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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgttgtgtttgtatgttataattcaaaacctcctgtagtttctatggtctatctttttttacatttccttcaaagtaatttatcatgctgcaactttcacttttcgtccttgtag

Basic information

species Oryza sativa
transcript LOC_Os08g25734.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25734.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G068506_T03 (Zea mays), 5'ss of exon 6
GTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgttgtgtttgtatgttataattcaaaacctcctgtagtttctatggtctatctttttttacatttccttcaaagtaatttatcatgctgcaactttcacttttcgtccttgtag------
 | |||||||||||||||||||||||||||| |||| ||||| |||||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| | ||  | ||  | |   ||| || |||||||        ||||    | ||| || |   |  |    |   |  ||||| ||  | ||  ||| || |    | |  |||||        
TTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGATGTGTTATTAAAgtaagca-gtgcttttactgtagcatatttgaaaacctttctatacttct----tttattttctccaaagtaatttctca--taattcatt-tactaaaacgtttatgccttgatcttgtgcacacag

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G163437_T01 (Zea mays), 5'ss of exon 6
GTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagta-tgttgtgtttg--tatgttataattcaaaacctcc-tgtagtttctatggtctatctttttttacatttccttcaaagtaatttatcatgctgcaactttcacttttcgtccttgtag------
 ||||||||||| |||||||||||||||||  |||| ||||| |||||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||||| |||| |||||   |||   ||| || |||||||   | |||  | |||     ||| |       ||||    |   |||||| ||  | ||  ||| || |    | |  |||||        
TTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGATGTGTTATTAAAgtaagtagtgttttgttttactatagcatatttgaaaacctatatatagactttat-----atcctccaaagtatttttccc---gtaattcatt-tactaaaacatttatgccttgatcttgtgcacacag

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 6
GTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgtt-gtgtttgtatgttataattcaaaacctcctgtagtttctatggtctatctttttttacatttccttcaaagtaatttatcatgctgcaactttcacttttcgtccttgtag-------------------
 ||  ||||||| || || ||||| ||| | |||||||| || ||| | |||||||||||||| || || ||||| ||||||||||| ||||| ||||| |||||||| |  |    |  |  || || |   |      || ||  |   ||  | ||   || || |||      |||||   | | |   || |  |  | |          | |||||                    
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtatttcagaaccttcacattctact--gatctgctctataaatgagatt-tatacaattcttaacaaagatgtcaaatataatgagattgatttatttataggaaactaactttgtattccatattttgttccatag

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 6
GTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgttgtg---tttgtatgttataattcaaaacct--cctgtagtttctatggtctatctttt---tttacatttccttcaaagtaatttatcatgctgcaact---ttcacttttcgt-ccttgtag-----
 ||  ||||||| || || ||||| ||| | |||||||| || ||| | |||||||||||||| || || ||||| ||||||||||| ||||| ||||| ||||| || |       ||   ||  ||    ||    |    | ||   ||| ||   |   |        | |  | |    | | | ||||||||      | ||||    |    || | | | ||||       
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcatttcagaaccttcacattctactgatctgctctgtacatgagatttatacaattcttaacaaagatgtcaaatataatgagattaatttatttataggaaactaaccttgtattccatactttgtgccatag

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 6
GTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgttgtgtttgtatgttataattcaaaacctcctgtagtttctatggtctatct-------ttttttacatttcctt-caaagtaatttatcatgctgcaacttt--cacttttcgtccttgtag
 ||  ||||||| || || ||||||||| | ||||| || || ||| | |||||||||||||| || || ||||| |||||||| || ||||| ||||| ||||||      ||           |   |       |    |||||  | |    |   |        |||||| | ||  |    | | | || |  | | | |   ||   |  |||  || | || ||
TTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttacacatgggcaagacaggtctcttgctgtgtttcatagttggtgtcacatgcttatgaaggctttttataattgttgattatgcagttaagtaagttccttgttcacccttttctgtgcatgcag

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 5'ss of exon 6
GTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagt---------atgttgtgtttgtatgttataattcaaaacctcctgtagtttc--tatggtctatctttttttacatttcctt---caaagtaatttat--catgctgcaactttcacttttcgtccttgtag-------------------
|||  |||| ||||| |||||  |||||  | | ||||| || ||  |  | || ||||||||||| |||||||| ||||| |||||||| ||||| || ||| ||         |   | || |   | ||| |   ||||  |      || | ||       | ||  ||| ||    | ||  |   | | |  |  |||  | || | ||| ||   |||   |       |                    
GTCGTCTCCTATTTACACACAGGCTCGATTCCTTCCTCCATCAAAAATGTTGGACGCTGATGTGACTGACAGTGTTATTGGAGAAGGTTGCGTTATCAAGgtaggttctgcaagaaccctttggtctgaagttttggatcaaggcaatgaataatctcacctcaatgtacatttattcctctctctctgcgccatgcgaagtattccttgatacaatttgtgcttactgattgaaaatatatatctatgatgtacag

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|29681077|gb|CB677352.1|CB677352
EST:     TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAA                         AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgt ... gtccttgtagAACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
EST: gi|58606969|gb|CK035002.1|CK035002
EST:     TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGGTGTGTTATTAAA                         AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgt ... gtccttgtagAACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
EST: gi|33681770|gb|CF310009.1|CF310009
EST:     TGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGGTTGTGTTATTAAA                         AACTGTAAGATACGCCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
genomic: TGATGCTGATGTGACAGACAGTGTCATTGGTGAAGG-TTGTGTTATTAAAgtaagtatgt ... gtccttgtagAACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
EST: gi|86417728|gb|CI031937.1|CI031937
EST:     TGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAA                         AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
genomic: TGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgt ... gtccttgtagAACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
EST: gi|29612859|gb|CB617872.1|CB617872
EST:     TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGGTGTGTTATTAAA                         AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgt ... gtccttgtagAACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
EST: gi|38472262|gb|CF956393.1|CF956393
EST:     TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGGTGTGTTATTAAA                         AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgt ... gtccttgtagAACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
EST: gi|29671442|gb|CB667717.1|CB667717
EST:     TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAA                         AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgt ... gtccttgtagAACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
EST: gi|86599888|gb|CI256050.1|CI256050
EST:     GACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAA                         AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
genomic: GACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgt ... gtccttgtagAACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
EST: gi|29660395|gb|CB656670.1|CB656670
EST:     TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAA                         AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgt ... gtccttgtagAACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
EST: gi|2797145|gb|AA750439.1|AA750439
EST:     TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGGTGTGTTATTAAA                         AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgt ... gtccttgtagAACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
EST: gi|29620180|gb|CB625192.1|CB625192
EST:     TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGGTGTGTTATTAAA                         AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgt ... gtccttgtagAACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgttgtgtttgtatgttataattcaaaacctcctgtagtttctatggtctatctttttttacatttccttcaaagtaatttatcatgctgcaactttcacttttcgtccttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT