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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatttttttgtgccatgtttgtctgcttttagttgatacaatttcaatgtgttggtttctggctgggctttttttgaggtggaaatttgttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGATAATCCAAAGCAACTTGAGCAGTATCGGTCCGGGAAAACTAAATTGCAAG

Basic information

species Oryza sativa
transcript LOC_Os11g34210.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g34210.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G091560_T01 (Zea mays), 3'ss of exon 6
taatttttttgtgccatgtttgtctgcttttagttgatacaatttcaatgtgttggtttctggctgggctttttt-tgaggtg----gaaatttgttgtgct----cagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGATAATCCAAAGCAACTTGAGCAGTATCGGTCCGGGAAAACTAAATTGCAAG
        | | |||||  ||||  | | | |||||||  ||||||| | |      |||| | |||||| | |  ||   ||     ||| |  |||        |||||||||||||| |||||||||||||||||||||||| ||||| | ||||||||||||||||||||||||||||| ||  | || ||||||||  | ||||
-------ctcgagccattgttgt--gttctcagttgatgtaatttcattattcaaacttcttgttgggctgtctaatggaatgcaaaaaaaatacttgaaaaatgacagATAGCAGATCCAGCAGCAATTGAGGCAATGGTAGATAAAGTAATTGCTGATAATCCAAAGCAACTTGAGCAGTACCGTGCTGGAAAAACTAAGCTACAAG
















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|86882758|gb|CI327383.1|CI327383
EST:     CGAAAGGTGGAACTCTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTTAGCCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|88901789|gb|CI374397.1|CI374397
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|86845186|gb|CI340316.1|CI340316
EST:     GTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAT                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGGCTGA
genomic: GTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTA-GCTGA
EST: gi|29616532|gb|CB621544.1|CB621544
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|86862767|gb|CI331650.1|CI331650
EST:     TCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: TCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|58606373|gb|CK034406.1|CK034406
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|3760962|gb|C98216.1|C98216
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|89175846|gb|CI042867.1|CI042867
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|86883589|gb|CI338107.1|CI338107
EST:     GGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: GGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|89181776|gb|CI113282.1|CI113282
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|86864344|gb|CI334102.1|CI334102
EST:     AGATTTGGTTCAG                         ATAGGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGA
genomic: AGATTTGGTTCAGgtaactgtag ... ttgtgctcagATA-GCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGA
EST: gi|86493642|gb|CI136275.1|CI136275
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|86600803|gb|CI356560.1|CI356560
EST:     GTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: GTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|88252153|gb|CI350581.1|CI350581
EST:     GAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATACCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: GAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|86839311|gb|CI331559.1|CI331559
EST:     CCAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTTAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|86498082|gb|CI140715.1|CI140715
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|89169673|gb|CI110032.1|CI110032
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|86433685|gb|CI094028.1|CI094028
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|29646032|gb|CB651039.1|CB651039
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|29641132|gb|CB646139.1|CB646139
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
EST: gi|86834558|gb|CI344489.1|CI344489
EST:     CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAG                         ATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT
genomic: CGAAAGGTGGAACTGTCAAGTCTGTGATAGAGGAGAAAGATTTGGTTCAGgtaactgtag ... ttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgtgttggtttctggctgggctttttttgaggtggaaatttgttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGATAATCCAAAGCAACTTGAGCAGTATCGGTCCGGGAAAACTAAATTGCAAG
                        tttttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatttttttgtgccatgtttgtctgcttttagttgatacaatttcaatgtgttggtttctggctgggctttttttgaggtggaaatttgttgtgctcagATAGCAGATCCTGCAGCAATTGAGGCAATGGTAGATCAAGTATTAGCTGATAATCCAAAGCAACTTGAGCAGTATCGGTCCGGGAAAACTAAATTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - -tttgtgc
- - - - - - - - tgtttgt
- - - - - - - - - - - -ctgcttt
- - - - - - - - - - - - - - - - - -gatacaa
- - - - - - - - - - - - - - - - - - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctgg