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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagagtcacttgattctcaaggaaacataaagcagattattattgtcggtgcttctatgccatggtgtcaaaaggaaaataaaatatcattgcattgccccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCAAACGATTACAACAACTTCACAAAGAGGGCGTACGTTGGGAAGGCGAAGA

Basic information

species Oryza sativa
transcript LOC_Os06g51290.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G300348_T01 (Zea mays), 3'ss of exon 2
gtaagaagagtcacttgattctcaaggaaacataaagcagattattattgtcggtgcttctatgccatggtgtcaaaaggaaaataaaatatcattgcattgcc-ccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCAAACGATTACAACAACTTCACAAAGAGGGCGTACGTTGGGAAGGCGAAGA
                                      ||   | |    |      |||    |||  || |   |  | |     | |  | || | |||   || |||||||| ||||| || |||||||| ||| |||| ||||| || ||||| ||||| ||||| |||||||||||||| ||||||||||| ||||| || | |||||
-----------------------------------gtaagtccactcaacttcacatttcccaccca--gtatagcacagcatcctcacttccttttctttgttaccattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCCAACGACTACAACAACTTCACGAAGAGGGCGTATGTTGGTAAAGGGAAGA

upper sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 6
-gtaagaagagtcacttgattctcaaggaaacataaagcagattattattgtcggtgcttctatgccatggtgtcaaaaggaaaataaaatatcattgcattgccccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCAAACGATTACAACAACTTCACAAAGAGGGCGTACGTTGGGAAGGCGAAGA
 || || | | |  ||  | | |        |||   |   |||||||    | |   ||   ||   |    |    |      |  ||| || ||| ||      ||||||||| ||||| ||| |  |||| || |||||||| || || ||||| ||||| |||||||||||||||||||| | ||| || || ||  | || || ||||
tgtcaggaaaatttctataatttt-------cattgggttcattattagcaacagatgtttcctgatgtatgttttggaatgttttggaatgtc-ttggat------gttgcagGTATGGGCATCTTTTCTGTTGTATCGGCAAATACTGGATGAGATTGAAGCTAACGATTACAACAACTTCACTAGGAGAGCTTATGTGAGCAAAGCTAAGA
















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|29619022|gb|CB624034.1|CB624034
EST:     AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCG                         GTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
genomic: AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
EST: gi|86601906|gb|CI258582.1|CI258582
EST:     AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCG                         GTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
genomic: AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
EST: gi|29617651|gb|CB622663.1|CB622663
EST:     AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCG                         GTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
genomic: AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
EST: gi|86482399|gb|CI125032.1|CI125032
EST:     AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCG                         GTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
genomic: AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
EST: gi|88226109|gb|CI226025.1|CI226025
EST:     AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCG                         GTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
genomic: AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
EST: gi|29617544|gb|CB622556.1|CB622556
EST:     AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCG                         GTTTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
genomic: AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
EST: gi|15854009|gb|BI806805.1|BI806805
EST:     AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCG                         GTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
genomic: AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
EST: gi|86430283|gb|CI082706.1|CI082706
EST:     CCGAGCTCAGCCAGGCAAGCCGGTGGCCG                         GTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
genomic: CCGAGCTCAGCCAGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
EST: gi|29613195|gb|CB618208.1|CB618208
EST:     AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCG                         GTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
genomic: AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
EST: gi|86430747|gb|CI083170.1|CI083170
EST:     AGGCAAGCCGGTGGCCG                         GTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTGGACGAGATAGAAGCA
genomic: AGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
EST: gi|89184023|gb|CI046588.1|CI046588
EST:     AGGCAAGCCGGTGGCCG                         GTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCC
genomic: AGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA
EST: gi|29612902|gb|CB617915.1|CB617915
EST:     AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAACCGGTGGCCG                         GTCTGGGCGTTTTTGTTGTTATTCCGGCAAATCCTTGACGAGATAGAAGCA
genomic: AGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCGgtaagaagag ... cccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatgccatggtgtcaaaaggaaaataaaatatcattgcattgccccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCAAACGATTACAACAACTTCACAAAGAGGGCGTACGTTGGGAAGGCGAAGA
                                         ttgcccc  CT-rich tract
                aaaaggaaaataaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaagagtcacttgattctcaaggaaacataaagcagattattattgtcggtgcttctatgccatggtgtcaaaaggaaaataaaatatcattgcattgccccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCAAACGATTACAACAACTTCACAAAGAGGGCGTACGTTGGGAAGGCGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA