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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcactgttaggttctaactttgacatctgtctcaactgaatctttttttagcattgtaggcattcttctgacactgacaaaactaattaattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTGAAAAGAAAGGGTCATGTTGTGGCTGTTACTGGTGATGGCACAAATGATG

Basic information

species Oryza sativa
transcript LOC_Os08g40530.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40530.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 25
---------------------------------------------tggcactgttag-gttctaactttgacatctgtctcaactgaatctttttttagcattgtaggcattcttctgacactgacaaaactaattaattt--tgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTGAAAAGAAAGGGTCATGTTGTGGCTGTTACTGGTGATGGCACAAATGATG
                                             |  |  ||| |  | ||| | | |  | |   || |    || | |||||| ||   | |   ||||||| |         | | |||||||| ||  | ||||||||||| ||||| || |||||||| ||||||||||||||||||||||| ||| |||| || |||||||| ||||||||||||||||||||||||||||
gtaactctctctcactatgtctcacaagttgtttggtgctttctttcactttgtcaatgctctcattctagccttcatc-ctctggagtattttttaagtccttt---cattctttttggttctgtagagctaattaacttgtttcagGTGATGGGGAGATCCTCGCCAAATGATAAACTTTTGCTTGTCCAAGCTTTAAAACGAAAAGGCCATGTTGTAGCTGTTACTGGTGATGGCACAAATGATG
















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|29665351|gb|CB661626.1|CB661626
EST:     TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACA                         GTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
genomic: TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACAgtaactctct ... aattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
EST: gi|88591696|gb|CI709748.1|CI709748
EST:     TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACA                         GTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
genomic: TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACAgtaactctct ... aattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
EST: gi|88371699|gb|CI680802.1|CI680802
EST:     NTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTNGACAAAATAACA                         GTGATGGGAAGATCATCTCCAAATGACAAA
genomic: TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACAgtaactctct ... aattttgcagGTGATGGGAAGATCATCTCCAAATGACAAA
EST: gi|88412431|gb|CI688779.1|CI688779
EST:     TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACA                         GTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
genomic: TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACAgtaactctct ... aattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
EST: gi|33678328|gb|CF306567.1|CF306567
EST:     TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACA                         GTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
genomic: TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACAgtaactctct ... aattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
EST: gi|33678453|gb|CF306692.1|CF306692
EST:     TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACA                         GTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
genomic: TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACAgtaactctct ... aattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
EST: gi|29681421|gb|CB677696.1|CB677696
EST:     TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACA                         GTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
genomic: TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACAgtaactctct ... aattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
EST: gi|88328484|gb|CI676694.1|CI676694
EST:     TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACA                         GTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
genomic: TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACAgtaactctct ... aattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
EST: gi|88589477|gb|CI707360.1|CI707360
EST:     TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACA                         GTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
genomic: TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACAgtaactctct ... aattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
EST: gi|88589322|gb|CI707190.1|CI707190
EST:     TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTCGACAAAATAACA                         GTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
genomic: TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACAgtaactctct ... aattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
EST: gi|88388660|gb|CI683447.1|CI683447
EST:     TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACA                         GTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG
genomic: TTCGCGAGATGTCTGAAGCTGCTAGAGGAGATATTGTTGACAAAATAACAgtaactctct ... aattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttagcattgtaggcattcttctgacactgacaaaactaattaattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTGAAAAGAAAGGGTCATGTTGTGGCTGTTACTGGTGATGGCACAAATGATG
                                 acaaaactaattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcactgttaggttctaactttgacatctgtctcaactgaatctttttttagcattgtaggcattcttctgacactgacaaaactaattaattttgcagGTGATGGGAAGATCATCTCCAAATGACAAACTTTTGCTTGTCCAAGCTTTGAAAAGAAAGGGTCATGTTGTGGCTGTTACTGGTGATGGCACAAATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT