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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcagtttttctccttgaagtttactattcaataaactacctgtgctgaaaacctttattttgtgtctcattgtatctgactgaatttctctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAACCTGGTACTGGAAGTATGCAGTAGATGGAGCTCATGTGAAGTTGGAAAT

Basic information

species Oryza sativa
transcript LOC_Os05g39230.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g39230.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AC197705.4_FGT011 (Zea mays), 3'ss of exon 20
atcagtttttctccttgaagtttactattcaataaactacctgtgctgaaaacctttattttgtgt-ctcattgtatctgac---tgaatttctctat---caccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAACCTGGTACTGGAAGTATGCAGTAGATGGAGCTCATGTGAAGTTGGAAAT
     |||||    |  ||||| |||  |   | ||||  |    |     ||  |||| |  ||  | ||  |   ||||    |||||| ||   |   ||  || |||||||| ||| || ||||  ||| |  | ||| |||||||||||||||||||| | |||||||||||||| ||||| |  |||              
----atttttggattgaaagttcacttctgtcttaactctcccaccc---cactattatgtcatggacccaacgctcctgatgaatgaattccttcttgtccaatagGATTTGTTGTTAAATTGGATCTTATACGTGACGAATTGATGGACAGTGGAACCTGGCATTGGAAGTATGCAGTTGATGGTGTCCAT--------------
















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|8856718|gb|AU094036.1|AU094036
EST:     CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAG                         AATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
genomic: CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAGgtttgttaat ... ctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
EST: gi|88245697|gb|CI245546.1|CI245546
EST:     CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAG                         AATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
genomic: CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAGgtttgttaat ... ctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
EST: gi|27547089|gb|CA765265.2|CA765265
EST:     CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAG                         AATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACGGTGGAA
genomic: CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAGgtttgttaat ... ctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
EST: gi|29623422|gb|CB628433.1|CB628433
EST:     CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAG                         AATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACGGTGGAA
genomic: CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAGgtttgttaat ... ctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
EST: gi|88478394|gb|CI415665.1|CI415665
EST:     CCACTGTTCATAGGATGCGCATTGTTCAAGATGGACCAG                         AATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACGGTGGAA
genomic: CCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAGgtttgttaat ... ctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
EST: gi|86250775|gb|CI007638.1|CI007638
EST:     CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAG                         AATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
genomic: CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAGgtttgttaat ... ctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
EST: gi|88478559|gb|CI415830.1|CI415830
EST:     TGGTCATAGAATGCGCATTGTTCAAGATGGACCAG                         AATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACGGTGGAA
genomic: TGGTCATAGAATGCGCATTGTTCAAGATGGACCAGgtttgttaat ... ctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
EST: gi|58607689|gb|CK035722.1|CK035722
EST:     CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAG                         AATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACGGTGGAA
genomic: CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAGgtttgttaat ... ctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
EST: gi|88828339|gb|CI000448.1|CI000448
EST:     CTTTGAAGTTCCCACTGGTCATAGAATGTGCATTGTTCAAGATGGACCAG                         AATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
genomic: CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAGgtttgttaat ... ctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
EST: gi|86840134|gb|CI332756.1|CI332756
EST:     CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAG                         AATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA
genomic: CTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAGgtttgttaat ... ctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaaaacctttattttgtgtctcattgtatctgactgaatttctctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAACCTGGTACTGGAAGTATGCAGTAGATGGAGCTCATGTGAAGTTGGAAAT
                             atctgac  putative branch site (score: 3)
                                        tttctctatc  putative PPT
         tttattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcagtttttctccttgaagtttactattcaataaactacctgtgctgaaaacctttattttgtgtctcattgtatctgactgaatttctctatcaccagAATTTGTTGCTAAGTTAGATCCCATAAGCAAGGAAATGATGGACAGTGGAACCTGGTACTGGAAGTATGCAGTAGATGGAGCTCATGTGAAGTTGGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - ctccttg
- - - - - - - - - - - - - - -caataaa
- - - - - - - - - - - - - - - - - - ctacctg
- - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgactg