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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAGgttggcatgtttatgttattttaacttgattgttctctgcatatcgttgcatgttagaaattaaacactgatgtggatgattataatgtgacatatttag...

Basic information

species Oryza sativa
transcript LOC_Os03g58700.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G825524_T02 (Zea mays), 5'ss of exon 8
TGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAGgttggcatgtttatgttattttaacttgattgttctctgcatatcg-ttgcatgttagaaattaaacactgatgtggatgattataatgtgacatat--ttag
|||||| ||||||||||||||||||||||| |||||||||||||| |||||||||||||| |||||||||||||| ||||  |||||||| || || ||||||| ||  || |  || ||| | ||||||  ||     | |  || || ||  ||    |||  |        ||   || |   ||| ||| |||  ||  
TGCACAGTTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGATGAATACCATTTACAAACATTGGAAACATTATTGAATGCATTTCCCCAGCTTCAGgttgacaacttcacctt-tttcagcttgatccttactgccttcgcgattacaaattcttcattgtaatgcatcatgctggacttcgatg-gacgtatggttg-

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 9
TGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAGgttggcatgtttatgttattttaacttgattgtt-ctctgcatatcgttgcatgttagaaatta-aacac-tgatgtggatgattataatgtgacatatttag
|||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| || |||||||||||||| || || ||||||||||  ||||  || ||| | |||||||  | ||     |  | || ||  ||    |||  ||  | | |||  | |     ||     |   | ||  
TGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTATTGAGCGCATTTCCCCAGCTTCAGgttggcaactttacctt-tttcagcttgattcctactgcatttgccattacaaattcctcattgtaatgcatcatgctggtaccagtaccaccaaggactt--

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G75850.1 (Arabidopsis thaliana), 5'ss of exon 8
TGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAGgttggcatgtttatgttattttaacttgattgttctctgcatatcgttgca-tgttagaaat-taaacactgatgtggatgattataatgtgacatatttag
 || || |  || |||||||| |||||||| ||||||||||| || || |||||||| |||||  | || || || |||   || | | | |||||   ||| || | | |      ||    | ||   | || ||| |    |  |||| |  |||  || | ||  ||    | | || ||      | ||   | |  
GGCTCAGTATTATCTGATGGAGTGCATAATTCAAGTCTTTCCTGATGAGTACCATTTGCAGACTCTTGAGACCTTATTGGCTGCTTGTACCCAACTGATGgtgggtaggctagca--atcgatatttttctcttttctactctccaatgcaattctagttatctcaatgctttgtttggtgctttctgattaactcttctta

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|29627051|gb|CB632062.1|CB632062
EST:     ACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAG                         CCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
genomic: ACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAGgttggcatgt ... tttgtggcagCCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
EST: gi|58664362|gb|CK053048.1|CK053048
EST:     ACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAG                         CCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
genomic: ACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAGgttggcatgt ... tttgtggcagCCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
EST: gi|29621778|gb|CB626789.1|CB626789
EST:     GAGCGCATTTCCGCAACTACAG                         CCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
genomic: GAGCGCATTTCCGCAACTACAGgttggcatgt ... tttgtggcagCCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
EST: gi|29622156|gb|CB627167.1|CB627167
EST:     GAGCGCATTTCCGCAACTACAG                         CCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
genomic: GAGCGCATTTCCGCAACTACAGgttggcatgt ... tttgtggcagCCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
EST: gi|58693863|gb|CK082550.1|CK082550
EST:     A-CATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAG                         CCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
genomic: ACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAGgttggcatgt ... tttgtggcagCCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
EST: gi|58611844|gb|CK039556.1|CK039556
EST:     ACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAG                         CCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
genomic: ACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAGgttggcatgt ... tttgtggcagCCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
EST: gi|29613031|gb|CB618044.1|CB618044
EST:     ACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAG                         CCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
genomic: ACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAGgttggcatgt ... tttgtggcagCCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
EST: gi|33794974|gb|CF323367.1|CF323367
EST:     ACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAG                         CCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA
genomic: ACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAGgttggcatgt ... tttgtggcagCCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCA

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: 69 (upstream exon), 73 (downstream exon)
Score: 53

TGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGTTGAGCGCATTTCCGCAACTACAGgttggcatgt ... tttgtggcagCCAAATGTTGATATCAAAACCGTGCTGTCTCAACTCATGGACAGGTTATCAAGCTATGCTGCCGCAAGTCCTGAA




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