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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaatttcaattttccatggaggaacttgttcttatgaagaagattaattgcaagattgtttgcacctgtctgacttgatcaaggatgtgttttcgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTCATGCTTGTGCCCACAACCCTACTGGAGTAGACCCAACTTTGGACCAGTG

Basic information

species Oryza sativa
transcript LOC_Os01g55540.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55540.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G506218_T01 (Zea mays), 3'ss of exon 1
----------------------------------------gtaccaatttcaattttccatggaggaacttgttcttatgaagaagattaattgcaagattgtttgcacctgtctgacttgatcaaggatgtgttttcgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTCATGCTTGTGCCCACAACCCTACTGGAGTAGACCCAACTTTGGACCAGTG
                                         ||  ||| | ||| | | |   |    |       ||| |       ||  |     | |  |  ||    |||| | |   |    || |||||| |  ||||||| || || ||||| ||| |||| ||||||||||||  ||||||||| || ||||| |||||||||||||||||| ||||||| |  ||| | || |  ||
ttatggatttcatttttcatgctagatctgttagaatgctttaataatgtgaatatgctagacacattcgcaaatgtattatatgttctatctttgcaaattatgtcatggctctgccattgacccaaatttgtttt-gctttacagGACTCTTGGAAGACCTCTGTTCTGCTCCTTCAGGTTTAATTGTACTACTGCATGCCTGTGCCCACAACCCTACTAGAGTAGATCATACTATTGATCGATG

upper sequence: LOC_Os01g55540.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G094712_T04 (Zea mays), 3'ss of exon 4
----------------------------------------gtaccaatttcaattttccatggaggaacttgttcttatgaagaagattaat-tgcaagattgtttgcacctgtctgac-ttgatcaaggatgtgttttcgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTCATGCTTGTGCCCACAACCCTACTGGAGTAGACCCAACTTTGGACCAGTG
                                         ||  ||| | | | | |  | |   || |      | ||    |  ||  | |    | |  |||     || ||| | |||| |||  || |  | | |  || |||| ||  | ||||| |||||||| |||||||||||| ||||||||||||| ||||| ||||| |||||||||||||||||||| || ||  | || |||||
gtatggatttcattttcatgctagatctattagatatgctataataatgtgagtatgc--tagtcaaattgacaactgtgttatatttttttatattcgttaatttttttatggctgtcattgaccaa--attttgtgttgctttgcagGACTCCTGGAAGACCTCGGTTCTGCTCCTTCAGGTTCAATTGTACTGCTGCATGCCTGTGCTCACAACCCTACTGGAGTAGATCCTACCATCGAACAGTG
















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|33678230|gb|CF306469.1|CF306469
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|218483847|gb|FG951547.1|FG951547
EST:     TAGGAGTTACCGCTATTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCATCTCAGGTGCAATTGTACTGCT
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCC-T-TCAGGTGCAATTGTACTGCT
EST: gi|33794428|gb|CF323098.1|CF323098
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|425867|gb|D22545.1|D22545
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|218496561|gb|FG955449.1|FG955449
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|58596195|gb|CK006723.1|CK006723
EST:     GCAACCCGTGGACTGGATTTGCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: GCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|29639571|gb|CB644580.1|CB644580
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
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|32948311|gb|BP184883.1|BP184883
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTT
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTT
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|218491933|gb|FG950038.1|FG950038
EST:     CCGCTACTATGATCCTGCAACCCGTGGACTGGA-TTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: CCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|33794958|gb|CF323359.1|CF323359
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCA-G                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... 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|29679665|gb|CB675940.1|CB675940
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTC-AAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGAAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|29660055|gb|CB656330.1|CB656330
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|163926589|gb|EG713605.1|EG713605
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|32948296|gb|BP184868.1|BP184868
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|2310086|gb|C26241.1|C26241
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTNGCTT
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACT-GCTT
EST: gi|29658837|gb|CB655112.1|CB655112
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|33680310|gb|CF308549.1|CF308549
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|33678676|gb|CF306915.1|CF306915
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|58694708|gb|CK083395.1|CK083395
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|33793380|gb|CF322571.1|CF322571
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAG
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAG
EST: gi|33795088|gb|CF323417.1|CF323417
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCA-G                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
EST: gi|58669037|gb|CK057723.1|CK057723
EST:     TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAG                         GGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC
genomic: TAGGAGTTACCGCTACTATGATCCTGCAACCCGTGGACTGGATTTCCAAGgtaccaattt ... cgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaagattgtttgcacctgtctgacttgatcaaggatgtgttttcgtgttacagGGCTGTTAGAAGATCTCGGTTCAGCTCCTTCAGGTGCAATTGTACTGCTTCATGCTTGTGCCCACAACCCTACTGGAGTAGACCCAACTTTGGACCAGTG
                                       tgttttc  CT-rich tract
      attgttt  TA-rich tract