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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgctttccccttttttaatgcactatatggtcatccttcgcttgaattagtaatcatggtttgacaggtcatatgctaaatcttttgccaattttcagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGCGGAAGCCTAACAGCGGCATAAGAGGTGGAA

Basic information

species Oryza sativa
transcript LOC_Os02g03890.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03890.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G167932_T01 (Zea mays), 3'ss of exon 7
------------------------------------------------------------tctgctttcccctttttt-----aatgcactatatggtcatccttcgc--ttgaattag------taatcatggtttgacaggtcatatg-ctaaatctt-ttgccaattttcagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGCGGAAGCCTAACAGCGGCATAAGAGGTGGAA
                                                            |||| | ||   || | |     || ||  ||| |  || | ||||    |||  ||        |||||||| ||  || ||||||||  ||||||  | | | |   ||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||||| || ||||| |||||||||||||
gtgactgttagcatcaatgcatttcaaaatcatttgtgtgttagttccttcagtttcttttctgttctctttttctgttgagaaaagctatatgttttctttcttcatcattgttttgtgtcttttaatcatgtttcaacgggtcatatatctaaattatatcgtcccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAGCCAAATAGCGGAATAAGAGGTGGAA
















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|86496369|gb|CI139002.1|CI139002
EST:     ATGCGTTCGTGGAATTCGAAGAACTTAGTGGTGTTCACAATGCATTGAAG                         GCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGCGGAAG
genomic: ATGCGTTCGTGGAATTCGAAGAACTTAGTGGTGTTCACAATGCATTGAAGgtggcaaact ... caattttcagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGCGGAAG
EST: gi|88908284|gb|CI090877.1|CI090877
EST:     ATGCGTTCGTGGAATTCGAAGAACTTAGTGGTGTTCACAATGCATTGAAG                         GCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGCGGAAG
genomic: ATGCGTTCGTGGAATTCGAAGAACTTAGTGGTGTTCACAATGCATTGAAGgtggcaaact ... caattttcagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGCGGAAG
EST: gi|58680181|gb|CK068868.1|CK068868
EST:     ATGCGTTCGTGGAATTCGAAGAACTTAGTGGTGTTCACAATGCATTGAAG                         GCTTCACCAATTGAAATAAATGGGC
genomic: ATGCGTTCGTGGAATTCGAAGAACTTAGTGGTGTTCACAATGCATTGAAGgtggcaaact ... caattttcagGCTTCACCAATTGAAATAAATGGGC
EST: gi|163920587|gb|EG709594.1|EG709594
EST:     ATGCGTTCGTGGAATTCGAAGAACTTAGTGGTGTTCACAATGCATTGAAG                         GCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGCGGAAG
genomic: ATGCGTTCGTGGAATTCGAAGAACTTAGTGGTGTTCACAATGCATTGAAGgtggcaaact ... caattttcagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGCGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattagtaatcatggtttgacaggtcatatgctaaatcttttgccaattttcagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGCGGAAGCCTAACAGCGGCATAAGAGGTGGAA
                              tgctaaa  putative branch site (score: 2)
                                     tcttttgcc  CT-rich tract
                                 taaatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgctttccccttttttaatgcactatatggtcatccttcgcttgaattagtaatcatggtttgacaggtcatatgctaaatcttttgccaattttcagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGCGGAAGCCTAACAGCGGCATAAGAGGTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA