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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttgctcgtataatggtaaactaattgtggtgcaatgtactgttgtggtgttgcctgtcttattagagcatttttacttgaaaatttattaacatttcgcatgaatcttcagGACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGATTTTTCCTTGCTGTGGCAGCTGGAGGTGACGGGGTTATTTAAAGAGAAT

Basic information

species Oryza sativa
transcript LOC_Os02g52810.2
intron # 6
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|58601551|gb|CK012079.1|CK012079
EST:     AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTG                         GACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA
genomic: AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTGgtgagttttt ... gaatcttcagGACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA
EST: gi|163929105|gb|EG713026.1|EG713026
EST:     AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTG                         GACGTTGCAGCTCATGTCAGCCAACAAATCAG
genomic: AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTGgtgagttttt ... gaatcttcagGACGTTGCAGCTCATGTCAGCCAACAAATCAG
EST: gi|29674430|gb|CB670705.1|CB670705
EST:     AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTG                         GACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA
genomic: AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTGgtgagttttt ... gaatcttcagGACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA
EST: gi|38476255|gb|CF960388.1|CF960388
EST:     AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTG                         GACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA
genomic: AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTGgtgagttttt ... gaatcttcagGACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA
EST: gi|88271447|gb|CI387500.1|CI387500
EST:     TACCTTTTTAGAAACTTTTTG                         GACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA
genomic: TACCTTTGTAGAAACTTTTTGgtgagttttt ... gaatcttcagGACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA
EST: gi|66914813|gb|CX101661.1|CX101661
EST:     AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTG                         GACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA
genomic: AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTGgtgagttttt ... gaatcttcagGACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA
EST: gi|163928622|gb|EG711183.1|EG711183
EST:     AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTG                         GACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA
genomic: AGTTGGTACCGTGGGCGTAGCAATGGATGTACCTTTGTAGAAACTTTTTGgtgagttttt ... gaatcttcagGACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttattagagcatttttacttgaaaatttattaacatttcgcatgaatcttcagGACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGATTTTTCCTTGCTGTGGCAGCTGGAGGTGACGGGGTTATTTAAAGAGAAT
                             tattaac  putative branch site (score: 1)
                                                tcttc  putative PPT
            atttttacttgaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttttgctcgtataatggtaaactaattgtggtgcaatgtactgttgtggtgttgcctgtcttattagagcatttttacttgaaaatttattaacatttcgcatgaatcttcagGACGTTGCAGCTCATGTCAGCCAACAAATCAGAATTAATCAGGAAGTCAGATTTTTCCTTGCTGTGGCAGCTGGAGGTGACGGGGTTATTTAAAGAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA