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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAACGTGCAACTGCATTCGGCCTCATGAAAATTGACGAGGAAGGGAGAATAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaatgacgtgcctttcttgctaacttgtgatatacagttgtgagatatcagttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtag

Basic information

species Oryza sativa
transcript LOC_Os08g25734.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G163437_T01 (Zea mays), 5'ss of exon 3
GAAACGTGCAACTGCATTCGGCCTCATGAAAATTGACGAGGAAGGGAGAATAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaa---tgacgtgcctttcttgctaacttgtgatatacagttgtgagatatcagttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtag------
|||||||||||| ||||| |||||||||||||||||||| |||||||| ||  |||| ||||| |||||||| |||||||| || ||||||||||||||||||  || |   || | |  |||||  |||||||||  | ||||| ||||     |||| ||| |  |||  | |  | |   |  ||| |   ||  |  | |||||  ||||  | |      
GAAACGTGCAACCGCATTTGGCCTCATGAAAATTGACGAAGAAGGGAGGATTATTGAGTTTGCTGAGAAACCGAAAGGAGATCAGTTGAAAGCAATGATGgtacacataatttgccttttctttcaagctaacttg--acatacatttgttgacaatcatttagtgaacctaaaatattcccctttaaaatgccttcatctcatatttctgtctgattgatgtag

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G068506_T03 (Zea mays), 5'ss of exon 3
GAAACGTGCAACTGCATTCGGCCTCATGAAAATTGACGAGGAAGGGAGAATAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaatgacgtgcctttcttgctaacttg--tgatatacagttgtgagatatcagttattacacc-acatacttccatatcaaaactcattttgttgcctattttcgtcttgtag
|||||||||||||||||| ||||||||||||||||| || |||||||| ||  |||| ||||| |||||||| |||||||| || ||||||||||||||||||  |  || |  ||| || ||| | | ||    |||| |||| |||||    |||| ||  || ||| |||   |||||| |    |||| ||| | |                   
GAAACGTGCAACTGCATTTGGCCTCATGAAAATTGATGAAGAAGGGAGGATCATTGAGTTTGCTGAGAAACCGAAAGGAGAGCAGTTGAAAGCAATGATGgtacac--ataatatgctttcctttcaagctaacttgatttacatttgtggacaatcattttgtaaacctacaatattccatttt---actcctttggattgtag--------------

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 3
GAAACGTGCAACTGCATTCGGCCTCATGAAAATTGACGAGGAAGGGAGAATAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgc--aaatgacgtgcctttcttgctaacttgtgatatacagttgtgagat-atcagttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtag
 || ||||| |||||||| ||||| ||||| ||||| || || ||| | ||| ||||||| || || || |||||||||||||| |||||||| |||| |||| ||  | || || ||  ||   || |    | |       | || | |  | | || ||  |  |  | || |  | |                                      
AAAGCGTGCCACTGCATTTGGCCTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagcccatataacatgtattatatgttgttatttatctggaaattattacctgagcaattgcttaa--aaatgccactag-------------------------------------

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 3
GAAACGTGCAACTGCATTCGGCCTCATGAAAATTGACGAGGAAGGGAGAATAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgc--aaatgacgtgcctttcttgctaacttgtgatatacagttgtgagatatcagttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtag
    ||||| |||||||| ||  | ||||| ||||| || || ||| | ||| |||||||||| || || |||||||||||||| |||||||| |||| || | ||  | || |  ||  ||   ||     |||| || ||    | ||       | ||||||| |   | | || | ||  ||  |   |||| ||  |||              
AGCGCGTGCCACTGCATTTGGTTTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagcccatataagatgtattatatg-----ttgttattta----tctgga-----aattattac-ctgaacaattgcttaaaaatgccacttttcttttctag-------------

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 3
GAAACGTGCAACTGCATTCGGCCTCATGAAAATTGACGAGGAAGGGAGAATAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaa---tgacgtgc-ctttcttgctaacttgtgatatacagttgtgagatat--cagttattacaccacatacttccatatcaaaactcat-----tttgttgcctattttcgtcttgtag-
 ||||| || |||||||| || || ||||| ||||| ||||||||  | ||| |||||||||||||||||||||||||||| ||||||||||| |||| ||||    |    |||  |   | ||| |  ||| || || | |   |||     ||    || || |        | | ||   ||  ||  || ||     ||  || |  |  |    ||| ||  
AAAACGAGCCACTGCATTTGGTCTAATGAAGATTGATGAGGAAGGCCGTATAATTGAATTTGCAGAGAAACCAAAAGGAGAGCAATTGAAAGCTATGAAGgtagatgatatttgaaataaacattcgtattaatttatgcttttgtgttcctctattctacaattttgtagttttaaagttggttaagaaggctgatacgttttcctttctgaactgttccttttaag

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|13420424|gb|AU174514.1|AU174514
EST:     GAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGANATGCCT
genomic: GAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|87012877|gb|CI297104.1|CI297104
EST:     GAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
genomic: GAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|33681770|gb|CF310009.1|CF310009
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|58678083|gb|CK066770.1|CK066770
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAGGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|88586416|gb|CI704115.1|CI704115
EST:     ATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
genomic: ATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|29614233|gb|CB619246.1|CB619246
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAGGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|58652879|gb|CK041559.1|CK041559
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAGCAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAGGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|58675386|gb|CK064073.1|CK064073
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAGGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|29681248|gb|CB677523.1|CB677523
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|88584775|gb|CI702352.1|CI702352
EST:     ATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
genomic: ATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|58668409|gb|CK057095.1|CK057095
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAGGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAACGTGCAACTGCATTCGGCCTCATGAAAATTGACGAGGAAGGGAGAATAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaatgacgtgcctttcttgctaacttgtgatatacagttgtgagatatcagttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA