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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttagatttcttctctctttctgtcagaaattgtcagttgattttattctatctttcaaattacttgctatgctaaactattgtctttgtgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG

Basic information

species Oryza sativa
transcript LOC_Os03g38960.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g38960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G086904_T01 (Zea mays), 3'ss of exon 4
-acttagatttcttctctctttctgtcagaaattgtcagttgatttta-ttctatctttcaaattacttgctatgctaaactattgtctttgtgcaaatt-agATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG
 | | |||||    ||   |  |  |||    |     |||    | | || ||  | | | | |   | ||     | |    ||| ||| | ||| || ||||||| ||||| ||||||||||| |||||||| || ||||| || || |||||||||||||| |||||
taatgagattcaacct---tagcaatcacctttcaatggttaccatcacttttagttcttatactgtgtactcaatgatatatatgtatttttacaattttagATTGCAATGAAGGAGCTGAGAGCGCGCAAGATACCCTTCACGATCAGACGGTACTTACCTGATGGAAG
















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|88376199|gb|CI533101.1|CI533101
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|88215899|gb|CI215748.1|CI215748
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCCCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|86506229|gb|CI148862.1|CI148862
EST:     TGAATGCTCCAGTTATGCTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCGTGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|88517263|gb|CI444917.1|CI444917
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|38481397|gb|CF965486.1|CF965486
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|86416666|gb|CI030677.1|CI030677
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|86536627|gb|CI176833.1|CI176833
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|88216290|gb|CI216139.1|CI216139
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|86507172|gb|CI149805.1|CI149805
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|88518337|gb|CI445991.1|CI445991
EST:     ACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: ACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|88907433|gb|CI090227.1|CI090227
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|88289429|gb|CI555791.1|CI555791
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|88323979|gb|CI561388.1|CI561388
EST:     ATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: ATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|38468521|gb|CF952652.1|CF952652
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
EST: gi|86911562|gb|CI296648.1|CI296648
EST:     TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG                         ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG
genomic: TGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAGgtaaattcta ... tgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctatctttcaaattacttgctatgctaaactattgtctttgtgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG
                          tgctaaa  putative branch site (score: 2)
                                       tctttgt  putative PPT
     tatctttcaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttagatttcttctctctttctgtcagaaattgtcagttgattttattctatctttcaaattacttgctatgctaaactattgtctttgtgcaaattagATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA