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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgtcagttttttccccttgaaattttttgaagttttaatgcccccatttatgatgcttgtttccttgtttagAACAATGATGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTACAAGTCATTTGTTAGTGAATACCCAATTGTCTCGATCGAAGACCCATTTG

Basic information

species Oryza sativa
transcript LOC_Os03g14450.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14450.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------gtaaatgtcagttttttccccttgaaattttttgaagttttaatgcccccatttatgatgcttgtttccttgtttagAACAATGATGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTACAAGTCATTTGTTAGTGAATACCCAATTGTCTCGATCGAAGACCCATTTG
                           |   | ||| | ||||   |   ||||  ||  ||  ||| | || || |  |   ||  |      ||  |  ||||||||||||| || || || ||||||||||| ||| |||||||||| ||||| |||||||| | ||| ||||||||||| || || |||||||||||||
ccatcacttcagaaactaaattaggatttcctatcaatattttgagcagaaaatccttgtaa--tttgaagcacctaactg-aataataaccatctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTACAAATCATTTGTGAATGATTACCCAATTGTTTCAATTGAAGACCCATTTG
















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|27576854|gb|CA999548.1|CA999548
EST:     CAGAGTTCTACACTGAGGACCAAACCTATGATCTTAACTTCAAGGAAGAG                         AACAATGATGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTAC
genomic: CAGAGTTCTACACTGAGGACCAAACCTATGATCTTAACTTCAAGGAAGAGgtaaatgtca ... ccttgtttagAACAATGATGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTAC
EST: gi|29678594|gb|CB674869.1|CB674869
EST:     CAGAGTTCTACACTGAGGACCAAACCTATGATCTTAACTTCAAGGAAGAG                         AACAATGATGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTAC
genomic: CAGAGTTCTACACTGAGGACCAAACCTATGATCTTAACTTCAAGGAAGAGgtaaatgtca ... ccttgtttagAACAATGATGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTAC
EST: gi|218503770|gb|FG954179.1|FG954179
EST:     AGAG-TCTACACTGAGGAGCAAACCTATGATCTTAACTTCAAGGGAAGAG                         AACAATGACGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTA
genomic: AGAGTTCTACACTGAGGACCAAACCTATGATCTTAACTTCAA-GGAAGAGgtaaatgtca ... ccttgtttagAACAATGATGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTA
EST: gi|2797284|gb|AA750578.1|AA750578
EST:     CTTAACTTCAAGGAAGAG                         AACAATGATGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTAC
genomic: CTTAACTTCAAGGAAGAGgtaaatgtca ... ccttgtttagAACAATGATGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaattttttgaagttttaatgcccccatttatgatgcttgtttccttgtttagAACAATGATGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTACAAGTCATTTGTTAGTGAATACCCAATTGTCTCGATCGAAGACCCATTTG
               ttttaat  putative branch site (score: 3)
                                      cttgtttccttgttt  putative PPT
     ttttttgaagttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgtcagttttttccccttgaaattttttgaagttttaatgcccccatttatgatgcttgtttccttgtttagAACAATGATGGTTCCCAGAAGATATCTGGAGATAGCCTGAAGAATGTGTACAAGTCATTTGTTAGTGAATACCCAATTGTCTCGATCGAAGACCCATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA