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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTCGGGTAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatgactttaccaggtttcccagataatcaaatcaaatatagctattaaattcatctacctttacattttaccggcaatatttttcttgttacatttctgttctaatgctctctgtacgcatatgccatactttcag

Basic information

species Oryza sativa
transcript LOC_Os01g60120.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60120.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G021589_T03 (Zea mays), 5'ss of exon 8
GTTGCTCGGGTAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatgactttaccaggtttcccagataatcaaatcaaatatagctattaaattcatctacctttacattttaccggcaatatttttcttgttacatttctgttc-taatgctctctgtacgcatatgccatactttcag
 |||||||| ||||||| ||||||||| | ||||| || ||||| || ||| |||||||||||||  | | || |        ||| || |   |   | | | ||||      ||   |  |  |  |     | | | |||| | | | |  ||| | |    | |  | || | | | |  |   |    |         
ATTGCTCGGATAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAGGTATGGGT-ATTTGAATTTTCCACCCCGAGAGgtactaccagt-tagcctgggcatctgtggaaatccattgacttctgacaatgtatattt--ttagaataagatccacagtgttttttttctgttaacattaa--------

upper sequence: LOC_Os01g60120.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G021589_T05 (Zea mays), 5'ss of exon 8
GTTGCTCGGGTAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatgactttaccaggtttcccagataatcaaatcaaatatagctattaaattcatctacctttacattttaccggcaatattt-ttcttgttacatttctgttctaatgctctctgtacgcatatgccatactttcag
 |||||||| ||||||| ||||||||| | ||||| || ||||| || ||| |||||||||||||  | | || |        ||| || |   |   | | | ||||      ||   |  |  |  |     | | | |||| | | || ||   | |                                           
ATTGCTCGGATAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAGgtatgggt-atttgaattttccaccccgagaggtactaccagt-tagcctgggcatctgtggaaatccattgacttctgacaatgtatatttttagaataag-----------------------------------------

upper sequence: LOC_Os01g60120.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G021589_T02 (Zea mays), 5'ss of exon 7
----------------------------------------GTTGCTCGGGTAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatgactttaccaggtttcccagataatcaaatcaaatatagctattaaattcatctacctttacattttaccggcaatattt-ttcttgttacatttctgttctaatgctctctgtacgcatatgccatactttcag
                                         |||||||| ||||||| ||||||||| | ||||| || ||||| || ||| |||||||||||||  | | || |        ||| || |   |   | | | ||||      ||   |  |  |  |     | | | |||| | | || ||   | |                                           
GATGGATAGTTTTGATTAACTTGTCTTTCGTCTGATACAGATTGCTCGGATAATCTTATTCATATATATGTTCACCCATATGTATTTTCATCTTGATCAGgtatgggt-atttgaattttccaccccgagaggtactaccagt-tagcctgggcatctgtggaaatccattgacttctgacaatgtatatttttagaataag-----------------------------------------

upper sequence: LOC_Os01g60120.2 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ27642 (Selaginella moellendorffii), 5'ss of exon 7
GTTGCTCGGGTAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatgactttaccag--gtttcccagataatcaaatcaaatatagctattaaattcatctacctttacattttaccggcaatatttttcttgttacatttctgttctaatgctctctgtacgcatatgccatactttcag
 |   ||| ||  |  | ||  | || ||||||||||| || ||| ||||||||||||||||| || |     ||   |  ||||  |   | |||    ||                                                                                                      
ATCTTTCGAGTGCTGCTCTTTGTCTACTTCTTCACTCATATTTACCTCCATTTTGATCAGgtaagcgttttggtaattgttgttttactcgttatcttgacag-----------------------------------------------------------------------------------------------------

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|29664737|gb|CB661012.1|CB661012
EST:     TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAG                         GTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
genomic: TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatga ... atactttcagGTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
EST: gi|86261222|gb|CI004787.1|CI004787
EST:     TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAG                         GTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
genomic: TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatga ... atactttcagGTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
EST: gi|8859152|gb|AU096470.1|AU096470
EST:     TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAG                         GTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
genomic: TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatga ... atactttcagGTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
EST: gi|29669063|gb|CB665338.1|CB665338
EST:     TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAG                         GTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTG
genomic: TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatga ... atactttcagGTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTG
EST: gi|29669062|gb|CB665337.1|CB665337
EST:     TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAG                         GTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
genomic: TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatga ... atactttcagGTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
EST: gi|313084023|gb|HO213806.1|HO213806
EST:     TTCCATTTTGATCAG                         GTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
genomic: TTCCATTTTGATCAGgtatgcatga ... atactttcagGTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
EST: gi|29664738|gb|CB661013.1|CB661013
EST:     TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAG                         GTGAAGTCCATTTTCCCCCTGGGCTTTTACAGTATACTGACGGTGCCACCG
genomic: TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatga ... atactttcagGTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
EST: gi|8527754|gb|AU092569.1|AU092569
EST:     TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAG                         GTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
genomic: TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatga ... atactttcagGTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG
EST: gi|29669064|gb|CB665339.1|CB665339
EST:     TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAG                         GTGAAGTCCATCTTCCCCCTGGGCTTTTACAGTATACTGACGGTGCCACCG
genomic: TAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatga ... atactttcagGTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCG

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), 64 (downstream exon)
Score: 11

GTTGCTCGGGTAATCTTGTTCATATATTTCTTCACTCACATGTACTTCCATTTTGATCAGgtatgcatga ... atactttcagGTGAAGTCCATCTTCCCCCTGGGCTTCTACAGTATACTGACGGTGCCACCGGCGCTGGCAGTGATGAACCTATTTTGGTTCTGGAAGATATTCAAGGGAA




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