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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgtgaacatctctttctgggtggatggcttttgttattttcttaaatatcccttgcttagttgacattgtggttaatatttttttttgtatgttccagAAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACATTAGATTTTGTCAAGGCTATGTTGGATGAGTTTGAGAAACAGAAATGCAT

Basic information

species Oryza sativa
transcript LOC_Os05g11550.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 4
------cctgtgaacatctctttctgggtggatggcttttgttattttcttaaatatcccttgcttagttgacattgtggttaatatttttttttgtatgttccagAAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACATTAGATTTTGTCAAGGCTATGTTGGATGAGTTTGAGAAACAGAAATGCAT
         ||| | |  ||| | |   || |   ||| |||    || ||  | || |  ||     ||   |||  |||  | | || |||||  ||   | ||||||||||||||| ||| | ||||| ||| ||||||| ||   ||||||  |||| |||||||| || ||||||||||| ||| |||| |||||||||||
tttgagtgggtggagacttctct-tatttgtacaacttatgtctgcttgtttcacattctatg----attctaattaaggtgcacaattcttttt-cattcgctagAAGTAGAGCCACATTATGCGGGACCGAGAATTGATGGGGAAGAAATAACGATAGAGTTTGTCAAAGCAATGTTGGATGAATTTAAGAAGCAGAAATGCAT
















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|33794510|gb|CF323142.1|CF323142
EST:     GGATGAAGAGAAGCGCTCTGTAGCTGATTCTATTGACTACCGTATCATAG                         AAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACAT
genomic: GGATGAAGAGAAGCGCTCTGTAGCTGATTCTATTGACTACCGTATCATAGgtatctggtg ... tatgttccagAAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACAT
EST: gi|29630243|gb|CB635252.1|CB635252
EST:     GGATGAAGAGAAGCGCTCTGTAGCTGATTCTATTGACTACCGTATCATAG                         AAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACAT
genomic: GGATGAAGAGAAGCGCTCTGTAGCTGATTCTATTGACTACCGTATCATAGgtatctggtg ... tatgttccagAAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACAT
EST: gi|29676952|gb|CB673227.1|CB673227
EST:     GGATGAAGAGAAGCGCTCTGTAGCTGATTCTATTGACTACCGTATCATAG                         AAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACAT
genomic: GGATGAAGAGAAGCGCTCTGTAGCTGATTCTATTGACTACCGTATCATAGgtatctggtg ... tatgttccagAAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACAT
EST: gi|29681334|gb|CB677609.1|CB677609
EST:     GGATGAAGAGAAGCGCTCTGTAGCTGATTCTATTGACTACCGTATCATAG                         AAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACAT
genomic: GGATGAAGAGAAGCGCTCTGTAGCTGATTCTATTGACTACCGTATCATAGgtatctggtg ... tatgttccagAAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACAT
EST: gi|33793725|gb|CF322745.1|CF322745
EST:     GGATGAAGAGAAGCGCTCTGTAGCTGATTCTATTGACTACCGTATCATAG                         AAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACAT
genomic: GGATGAAGAGAAGCGCTCTGTAGCTGATTCTATTGACTACCGTATCATAGgtatctggtg ... tatgttccagAAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatcccttgcttagttgacattgtggttaatatttttttttgtatgttccagAAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACATTAGATTTTGTCAAGGCTATGTTGGATGAGTTTGAGAAACAGAAATGCAT
                           ggttaat  putative branch site (score: 4)
                                   tttttttttgt  CT-rich tract
                             ttaatatttttttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgtgaacatctctttctgggtggatggcttttgttattttcttaaatatcccttgcttagttgacattgtggttaatatttttttttgtatgttccagAAGTAGAGCCACAATATACAGGACCAAGAGTTGATGGAGACACAATAACATTAGATTTTGTCAAGGCTATGTTGGATGAGTTTGAGAAACAGAAATGCAT

cctgtga
- - - - - - -ctttctg
- - - - - - - - - - -gtggatg
- - - - - - - - - - - - - - -cttttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - -cttgctt