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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcactttatcaataattagtacatgaagaaaaaaaattgagcatctggtttttctgattagtatagtttatatggtatgtacacaatctttactactttaactgaattgtctgctggtcggttctcctttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT

Basic information

species Oryza sativa
transcript LOC_Os02g46510.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 7
gtatcactttatcaataattagtacatgaagaaaaaaaattgagcatctggtttttctgattagtatagtttatatggtatgtacacaatctttactactttaactgaattgtctgctggtcggttctcctttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT
                                    | || | |    | ||||| || |||| || | ||| | ||| |  |      | |||   |  ||  || ||||   | ||| | |  ||| || || | || |||| || ||||| || || ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || ||||| || ||||||
-----------------------------------cagatcgtgg---tagttttgctcattaatacaatttttttggaacttt-----tttttgtcatctttgctaaatttgttactgattgtgtcttctcttgc-tctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGT

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatcactttatcaataattagtacatgaagaaaaaaaattgagcatctggtttttctgattagtatagtttatatggtatgtacacaatctttactactttaactgaattgtctgctggtcggttctcctttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT
                                                               |||||  || | |  ||  |  |  |||  ||   |  | |||    | | ||||    |  |||| ||||       ||| || || |||||||||||||||||||||||||| ||||||||||| ||| |||| ||||| ||||| || ||||| || || ||||| || || || || 
---------------------------------------------------------------gtatacgttgt-taatacattgaacatcagtagc-cactgacttttctttgtgctaactgactctcgttttgt----gcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 7
gtatcactttatcaataattagtacatgaagaaaaaaaattgagcatctggtttttctgattagtatagtttatatggtatgtacacaatctttactactttaactgaattgtctgctggtcggttctcctttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT
                                   | | ||  |  | |    | | |  ||   || | || | |  || |      || ||   |  ||| | | | ||     ||| |   | || | ||||     |||| || || |||||||||||||||||||| || ||||||||||| || || ||||| || ||||||||||||||||| ||||| |||||||| ||||| |||
----------------------------------tacagttttgtttatcacatatttatttcaaatggcttgttt--taggc-tgtgatgttggttgatttga-taacttagtctctgat-aatgctacctttt-----acagTGGCAAAACCATTGAGCTTGATGATGTTACTTTCCACCAGTGCGTAAATTTGACGAGGTTTAACTCAGAAAAGACCGTCAGTTTTGTGCCACCAGATGGT

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 7
---------gtatcactttatcaataattagtacatgaagaaaaaaaatt-----gagcatctggtttttctgattagtatagtt--tatatggtatgtacacaatct-ttactactttaac-----------tgaattgtctgctggtcggttctcct--------ttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT
         | |||          | ||   | | |  |  ||            | |  | |  ||||| |  ||| | || ||  | |||  | |   | || ||| || |  |||  ||           ||||  || |  |   | || ||| |        | || |   |||| || || || ||||||||||||||||| ||||||||||| ||||||||  | |||||||| |   | || ||||||||||| ||||| || || || || 
gttgaatgcgcatccacactcttgtgatggcttcgtttaacaatgttgccctcaagtgttttttatttttatttttattttatttactttattttttactctcattctcttgcagcttcgacatatttgggtttgaaaagtgttttacactgtgctcttgtgactcctctttcatgacagTGGGAAAACAATTGAGCTTGATGATGTTACATTCCACCAATGTGTCAATCTCACAAGATTCACTGCTGAGAAGACAGTCAGTTTTGTTCCACCCGATGGA

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 7
-------gtatcactttatcaataattagtacatgaagaaaaaaaattgagcatctggtttttctgattagtatagtttatatggtatgtacacaatctttactactttaactgaa-ttgtctgctggtc--ggttctcctttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT
       | | || |        |    |    ||          |||| |||    ||||  | ||   |  |  ||    | | |  |    ||| |||   | ||  |  | | ||| |     |||  | |     |  ||   | |||| || ||||| |||||||||||||| |||||||||||||||||||| ||  | || ||||| ||  | || ||||||||||| || || || || || || 
gttgaatgca-cattcctggggcaccctgattttgctatggcttcattgtgcaa--agtttccccgagatgcttctttccccttgcagatttgaaatgtttgaaaattggaaggtacttgacattccgtcctgatgtatttccttttacgacagTGGCAAGACAATTGAGCTTGATGACGTCACATTCCACCAGTGTGTGAATCTTACGAGATTCAATGCCGAGAAGACAGTCAGTTTCGTTCCACCGGATGGA

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 7
gtatcactttatcaataattagtacatgaagaaaaaaaattgagcatctggtttttctgattagtatagtttatatggtatgtacacaatctttactactttaactgaattgtctgctggtcggttctcctttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT
                                                                                 |||  |  |      ||| |||    ||   | |  || | | |     ||||||      || || || || || ||||| || |||||||| || || ||||| |||||||| || ||||||||||| || ||||| ||||||||||| || || || || 
---------------------------------------------------------------------------------gtatgctttaaggtgtacattagtgcaacctttt--tgattgataaaaatttttc------agTGGGAAAACGATAGAGCTGGACGATGTCACGTTTCATCAGTGCGTCAACTTAACCAGATTTAACTCCGAGAAGACGGTCAGCTTTGTTCCTCCGGATGGA

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 7
gtatcactttatcaataattagtacatgaagaaaaaaaattgagcatctggtttttctgattagtatagtttatatggtatgtacacaatctttactactttaactgaattgtctgctggtcggttctcctttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT
                                                                                 |||  |  |      ||| |||    ||   | |  || | | |     ||||       ||| || || || || ||||| || |||||||| || || ||||| |||||||| || ||||||||||| || ||||| ||||||||||| || || || || 
---------------------------------------------------------------------------------gtatgctttaaggtgtacattagtgcaacctttt--tgattgataaaaatttt------gcagTGGGAAAACGATAGAGCTGGACGATGTCACGTTTCATCAGTGCGTCAACTTAACCAGATTTAACTCCGAGAAGACGGTCAGCTTTGTTCCCCCGGATGGA

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|38469602|gb|CF953733.1|CF953733
EST:     AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAG                         CGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
genomic: AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAGgtatcacttt ... tcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
EST: gi|11565235|gb|AU165871.1|AU165871
EST:     AGATCGGGCTTGAAAAAGAAGCTCAACTCCAAGTCCAGGCCTGCAAAGAG                         CGGAAAGNCCATTGAGCCTGATGATGNCACATTCCACCAGTGTGTCA-CTT
genomic: AGATCGGGCTTGAAAAAGAAGCTCAACTC-AAGTCCAGGCCTGCAAAGAGgtatcacttt ... tcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
EST: gi|58672424|gb|CK061110.1|CK061110
EST:     AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAG                         CGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
genomic: AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAGgtatcacttt ... tcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
EST: gi|218499528|gb|FG946431.1|FG946431
EST:     AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAG                         CGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
genomic: AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAGgtatcacttt ... tcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
EST: gi|11025706|gb|AU162307.1|AU162307
EST:     AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAG                         CCGGNAAGACCATTGAGCCTGATGATGTCACATTCCACCAG
genomic: AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAGgtatcacttt ... tcctcaacagC-GGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAG
EST: gi|58679139|gb|CK067826.1|CK067826
EST:     AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAG                         CGGAAAGACCATTGAGCTTGATGATGTCACATTCCACC
genomic: AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAGgtatcacttt ... tcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACC
EST: gi|428998|gb|D25154.1|D25154
EST:     AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAG                         CGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
genomic: AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAGgtatcacttt ... tcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
EST: gi|33811253|gb|CF331516.1|CF331516
EST:     AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAG                         CGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
genomic: AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAGgtatcacttt ... tcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
EST: gi|58684077|gb|CK072764.1|CK072764
EST:     AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAG                         CGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT
genomic: AAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAGgtatcacttt ... tcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 73 (downstream exon)
Score: 34

TGAAGTGCTTCCTTTCTGGAATGCCTGATCTGAAATTGGGATTAAATGACAAGATCGGGCTTGAAAAAGAAGCTCAACTCAAGTCCAGGCCTGCAAAGAGgtatcacttt ... tcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttactactttaactgaattgtctgctggtcggttctcctttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT
         ctttaac  putative branch site (score: 34)
                               tcggttctcctttttc  putative PPT
       tactttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcactttatcaataattagtacatgaagaaaaaaaattgagcatctggtttttctgattagtatagtttatatggtatgtacacaatctttactactttaactgaattgtctgctggtcggttctcctttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT