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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactaacctttttttacagttgacaaaacttcggagaaagtaaaaaaaaatccgatctttatacgagacttaaatttccttccgttttggaaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGACGTGCGGTCCAACCAGCTGAAATCGCTGCCCAACTCCATCGGCTGCCTCT

Basic information

species Oryza sativa
transcript LOC_Os04g51580.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51580.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G072518_T01 (Zea mays), 3'ss of exon 1
tactaacctttttttacagttgacaaaacttcggagaaagtaaaaaaaaatccgatctttatacgagacttaaatttccttccgtt-ttggaaaa---------ccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGACGTGCGGTCCAACCAGCTGAAATCGCTGCCCAACTCCATCGGCTGCCTCT
         | | |    | ||  | || | |  |  |  || | |  |   |||     ||   |    ||| |  | | | ||  ||||||||         ||||||||||| |||||||| ||||||||  |||| |||||||||||||||||||||||||| ||||||||||| || ||||||||||||||||||||||||||||
---------tatgtggtggatgg-agaaatactcatcatatatacagtaccacgaaaaacatgtaattaataactaacgtgctgtcgttggaaaaaatctaaaaccgcagAGCATTCCGGAGTCCATAATCGCGAGGCTCCTGAACGTGGTGGTGCTGGACGTGCGCTCCAACCAGCTCAAGTCGCTGCCCAACTCCATCGGCTGCCTCT

upper sequence: LOC_Os04g51580.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G18210.1 (Glycine max), 3'ss of exon 1
tactaacctttttttacag--ttgacaaaacttcggagaaagtaaaaaaaaatccgatctttatacgagacttaaatttccttccg----ttttggaaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGACGTGCGGTCCAACCAGCTGAAATCGCTGCCCAACTCCATCGGCTGCCTCT
     |  ||     |  |   |  ||||| || |||  |  ||||              ||||| ||   | |  | |            |||  |      |||   || ||||| ||  |||  ||| | || || |||||||  ||| |||||||||| ||||||||||| || || || ||||| ||||| ||||||||||
-----attttaggagatggaactagcaaaattt-ggattatataaatgttttattagatattatatgaatttaatgtgtaaaaaaaaaaactttatactctgacagGAAATTCCGGAATCCTTAACGGCTAGACTTCTAAACGTGGAAGTGTTGGACGTGCGTTCCAACCAGCTAAACTCCCTTCCCAATTCCATTGGCTGCCTCT
















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|33665877|gb|CF296844.1|CF296844
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGNGTGGTGCTGGG
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTG-GTGGTGCTGG-
EST: gi|86906096|gb|CI292627.1|CI292627
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
EST: gi|88315471|gb|CI613740.1|CI613740
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
EST: gi|29660969|gb|CB657244.1|CB657244
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
EST: gi|87005576|gb|CI287400.1|CI287400
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
EST: gi|88413389|gb|CI581404.1|CI581404
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
EST: gi|117231077|gb|CT860181.1|CT860181
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
EST: gi|58695205|gb|CK083892.1|CK083892
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
EST: gi|33823855|gb|CF337739.1|CF337739
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGGTGCTGGA
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGG-TGCTGGA
EST: gi|87005049|gb|CI308925.1|CI308925
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
EST: gi|88409788|gb|CI571045.1|CI571045
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGG
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGG
EST: gi|88760090|gb|CI769646.1|CI769646
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAG
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAG
EST: gi|38472393|gb|CF956524.1|CF956524
EST:     TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAG                         AGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC
genomic: TGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGAC

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: 71 (upstream exon), 64 (downstream exon)
Score: 16

TAAGCTAGACATGAGTGGCATGTCCATGGATGCCCTCCCACACCTCACCATGTCTCTTGGTCAAGTCACCATCTTGGATCTCTCTAACAACAATCTTGAGgtagatttca ... aaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGACGTGCGGTCCAACCAGCTGAAATCGCTGCCCAACTCCATCGGCTGCCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaatccgatctttatacgagacttaaatttccttccgttttggaaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGACGTGCGGTCCAACCAGCTGAAATCGCTGCCCAACTCCATCGGCTGCCTCT
                      acttaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactaacctttttttacagttgacaaaacttcggagaaagtaaaaaaaaatccgatctttatacgagacttaaatttccttccgttttggaaaaccgcagAGCATCCCGGAGTCAATAATCGCTCGGCTGCTGAACGTGGTGGTGCTGGACGTGCGGTCCAACCAGCTGAAATCGCTGCCCAACTCCATCGGCTGCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - -gacaaaa
- - - - - - - - - - - - - - - - - -gaaagtaa
- - - - - - - - - - - - - - - - - - - - -aaaaaaa