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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccatacatcttttataatgtcttgcattattaatgatgcaataccagcaatcttgaaattgatgtaatatttcaaacttattattgtatgatttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCA

Basic information

species Oryza sativa
transcript LOC_Os04g58750.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 4
gccatacatcttttataatgtcttgcattattaatgatgcaataccagcaatcttg--aaattgatgtaatatttcaaacttattattgtatg-atttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCA
  |||    ||      |   |||  ||  || || |     |   |  |  |||   | |||| |    || ||    | ||||||| |||| ||||| |||||||| | ||| ||||||||||| ||||||||||||| |||||||||| ||| ||||||||||||||||||||||| | || ||| |||||||| |||||
-tcattttactcaaccgaca-cttaaatatttgat-acattgttttaaaagccttactagattggtagtgtaattaccccatattattttatgcatttctcagGGGAGTCACAATCAATGAAATGGACCATGAGATTAAGGGTTGTTCTCTGTCTCGCTGAGGCTTTAGAATATTGCACTAACAGGGGCCGTGCTCTCTACCA
















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|33794016|gb|CF322898.1|CF322898
EST:     TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATT                         GGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
genomic: TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgcc ... gatttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
EST: gi|33675914|gb|CF304153.1|CF304153
EST:     TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATT                         GGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
genomic: TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgcc ... gatttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
EST: gi|29624788|gb|CB629799.1|CB629799
EST:     TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATT                         GGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
genomic: TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgcc ... gatttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
EST: gi|58669011|gb|CK057697.1|CK057697
EST:     TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATT                         GGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTAGTTCTCTATC
genomic: TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgcc ... gatttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcaatcttgaaattgatgtaatatttcaaacttattattgtatgatttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCA
            aattgat  putative branch site (score: 4)
                                               tttccc  putative PPT
           aaattgatgtaatatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccatacatcttttataatgtcttgcattattaatgatgcaataccagcaatcttgaaattgatgtaatatttcaaacttattattgtatgatttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG