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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAAACGGAAGAGCTGGCCAAGAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgctataaccccgtcctgatgtaactgatagtgcacaatgcagatctatatggccaatgctttctcccttttcttttttaccttgagataaaggg...

Basic information

species Oryza sativa
transcript LOC_Os01g43090.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43090.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G024315_T01 (Zea mays), 5'ss of exon 6
CTGAAAACGGAAGAGCTGGCCAAGAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtga-gtgctataaccccgtcctgatgtaactgatagtgcacaatgc----agatctatatggccaatgctttctcccttttcttttttaccttgagataaaggg
 ||  || |||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||| || ||||||||||      ||||| | | | ||  | | | |||    |  |  |||    |||   ||  |    |  ||||          | | || | |   | |      
TTGCGAATGGAAGAACTGGCCAATAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttaccttataatctcattctcttatcattgacgacggtctgtgctttcagactgatgagttatacactttgagagaacagtgtattgcatcatgttc-----

upper sequence: LOC_Os01g43090.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv14s0030g01960.t01 (Vitis vinifera), 5'ss of exon 6
CTGAAAACGGAAGAGCTGGCCAAGAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgctataaccccgtcctgatgtaactgatagtgcacaatgcagatctatatggccaatgctttctcccttttcttttttaccttgagataaaggg--
     ||  ||| | || || || |||||    || |  |||||||| |||||  |||| |||||||| || |||||||||||||| || || ||||| ||||||| |  |  | |  |    |  | | | ||       ||| |||  |          ||   |     | | | | |  |   | ||  | ||||   
ACTCGAATAGAAAACCTTGCAAATAAGCATGGTTGTACTCCTGCTCAACTAGCACTAGCATGGGTTCTCCAACAAGGGGATGATGTTGTACCTATACCTGgtgagt-cacttcctctttttctaccttattaatctattttaat-caggccatgtcatttgatatatatgtacatatatatcctgtttggattttaaggaaa

upper sequence: LOC_Os01g43090.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv14s0030g02050.t01 (Vitis vinifera), 5'ss of exon 6
CTGAAAACGGAAGAGCTGGCCAAGAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgctataaccccgtcctgatgtaactgatagtgcacaatgcagatctatatggccaatgctttctcccttttcttttttaccttgagataaaggg
   |||| |||   | ||||  | ||||||   |||| | |||| ||||| ||  ||||||||||||||| ||||||||||||||| |  || || || ||||||||  ||     |  ||  ||  || | |||       | |  |    | ||    |||   | ||     | ||| ||     |||  ||     
ACTAAAATGGAGATGTTGGCTGAAAAGCACGGATGCACCGCTGCACAGCTTGCGCTAGCTTGGGTTCTTCGTCAAGGGGATGATGTTGCTCCTATCCCTGgtgagtgaaattttttctgcc--atacaagttatacccttggaggttgggacaaatcctaaatatgtgcttttgatccttattccatatgatgtag----

upper sequence: LOC_Os01g43090.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv14s0030g01980.t01 (Vitis vinifera), 5'ss of exon 6
CTGAAAACGGAAGAGCTGGCCAAGAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgctataaccc-cgtcctgatgtaac-tg-atagtgcacaatgcagatctata-tggccaatgctttctcccttttcttttttaccttgagataaaggg
   |||| |||   | ||||  | ||||||   |||| |||||| ||||| ||  |||||||||||||||||||||||||||||||||  || || || |||||||    |   |  | ||   |  || | || | ||  ||   |  | |||| |  | | |    |  |  |    ||| | | |   ||||         
ACTAAAATGGAGATGTTGGCTGAAAAGCACAGATGCACCCCTGCACAGCTTGCACTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGCACCTATCCCTGgtgagtcacgtgttcttcctctcaacctagcatgcaaagaacatgcttaacatctgttcttgtcctcacaataacatcattcatatctcttttgattgtc----

upper sequence: LOC_Os01g43090.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv14s0030g02020.t01 (Vitis vinifera), 5'ss of exon 6
CTGAAAACGGAAGAGCTGGCCAAGAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgctataaccc-cgtcctgatgtaactgatagtgcacaatgcagatctatatggccaatgctttctcccttttcttttttaccttgagataaaggg
   |||| |||   | ||||  | ||||||   |||| |||||| ||||| ||  |||||||||||||||||||||||||||||||||  || || || |||||||    |   |  | ||   |  || |  | |  | |||  |   |  | |||                  |   |  | |  |||  |||   || 
ACTAAAATGGAGATGTTGGCTGAAAAGCACAGATGCACCCCTGCACAGCTTGCACTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGCACCTATCCCTGgtgagtcacgtgttcttcctctcaacctagcacacaaagaacatggttaacatctattcttgtcctcacaataactcattcatgtctcttttgatgtcgg-

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|87026936|gb|CI259589.1|CI259589
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|89168390|gb|CI109594.1|CI109594
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|66916219|gb|CX103067.1|CX103067
EST:     GCTTTAGCTTGGGTTCTTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGA
genomic: GCTTTAGCTTGGGTTCTT-CATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGA
EST: gi|86538047|gb|CI178253.1|CI178253
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|88259423|gb|CI363716.1|CI363716
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|58685243|gb|CK073930.1|CK073930
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|88281651|gb|CI403047.1|CI403047
EST:     CTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: CTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|88204861|gb|CI202712.1|CI202712
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAATAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|88271340|gb|CI387393.1|CI387393
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|86839806|gb|CI343719.1|CI343719
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATTTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|88846089|gb|CI372857.1|CI372857
EST:     TTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: TTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|86863542|gb|CI345249.1|CI345249
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|88993684|gb|CI112588.1|CI112588
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|88225703|gb|CI225619.1|CI225619
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|58611335|gb|CK039047.1|CK039047
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
EST: gi|86492326|gb|CI134959.1|CI134959
EST:     AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAG                         GAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA
genomic: AGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGA

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: 65 (upstream exon), 69 (downstream exon)
Score: 7

CTGAAAACGGAAGAGCTGGCCAAGAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgcta ... attttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGAACCTCACGGATGATGACCTGAAAGAGATCTCTAGCCAGGTACGCGAAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAAAACGGAAGAGCTGGCCAAGAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCTTGGGTTCTTCATCAAGGGGATGATGTGGTCCCAATACCAGgtgagtgctataaccccgtcctgatgtaactgatagtgcacaatgcagatctatatggccaatgctttctcccttttcttttttaccttgagataaaggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttctcc