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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcatacgaattagtaattttggcctacttattgacattcaacattggtcgtctcaattgtctttatctaattatgcaaacatttgttaaatggaggagACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAACGTGGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTT

Basic information

species Oryza sativa
transcript LOC_Os02g01710.2
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|86497902|gb|CI140535.1|CI140535
EST:     GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTG                         ACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGgtgcgtacaa ... aatggaggagACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG
EST: gi|86498521|gb|CI141154.1|CI141154
EST:     GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCT-                         ---GGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGgtgcgtacaa ... aatggaggagACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG
EST: gi|88831540|gb|CI083934.1|CI083934
EST:     GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTG                         ACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGgtgcgtacaa ... aatggaggagACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG
EST: gi|88845414|gb|CI084339.1|CI084339
EST:     GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTG                         ACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGgtgcgtacaa ... aatggaggagACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG
EST: gi|86504655|gb|CI147288.1|CI147288
EST:     GGAGCACCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCT-                         ---GGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGgtgcgtacaa ... aatggaggagACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG
EST: gi|88841179|gb|CI080633.1|CI080633
EST:     GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCT-                         ---GGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGgtgcgtacaa ... aatggaggagACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtcgtctcaattgtctttatctaattatgcaaacatttgttaaatggaggagACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAACGTGGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTT
                     atctaat  putative branch site (score: 3)
                tctttatctaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcatacgaattagtaattttggcctacttattgacattcaacattggtcgtctcaattgtctttatctaattatgcaaacatttgttaaatggaggagACAGGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAACGTGGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTT

- - - - - - - - - - - -gcctact
- - - - - - - - - - - - - - - - - - cattcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatttg