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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttgtaaaggcctgttgcttagatgtgatctatatattgttgctaatatgtctcatatccttgtag

Basic information

species Oryza sativa
transcript LOC_Os09g34040.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G142806_T01 (Zea mays), 5'ss of exon 9
AACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttgtaaaggcctgttgcttagatgtgatctatatattgttgctaatatgtc--tcatatccttgtag
||||||| || |||||||| || || |||||||| || |||||||||||||| || || |||||||| || ||| |||| || |||||  |  ||||||    |  ||| | |||| |    |||| |      | ||   | |   ||| || ||| ||
AACCTGTTTCCAAGCACATTGAAGAGCAAGGATTAGAGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttgtaa----cacttgatgagatatttattatacac-accacaaaatagccaaccatttcgttgcag

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA15G03200.1 (Glycine max), 5'ss of exon 8
AACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttgta-------------aaggcctgttgcttagatgtgatct--atatattgttgctaatatgtct-catatccttgtag--------------------------------------------------------------------------------------------------
| ||||  ||||| || |||||||| ||||||||||| |||||||| ||||| || || |||||||| |||||| | || || |||||  ||  || |             |||  | || |  |      || ||  || |||  ||  |||   | || ||||||     ||                                                                                                  
ATCCTGCTTCAAACCATATGGAGGAGCAAGGATTGGAATTTCTTCAATTTGCTTTCCGCTGGTTCAACTGTCTTCTAATCCGCGAGgtttgctctgaattttttctctcaaaagtgcagtagtcttcgccagagctgcatgtataatttgtaaatcgactgcatatcaagccagaaggacttgttaatttagttagagggaattatggagtacaaaaaatttggcccaattttatgcttttgttaactctgatttctgctttatgtaatcag

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G42180.1 (Glycine max), 5'ss of exon 8
AACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttgtaaaggcctgttgcttagatgtgat----ctatatattgttgctaatatgtctcatatccttgtag---------------------------------------------------------------------------------------------------------------
| ||||| ||||| || |||||||| ||||||||||| |||||||| ||||| || || |||||||| |||||| | || || |||||  ||     |      |||  |  |  ||  ||     |    |  | |||   |||  ||| ||   |    |                                                                                                               
ATCCTGTTTCAAACCATATGGAGGAGCAAGGATTGGAATTTCTTCAATTTGCTTTCCGCTGGTTCAACTGTCTTCTAATCCGCGAGgtttgctcataatttttttgtctcaaaagtgcaatagtcttccccagagctgcatgtataactcgtaaattgactgcatatcaagcccgaaggagttgttaatttggtttgagggaattatggagtacaaaaaatttggcccaattttatgcttttgttaactctgatttctgctttatgtaatcag

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv05s0094g00070.t01 (Vitis vinifera), 5'ss of exon 8
AACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttgtaaaggcctgttgcttagatgtgatctatat-attgttgctaatatgtctcatatccttgtag----------------------------
||||||| |||| |||||||||||| |||||  | || |||||||| ||||| || ||||||||||| |||||| | || || |||||  |  |    |       |  ||    |||| || |  | ||  || |    |  | || | ||||| |                              
AACCTGTTTCAAGGCACATGGAGGAGCAAGGGCTTGAGTTTCTTCAATTTGCTTTCCGTTGGTTCAACTGTCTTCTAATACGAGAGgtttgtctcactact-tgcatcactagtttgtgctccaagtcatgatttcctcgagttttcttttccttatttagtccagagcatgggtcaatcttaagaa

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|16753794|gb|BM038173.1|BM038173
EST:     ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTGTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGG
genomic: ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCT-TGTAACACGCTTGTGGGATACCTACCTTGCTGAAGG
EST: gi|88961123|gb|CI096526.1|CI096526
EST:     ACTTTCTTCAGTGTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|88965042|gb|CI097910.1|CI097910
EST:     ACTTTCTTCAGTNTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|88957061|gb|CI095105.1|CI095105
EST:     ATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGGTGAAGGC
genomic: ATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|89164629|gb|CI101717.1|CI101717
EST:     TGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: TGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|86501940|gb|CI144573.1|CI144573
EST:     ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|88849204|gb|CI087726.1|CI087726
EST:     ACTTTCTTCAGTGTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|86493863|gb|CI136496.1|CI136496
EST:     ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|7332463|gb|AU085809.1|AU085809
EST:     ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGNCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACNCGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|88223252|gb|CI223101.1|CI223101
EST:     ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|88833583|gb|CI077064.1|CI077064
EST:     GTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: GTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|88224054|gb|CI223903.1|CI223903
EST:     TTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: TTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|86494239|gb|CI136872.1|CI136872
EST:     TTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: TTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|88956561|gb|CI092786.1|CI092786
EST:     CGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: CGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|27547564|gb|CA767379.2|CA767379
EST:     ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: ACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|88848200|gb|CI086722.1|CI086722
EST:     TTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: TTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
EST: gi|89165919|gb|CI103009.1|CI103009
EST:     TGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG                         ATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC
genomic: TGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGC

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: 73 (upstream exon), 74 (downstream exon)
Score: 24

AACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAGgtcagcgttg ... atccttgtagATTCCTTTTCATCTTGTAACACGCTTGTGGGATACCTACCTTGCTGAAGGCGATTATCTACCGGATTTTCTTGTATATATATCAGCTAGCTTTTTGTTAA




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