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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtgctaaacatgcactgcagaaaactccatctcagatattttattagctatggtaattacacacattactaatttgatttcatatttcttccttcagTGTGCCTTGGCTGCAATTGTTATTTCTGCAGTCACTAGCCTG

Basic information

species Oryza sativa
transcript LOC_Os09g06499.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g06499.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 10
-------attgtgctaaacatgcactgcagaaaactccatctcagatattttattagctatggtaattacacacattactaatttgatttcatatttcttccttcagTGTGCCTTGGCTGCAATTGTTATTTCTGCAGTCACTAGCCTG
       | | || | ||| | || |   |   |||       | | ||| ||| | | |   || | |      || || |||| || |||| ||| |||   |||||||| |||||||||||||| |||||||| || ||| |||||
tatttttagtatgatcaactt-catttaggtttactatgataaataaattatataatccagaatactcat---ttttgctgattttatgtcatcttttttc---cagTGTGCATTGGCTGCAATTGTGATTTCTGCTGTTACTGGCCTG
















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|29613614|gb|CB618627.1|CB618627
EST:     TTGGTGGTGCTCTCTTGTTTATGACACCCTTGTTTACGGATATACCTCAG                         TGTGCCTTGGCTGCAATTGTTATTTCTGCAGTCACTAGCCTG
genomic: TTGGTGGTGCTCTCTTGTTTATGACACCCTTGTTTACGGATATACCTCAGgttagactcc ... cttccttcagTGTGCCTTGGCTGCAATTGTTATTTCTGCAGTCACTAGCCTG
EST: gi|29661763|gb|CB658038.1|CB658038
EST:     TTGGTGGTGCTCTCTTGTTTATGACACCCTTGTTTACGGATATACCTCAG                         TGTGCCTTGGCTGCAATTGTTATTTCTGCAGTCACTAGCCTG
genomic: TTGGTGGTGCTCTCTTGTTTATGACACCCTTGTTTACGGATATACCTCAGgttagactcc ... cttccttcagTGTGCCTTGGCTGCAATTGTTATTTCTGCAGTCACTAGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagctatggtaattacacacattactaatttgatttcatatttcttccttcagTGTGCCTTGGCTGCAATTGTTATTTCTGCAGTCACTAGCCTG
                                   tttcatatttcttcct  CT-rich tract
                      attactaatttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgtgctaaacatgcactgcagaaaactccatctcagatattttattagctatggtaattacacacattactaatttgatttcatatttcttccttcagTGTGCCTTGGCTGCAATTGTTATTTCTGCAGTCACTAGCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG