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'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattttatttgcatgacgtgggaacatatatttgcatgagagtggaatgggtgttatcctgaagttcgctatcatatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG

Basic information

species Oryza sativa
transcript LOC_Os03g63020.3
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.4 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G045241_T05 (Zea mays), 3'ss of exon 16
gtgagattttatttgcatgacgtgggaacatatatttgcatgagagtggaatgggtgttatcctgaagttc--gctatcatatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
||||||  ||||| |  ||  |   ||    || |||         || ||||||||   || |||  ||   |||||| |  | ||||||||||||| |||||||| |||||||| ||| | |||||| |||| |
gtgagaaattattagggtg-tgcaagatatcattttta--------tgcaatgggtgccgtcatgatatttttgctatcctgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
















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|29613120|gb|CB618133.1|CB618133
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|29644979|gb|CB649986.1|CB649986
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|89167683|gb|CI018289.1|CI018289
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|29663527|gb|CB659802.1|CB659802
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|34996388|gb|CF569133.1|CF569133
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|29666009|gb|CB662284.1|CB662284
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGT---CAG
EST: gi|29666008|gb|CB662283.1|CB662283
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGT---CAG
EST: gi|29638287|gb|CB643296.1|CB643296
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|29656192|gb|CB652467.1|CB652467
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|29613155|gb|CB618168.1|CB618168
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|33801021|gb|CF326384.1|CF326384
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|29633044|gb|CB638053.1|CB638053
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|33381337|gb|CF196680.1|CF196680
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|218497584|gb|FG955131.1|FG955131
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|29613395|gb|CB618408.1|CB618408
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|29628841|gb|CB633852.1|CB633852
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTTTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
EST: gi|8856640|gb|AU093958.1|AU093958
EST:     ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG                         GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
genomic: ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG

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: 35 (upstream exon), 46 (downstream exon)
Score: 27

ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAGgtgagatttt ... tatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgcatgagagtggaatgggtgttatcctgaagttcgctatcatatcatgcagGAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG
                                        tatcatat  TA-rich tract