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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaggaagagtttacattagcttgccactgtcatcactctctcatttacttaaaaaatgtatatggacatttcatgctataatgcatatctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTGCTCACATGTGGATTGAGTCAGAGATCATTGCAGGATCAGGCAGTAATGG

Basic information

species Oryza sativa
transcript LOC_Os06g08400.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g08400.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G017845_T01 (Zea mays), 3'ss of exon 11
-atgaggaagagtttacattagc--ttgccactgtcatcactctctcatttacttaaaaaatgtatatggacatttcatgctataatgcatatctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTGCTCACATGTGGATTGAGTCAGAGATCATTGCAGGATCAGGCAGTAATGG
  |       | ||  || | ||  |    | |  | |     ||  || ||||| |||    || | ||||||||| ||||  |||| |||| |  |  ||||||| || ||||| || |||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||| || ||||||||||||| || 
tcttgcattcatttggcaattgccataataatttgcgtacacatcctatctacttgaaactgttacaaggacatttc-tgct--aatgaatatgtcatcacagGATACCGGACACTGAGCCCAGACGTAGAAGAGGGCATTTGCCAAGTTCTTGCTCACATGTGGATCGAGTCAGAGATCATGGCCGGATCAGGCAGTAGTGC
















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|87024665|gb|CI259380.1|CI259380
EST:     AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG                         GATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
genomic: AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAGgtaattttta ... ctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
EST: gi|3766689|gb|AU030799.1|AU030799
EST:     AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG                         GATATCGCACACTTATTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
genomic: AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAGgtaattttta ... ctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
EST: gi|89197154|gb|CI051884.1|CI051884
EST:     TGATGCATGCGTGGTTGCGACTTAAAG                         GATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
genomic: TGATGCATGCGTGGTTGCGACTTAAAGgtaattttta ... ctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
EST: gi|86481178|gb|CI123811.1|CI123811
EST:     AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGGCTTAAAG                         GATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
genomic: AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAGgtaattttta ... ctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
EST: gi|88847129|gb|CI001401.1|CI001401
EST:     GGTTGCGACTTAAAG                         GATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
genomic: GGTTGCGACTTAAAGgtaattttta ... ctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
EST: gi|86481569|gb|CI124202.1|CI124202
EST:     AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG                         GATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
genomic: AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAGgtaattttta ... ctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
EST: gi|86480801|gb|CI123434.1|CI123434
EST:     AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG                         GATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
genomic: AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAGgtaattttta ... ctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
EST: gi|86478774|gb|CI121407.1|CI121407
EST:     AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG                         GATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
genomic: AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAGgtaattttta ... ctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
EST: gi|29681610|gb|CB677885.1|CB677885
EST:     AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG                         GATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG
genomic: AGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAGgtaattttta ... ctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacttaaaaaatgtatatggacatttcatgctataatgcatatctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTGCTCACATGTGGATTGAGTCAGAGATCATTGCAGGATCAGGCAGTAATGG
                                            tctactt  CT-rich tract
     ttaaaaaatgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaggaagagtttacattagcttgccactgtcatcactctctcatttacttaaaaaatgtatatggacatttcatgctataatgcatatctacttgcagGATATCGCACACTTAGTCCAGACGTAGAAGAGGGCATATGCCAAGTTCTTGCTCACATGTGGATTGAGTCAGAGATCATTGCAGGATCAGGCAGTAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA