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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctcatccccttaaaatgctagcctttttgtttgccacttcgtaattctgttttttctattcagattctaatcagttgcagacttttttaaagaattaactcaaatattttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTTTCATGAAGGGCCGTCTCTTTGTGGAATTCAATGTTGAGTTCCCTGAATC

Basic information

species Oryza sativa
transcript LOC_Os04g46390.3
intron # 7
splice site 3'
intron type U2

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|29644137|gb|CB649144.1|CB649144
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|88988719|gb|CI039138.1|CI039138
EST:     CAGTAGACAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|218494336|gb|FG947221.1|FG947221
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCAGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|3762040|gb|C99288.1|C99288
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAANCCTG                         GTCAACACAAGGCCAT-AATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|8858764|gb|AU096082.1|AU096082
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|86261580|gb|CI017322.1|CI017322
EST:     GAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: GAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29678522|gb|CB674797.1|CB674797
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29640000|gb|CB645009.1|CB645009
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|218481590|gb|FG960931.1|FG960931
EST:     GCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         TTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGNCCGGCCTT
genomic: GCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|109712005|gb|CI029175.1|CI029175
EST:     CTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|25798325|gb|CA754286.1|CA754286
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29644138|gb|CB649145.1|CB649145
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29643237|gb|CB648244.1|CB648244
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|89192792|gb|CI050090.1|CI050090
EST:     TTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: TTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29663532|gb|CB659807.1|CB659807
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|86901901|gb|CI298548.1|CI298548
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29637041|gb|CB642050.1|CB642050
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|27577316|gb|CB000011.1|CB000011
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|8858763|gb|AU096081.1|AU096081
EST:     GTNGGCAGCTCCCTAAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: GTAGGCAGCT-CCT-AATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29614043|gb|CB619056.1|CB619056
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCAGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|15852528|gb|BI805324.1|BI805324
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCT-GCGAAATTATTAAACCTG                         GTCAACACAA-GCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29668765|gb|CB665040.1|CB665040
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACCCCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|88979252|gb|CI025754.1|CI025754
EST:     TATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: TATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29685950|gb|CB682225.1|CB682225
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29678573|gb|CB674848.1|CB674848
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29643292|gb|CB648299.1|CB648299
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29683515|gb|CB679790.1|CB679790
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29645125|gb|CB650132.1|CB650132
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29670818|gb|CB667093.1|CB667093
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29683516|gb|CB679791.1|CB679791
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|89188868|gb|CI048604.1|CI048604
EST:     AATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: AATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|8528315|gb|AU093130.1|AU093130
EST:     AGTAGGCAGCTCCTAATCAAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATNAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: AGTAGGCAGCTCCTAATC-AAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|86903742|gb|CI300596.1|CI300596
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|88901709|gb|CI001817.1|CI001817
EST:     ATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: ATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|218492135|gb|FG957408.1|FG957408
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|58684853|gb|CK073540.1|CK073540
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|700654|gb|D46945.1|D46945
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGGATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|29670817|gb|CB667092.1|CB667092
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
EST: gi|38479739|gb|CF963828.1|CF963828
EST:     CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTG                         GTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT
genomic: CAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTT

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), 70 (downstream exon)
Score: 367

TCTTTAACTGAGGCATTGTGTGGGTTCCAATTCATCCTCACTCATCTGGACAGTAGGCAGCTCCTAATCAAGGCAAATCCTGGCGAAATTATTAAACCTGgtatctcatc ... ttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTTTCATGAAGGGCCGTCTCTTTGTGGAATTCAATGTTGAGTTCCCTGAATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctaatcagttgcagacttttttaaagaattaactcaaatattttccaaacagGTCAACACAAGGCCATAAATGATGAGGGAATGCCACACCATGGCCGGCCTTTCATGAAGGGCCGTCTCTTTGTGGAATTCAATGTTGAGTTCCCTGAATC
                             aattaac  putative branch site (score: 367)
                                         tattttcc  putative PPT
                 acttttttaaagaatt  TA-rich tract