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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacactcctggctctattctgcatttccttcaattgatagagttttgctctctcttggaatgtgcttcatccagcattttgtgttgtactatgaacgttgtacccttaaggtcccatacatttatttccaaaggttcaatttgtactcaaatggtttgcacactgtaatttaacaggaatttttttttttttttgcagATAAAGGAGATGTCTTCTGCTGGGGTTGGAACAAGTACGGTCAG

Basic information

species Oryza sativa
transcript LOC_Os05g38270.1
intron # 9
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|29665760|gb|CB662035.1|CB662035
EST:     TCATGCAAGAGGTGTTTCGTGTGGAGCCCGACACAGTGCAGTCATAACAG                         ATAAAGGAGATGTCTTCTGCTGGGGTTGGAACAAGTACGGTCAG
genomic: TCATGCAAGAGGTGTTTCGTGTGGAGCCCGACACAGTGCAGTCATAACAGgtacactcct ... ttttttgcagATAAAGGAGATGTCTTCTGCTGGGGTTGGAACAAGTACGGTCAG
EST: gi|9865082|gb|AU100832.1|AU100832
EST:     CATGCCAAGAGGTGTTTCGTGTGGAGCCCNACACAGTGCAGTCATAACAG                         ATAAAGGAGATGTCTTCTGCTGGGGTTGGAACAAGTACGGTCAG
genomic: CATG-CAAGAGGTGTTTCGTGTGGAGCCCGACACAGTGCAGTCATAACAGgtacactcct ... ttttttgcagATAAAGGAGATGTCTTCTGCTGGGGTTGGAACAAGTACGGTCAG
EST: gi|218498039|gb|FG964220.1|FG964220
EST:     GCATGCAAGAGGTGTTTCGTGTGGAGCCCGACACAGTGCAGTCATAACAG                         ATAAAGGAGATGTCTTCTGCTGGGGTTGGAACAAGTACGGTCAG
genomic: TCATGCAAGAGGTGTTTCGTGTGGAGCCCGACACAGTGCAGTCATAACAGgtacactcct ... ttttttgcagATAAAGGAGATGTCTTCTGCTGGGGTTGGAACAAGTACGGTCAG
EST: gi|2311383|gb|C27538.1|C27538
EST:     TCATGCAAGAGGTGTTTCGTGTGGAGCCCGACACAGTGCAGTCATAACAG                         ATAAAGGAGATGTCTTCTGCTGGGGTTGGAACAAGTACGGTCAG
genomic: TCATGCAAGAGGTGTTTCGTGTGGAGCCCGACACAGTGCAGTCATAACAGgtacactcct ... ttttttgcagATAAAGGAGATGTCTTCTGCTGGGGTTGGAACAAGTACGGTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactcaaatggtttgcacactgtaatttaacaggaatttttttttttttttgcagATAAAGGAGATGTCTTCTGCTGGGGTTGGAACAAGTACGGTCAG
                        atttaac  putative branch site (score: 3)
                                    tttttttttttttttg  putative PPT
                    tgtaatttaacaggaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacactcctggctctattctgcatttccttcaattgatagagttttgctctctcttggaatgtgcttcatccagcattttgtgttgtactatgaacgttgtacccttaaggtcccatacatttatttccaaaggttcaatttgtactcaaatggtttgcacactgtaatttaacaggaatttttttttttttttgcagATAAAGGAGATGTCTTCTGCTGGGGTTGGAACAAGTACGGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG