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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatcttgctattactaaatcaccatatgtgtgtatcatgcttctgctttatcctcttataatgatatattccagaaaggttgcttctttatcgagt...

Basic information

species Oryza sativa
transcript LOC_Os06g33710.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g33710.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G047867_T01 (Zea mays), 5'ss of exon 8
CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatcttgctattactaaatcaccatatgtgtgtatcatgcttct-gctttatcctcttataatgatatattccagaaaggttgcttctttatcgagt------
|||| |||||| |||| ||| | || ||||| |||||||||||||| ||||| |||||||| || |||||||||| |  |||||||| |  |    |  |      |||||  |  || |  ||| || | | |   || ||  |||      ||||||||||||  | || |      
CTGTTGATTTCCTGAGGAATTCTCCCGAAGGAAAATATGATGCTATTATTGTAGATTCATCAGATCCAATTGgtgggtacttgctataagaagtatagaactctcttgtatattttttatcacttcattcacatgccattatcgatt------aggttgcttctt-gttgatttatttt

upper sequence: LOC_Os06g33710.4 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G53120.4 (Arabidopsis thaliana), 5'ss of exon 9
CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatcttgctattactaaatcaccatatgtgtgtatcatgcttctgctttatcctcttataatgatatattccagaa---aggttgcttctttatcgagt-------------------
|||  || ||| |  | ||  ||||||||||||| |||||||| |||||||||||||| || || ||  | |||  |||    ||   |  || ||     || | ||  | || ||| |  | | |      || |  |     | ||||    || |     || |  ||  |                   
CTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAGgtatgattcatctgcaa--aactctttggatatctgagtgattcttattttgtttttctaaatcaaaactcggttcagacttcagctacaaactctcacgttttcactctatataatcatag

upper sequence: LOC_Os06g33710.4 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 5'ss of exon 8
CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatcttgctattactaaatcaccatatgtgtgtatcatgcttctgctt-tatcctcttataatgatatattccagaaaggttgcttctttatcgagt--
|||| || ||  | ||| |||  ||||||||||| |||||||| || |||||||||||||| || ||  | |||  |  |||  |   |  |  |  | || | | | |       ||  |  | |       |||| || | |     || | |||||    |  |   |    
CTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGGgtatgtcctt--tgccataatttttctatttatttcttgggaagttgggtgtgtgggtgtgtatagtg-tgtccatgagcagggttggggttggaataaaaac

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|33686636|gb|CF314875.1|CF314875
EST:     CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG                         GGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
genomic: CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatctt ... cacattatagGGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
EST: gi|29639075|gb|CB644084.1|CB644084
EST:     ATGCTATCATTGTTGATTCATCTGACCCAATTG                         GGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
genomic: ATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatctt ... cacattatagGGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
EST: gi|29678039|gb|CB674314.1|CB674314
EST:     CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG                         GGCCAGCTCANGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
genomic: CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatctt ... cacattatagGGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
EST: gi|29661773|gb|CB658048.1|CB658048
EST:     CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG                         GGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
genomic: CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatctt ... cacattatagGGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
EST: gi|29665561|gb|CB661836.1|CB661836
EST:     AAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG                         GGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
genomic: AAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatctt ... cacattatagGGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
EST: gi|29657895|gb|CB654170.1|CB654170
EST:     CATTGTTGATTCATCTGACCCAATTG                         GGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
genomic: CATTGTTGATTCATCTGACCCAATTGgtgagatctt ... cacattatagGGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
EST: gi|29674258|gb|CB670533.1|CB670533
EST:     CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG                         GGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
genomic: CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatctt ... cacattatagGGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
EST: gi|38468529|gb|CF952660.1|CF952660
EST:     CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG                         GGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
genomic: CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatctt ... cacattatagGGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
EST: gi|29674257|gb|CB670532.1|CB670532
EST:     CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG                         GGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTT-CAGACAATTGCTAGAG
genomic: CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatctt ... cacattatagGGCCAGCTCAGGAGCTTGTGGAGAAGCCCTTTTTTCAGACAATTGCTAGAG
EST: gi|58690531|gb|CK079218.1|CK079218
EST:     CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG                         GGCCAGCTCAGGAAGCTTGTGGAGAAGCCCT
genomic: CCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatctt ... cacattatagGGCCAGCTCAGGA-GCTTGTGGAGAAGCCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTGgtgagatcttgctattactaaatcaccatatgtgtgtatcatgcttctgctttatcctcttataatgatatattccagaaaggttgcttctttatcgagt

- - - - - - - - - - - - CTGAAG