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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgtttagtttgattcctgcaaatcctgacgttctgattttgtttagatgtaagccagtaactgaacttgtctgctaatttggtgctttcatgtgaatcttattagATGAAAGTAAGAGGCTAATATTTGGATGGAAATTGCGATACAAGATTATTCAGGGAATTGGGAGAGGATTATTGTACCTTCATCAGGATTCCAGGCTCAA

Basic information

species Oryza sativa
transcript LOC_Os04g54190.2
intron # 3
splice site 3'
intron type U2

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|157650178|gb|EX449812.1|EX449812
EST:     GTTGCTGTATGAATACATGCCCAACAAGAGCCTTGACTCATTTATTTTTG                         ATGAAAGTAAGAGGCTAATATTTGGATGGAAATTGCGATACAAGATTATTC
genomic: GTTGCTGTATGAATACATGCCCAACAAGAGCCTTGACTCATTTATTTTTGgtaacgttta ... atcttattagATGAAAGTAAGAGGCTAATATTTGGATGGAAATTGCGATACAAGATTATTC
EST: gi|32948092|gb|BP184664.1|BP184664
EST:     GTTGCTGTATGAATACATGCCCAACAAGAGCCTTGACTCATTTATTTTTG                         ATGAAAGTAAGAGGCTAATATTTGGATGGAAATTGCGATACAAGATTATTC
genomic: GTTGCTGTATGAATACATGCCCAACAAGAGCCTTGACTCATTTATTTTTGgtaacgttta ... atcttattagATGAAAGTAAGAGGCTAATATTTGGATGGAAATTGCGATACAAGATTATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagccagtaactgaacttgtctgctaatttggtgctttcatgtgaatcttattagATGAAAGTAAGAGGCTAATATTTGGATGGAAATTGCGATACAAGATTATTCAGGGAATTGGGAGAGGATTATTGTACCTTCATCAGGATTCCAGGCTCAA
                     tgctaat  putative branch site (score: 2)
                                              tcttatt  putative PPT
                                            aatcttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgtttagtttgattcctgcaaatcctgacgttctgattttgtttagatgtaagccagtaactgaacttgtctgctaatttggtgctttcatgtgaatcttattagATGAAAGTAAGAGGCTAATATTTGGATGGAAATTGCGATACAAGATTATTCAGGGAATTGGGAGAGGATTATTGTACCTTCATCAGGATTCCAGGCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT