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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAACCTGGGGGAATCACCCCAAAGTGTTCACTTTAGCTGGCCTGACTGTTAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaatttcaattttccatggaggaacttgttcttatgaagaagattaattgcaagattgtttgcacctgtctgacttgatcaaggatgtgttttcgtgttacag

Basic information

species Oryza sativa
transcript LOC_Os01g55540.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55540.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G094712_T04 (Zea mays), 5'ss of exon 4
CCAACCTGGGGGAATCACCCCAAAGTGTTCACTTTAGCTGGCCTGACTGTTAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaatttcaattttccatggaggaacttgttcttatg----aagaagattaat-tgcaagattgtttg-cacctgtctgacttgatcaaggatgtgttt-tcgtgttacag---------------------------------
||||||||||| |||||||| ||||| |||||  || ||||| |||  |||||||| |||||||| ||||||||||||||  |  | ||  | ||| ||||||   ||||||  ||| ||||   || ||  |   ||||    || ||  | | | ||| ||     ||| || |||| | |  |  |     ||  |||  |  | |||  |                                 
CCAACCTGGGGAAATCACCCAAAAGTCTTCACCCTATCTGGCTTGAACGTTAGGAGCTACCGCTATTATGATCCTGCAACATGCAGCCTTCACTTCGAAGgtatggatttca--ttttcatgctagatctattagatatgctataataatgtgagtatgctagtcaaattgacaactgtgttatatttttttatattcgttaatttttttatggctgtcattgaccaaattttgtgttgctttgcag

upper sequence: LOC_Os01g55540.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G19550.1 (Arabidopsis thaliana), 5'ss of exon 6
CCAACCTGGGGGAATCACCCCAAAGTGTTCACTTTAGCTGGCCTGACTGTTAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaatttcaattttccatggaggaacttgttcttatgaagaagattaattgcaagattgtttgcacctgtctg--acttgatcaaggatgtgttttcgtgttacag
||||| |||||||| || |||||||| ||||  || || ||| || ||||   |  || ||||||||||||||||||||||||||| || || ||| |||||   | | | || |||||||  |      | ||| | |  |   | ||      |   |  |||   | ||  |    |||||| |   || |  | |          
CCAACTTGGGGGAACCATCCCAAAGTTTTCAACTTGGCAGGCTTGTCTGTGGAGTATTTCCGCTACTATGATCCTGCAACCCGTGGTCTTGACTTCAAAGgt-tgattcttaactttccattaatttttgttttcatcttcatgtggttgcactgacattaatttagtcatggttattgcttgattatccatctactctac--------
















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|58669037|gb|CK057723.1|CK057723
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|29660055|gb|CB656330.1|CB656330
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|58606260|gb|CK034293.1|CK034293
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAG
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAG
EST: gi|29679665|gb|CB675940.1|CB675940
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTC-AAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGAAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|218483847|gb|FG951547.1|FG951547
EST:     TAGGAGTTACCGCTATTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCATCTCAGGTGCAATTGTACTGCT
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCC-T-TCAGGTGCAATTGTACTGCT
EST: gi|33678230|gb|CF306469.1|CF306469
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|33795088|gb|CF323417.1|CF323417
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCA-G                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|425867|gb|D22545.1|D22545
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|58694708|gb|CK083395.1|CK083395
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|32948296|gb|BP184868.1|BP184868
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|218496561|gb|FG955449.1|FG955449
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|29639571|gb|CB644580.1|CB644580
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|58596195|gb|CK006723.1|CK006723
EST:     GCAACCCGTGGACTGGATTTGCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: GCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|88358129|gb|CI605054.1|CI605054
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTANAAGATCTCGGTTCAACTTCTTCANGTGGCAATTGTACTGCTT
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTG-CAATTGTACTGCTT
EST: gi|27576897|gb|CA999591.1|CA999591
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|218485004|gb|FG945494.1|FG945494
EST:     CTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: CTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|218483959|gb|FG947666.1|FG947666
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|33793733|gb|CF322749.1|CF322749
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|33794958|gb|CF323359.1|CF323359
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCA-G                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|218491933|gb|FG950038.1|FG950038
EST:     CCGCTACTATGATCCTGCAACCCGTGGACTGGA-TTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: CCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|396941430|gb|HO188639.1|HO188639
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|425866|gb|D22544.1|D22544
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|29658837|gb|CB655112.1|CB655112
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|33793380|gb|CF322571.1|CF322571
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAG
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAG
EST: gi|163926589|gb|EG713605.1|EG713605
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|2310086|gb|C26241.1|C26241
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTNGCTT
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACT-GCTT
EST: gi|33678676|gb|CF306915.1|CF306915
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|33680310|gb|CF308549.1|CF308549
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|32948311|gb|BP184883.1|BP184883
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTT
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTT
EST: gi|33794428|gb|CF323098.1|CF323098
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC

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), 59 (downstream exon)
Score: 138

CCAACCTGGGGGAATCACCCCAAAGTGTTCACTTTAGCTGGCCTGACTGTTAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTCATGCTTGTGCCCACAACCCTACTGGAGTAGACCCAACTTTGGACCAGTG




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