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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacattcttcgctctgaatgttccaaaatattataataggtttagcattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG

Basic information

species Oryza sativa
transcript LOC_Os06g20340.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g20340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G174170_T02 (Zea mays), 3'ss of exon 2
---aacattcttcgctctgaatgttccaaaatatt-ataataggtttagcattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG
     ||  ||    |||   | |    |  | || ||  || ||| | ||||      ||| |  ||        ||||| |  | | |  ||| ||||||||| || || || || || |||||||| || ||||||||||||||||| |||||||||||
gtatgcacactattttcttcttctgtgtacctgttgattgtaagttaaccatttccctggtaagttctc-------ctaattaaat-gctcctttgaacttcagAGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG

upper sequence: LOC_Os06g20340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G174170_T01 (Zea mays), 3'ss of exon 2
---aacattcttcgctctgaatgttccaaaatatt-ataataggtttagcattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG
     ||  ||    |||   | |    |  | || ||  || ||| | ||||      ||| |  ||        ||||| |  | | |  ||| ||||||||| || || || || || |||||||| || ||||||||||||||||| |||||||    
gtatgcacactattttcttcttctgtgtacctgttgattgtaagttaaccatttccctggtaagttctc-------ctaattaaat-gctcctttgaacttcagAGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA----

upper sequence: LOC_Os06g20340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G04550.1 (Arabidopsis thaliana), 3'ss of exon 2
aacattcttcgctctgaatgttccaaaatattataataggttta-gcattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG
               | |||||     ||  |||   | ||||    |||   ||  |||||  |||     |||   | || |  |  |||    |  ||| || || || |  || || ||||||||||| || ||||||||||| |||||||||||
---------------gtatgtt----gattctatctcaagtttctagatttcatctttatgattttt-----tcttgacggtct--tgctttg---tgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGAAAAGTAG

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|24468882|gb|CA305831.1|CA305831
EST:     TCAAGACGAGAAGACTTTGCAGTTTGATGATGCAATCCAATTTTTAG                         AACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGA
genomic: TCAAGACGAGAAGACTTTGCAGTTTGATGATGCAATCCAATTTTTAGgtattgatgc ... tcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGA
EST: gi|33675778|gb|CF304017.1|CF304017
EST:     CCTTCAAGACGAGAAGACTTTGCAGTTTGATGATGCAATCCAATTTTTAG                         AACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGA
genomic: CCTTCAAGACGAGAAGACTTTGCAGTTTGATGATGCAATCCAATTTTTAGgtattgatgc ... tcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG
                         atctaat  putative branch site (score: 3)
                                       ttattttc  putative PPT
                  tttctatatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacattcttcgctctgaatgttccaaaatattataataggtttagcattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA