BM419436.1|BM419436
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|29663318|gb|CB659593.1|CB659593
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|86429995|gb|CI082418.1|CI082418
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|29659581|gb|CB655856.1|CB655856
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88253485|gb|CI352111.1|CI352111
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         A-TGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88992255|gb|CI035393.1|CI035393
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88274864|gb|CI388322.1|CI388322
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
EST: gi|88840439|gb|CI079893.1|CI079893
EST:     CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTGGGCATCAG                         ATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG
genomic: CATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTG

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: 61 (upstream exon), 37 (downstream exon)
Score: 4

ACCTACATCCTTCCATGCGCCTGTTTCTTGGCCATCCTTAAGAGAAAAGTGACTTGGCATCAGgtacaaaaat ... tgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTGGGGACATACTCATCCCTCTCCAAGATTATCCAGAACTACACCTGACCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaatgagcgatgtattaattcactgtacattgtattgtggctttgatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTGGGGACATACTCATCCCTCTCCAAGATTATCCAGAACTACACCTGACCTG
           atgtattaatt  TA-rich tract