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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatgttactttttttcctttatctgtttccctcctatgcaaattggagccttgatatcatgattttatcattataaaatattctatgccgccttccagGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG

Basic information

species Oryza sativa
transcript LOC_Os03g62640.2
intron # 10
splice site 3'
intron type U2

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|29665629|gb|CB661904.1|CB661904
EST:     AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG                         GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
genomic: AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAGgtacattctt ... cgccttccagGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
EST: gi|86502553|gb|CI145186.1|CI145186
EST:     AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG                         GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
genomic: AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAGgtacattctt ... cgccttccagGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
EST: gi|58682879|gb|CK071566.1|CK071566
EST:     AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG                         GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
genomic: AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAGgtacattctt ... cgccttccagGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
EST: gi|454535|gb|D28304.1|D28304
EST:     AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG                         GAGGAGAGAAGTAAAAGAAGGAAGGCACCTTAAGATGACAGGCG
genomic: AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAGgtacattctt ... cgccttccagGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
EST: gi|86499113|gb|CI141746.1|CI141746
EST:     AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG                         GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
genomic: AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAGgtacattctt ... cgccttccagGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
EST: gi|29664073|gb|CB660348.1|CB660348
EST:     AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG                         GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
genomic: AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAGgtacattctt ... cgccttccagGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
EST: gi|29661288|gb|CB657563.1|CB657563
EST:     AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTCCAG                         GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
genomic: AGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAGgtacattctt ... cgccttccagGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagccttgatatcatgattttatcattataaaatattctatgccgccttccagGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG
     ccttgat  putative branch site (score: 5)
                                            ccgccttcc  putative PPT
       ttgatatcatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatgttactttttttcctttatctgtttccctcctatgcaaattggagccttgatatcatgattttatcattataaaatattctatgccgccttccagGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - tgttact
- - - - - - - - - - - - ctgtttc
- - - - - - - - - - - - - - - - - -ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctatgc