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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttgtttttcttacccatattctaatttcagatgaattcgtttttggtagaaaccactgtgagttgaagtcttgaagatcgtccatatatgaaa...

Basic information

species Oryza sativa
transcript LOC_Os12g07110.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07110.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G118286_T01 (Zea mays), 5'ss of exon 8
GTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttgtttttcttacccatattctaatttcagatgaattcgtt----tttggtagaaaccactgtgagttgaagtcttgaagatcgtccatatatgaaa
 |||||||| ||||| || ||||||||||| |||||||| |||||||||||| ||||||| ||||| |||||||||||||||||||||||||| |||||||| || ||  |||  |||| | || || || |   || ||  ||  |     | |  |     |   | |   ||| | | || | |     | || | || | 
TTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttcattt--cttaactattttgta-tcaaagctgtttttatcacgatgttatctgtgcggatctattttgtattttttatgcctaacaatgtttgta-

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 5'ss of exon 8
GTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttgttttt--cttacccatattctaatttcagatgaattcgtttttggt--agaaaccactgtgagttgaagtcttgaagatcgtccatatatgaaa
 ||||| || || ||||| |||||||| ||||| || || |||| ||| ||| |||| ||||| || |||||||||||||| ||||| || |   | |||||||  | | |   |   ||  |||  || ||||      | |  |  || || ||    |   |   ||   |||   || |     |    | | | | |  
ATATGGGCTCACAGAGACTTGTGCTGGTGGAACCTTCTCGGAGTTTGAGGACACATCCGTTGGCCGTGTTGGTGCTCCACTTCCTTGCTCCTTTGTAAAGgtaacctctttacctgatttgtccac-ttttaatactttgttagctatttattagtttgtatgtcgtagtctcttgtgatcatatgcttatatcttgtttcag-

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 5'ss of exon 9
GTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttt-------tgtttttcttacccatattctaatttcagatgaattcgtttttggtagaaaccactgtgagttgaagtcttgaagatcgtccatatatgaaa
|||||| || || ||||  |||||||| || |||||||| |||||||||||  ||||||||||||| |||||||||||||| ||||| || |  ||||||||||||         | |||| ||| |   |  | ||||   ||||   || |   |   |    ||   |   || ||||  |    |  | |     | |     
GTATGGCCTGACAGAGAGTTGTGCTGGTGGTACATTTTCCGAGTATGATGATACATCTGTTGGTCGTGTTGGTGCTCCACTTCCTTGCTCATTTATTAAGgtaagtggatgaaaatattttacttgcatgtgctttaatgcgagatc--ttggacctacatgtgcac--ttcctagctgaaaaccctgaccttggtagaaaaca---

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|29669841|gb|CB666116.1|CB666116
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGC
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGC
EST: gi|29614988|gb|CB620001.1|CB620001
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCT
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCT
EST: gi|29675500|gb|CB671775.1|CB671775
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAGAAAGTCCCCAATGCCT
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCT
EST: gi|58030548|gb|CX728091.1|CX728091
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACAATAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAGAGAGTCCCCAATG
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATG
EST: gi|29672201|gb|CB668476.1|CB668476
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACAATGAG                         CTGATTGACTGGTCAGAAGGTGGAT
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGAT
EST: gi|29614945|gb|CB619958.1|CB619958
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATGAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAA-GAGTCCCCAATGCCT
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCT
EST: gi|13420751|gb|AU174841.1|AU174841
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGC
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGC

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: 75 (upstream exon), 63 (downstream exon)
Score: 33

GTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCTCGAGGAGAGATTGTCATTGGTGGTCCCAATGTAACTAAAGGCTATTTCA




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