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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttcaacttgtctctttgtatgactcctctgctgtataattctgatcatgaccatatagcttgtgtgtgaagcttgattaatgtcttaagaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG

Basic information

species Oryza sativa
transcript LOC_Os02g15594.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15594.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G073788_T01 (Zea mays), 3'ss of exon 6
agttcaact-tgtctctttgtatgactcctctgctgtataattctgatcatgaccatatagcttgtgtg-tgaagcttgattaatgtcttaagaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG
  | ||||  |||   ||||| |          ||||| || |   ||||    | ||   |||  ||  | ||    | ||  | |  ||| | | | ||||||||||  |||| ||  |   |||||||||| ||||||||||| ||||| ||||||||||| ||||||||||||
--tgcaaccatgtgcatttgtttattggtcaacctgtagaacttccatcacagacttaggactttggtaattaataaagtttttttttctaatacactgcagGAAGAACAGGTCAGTGGTGGGCTGGAATGCCTGGTTCTTGCTAGTGATGGGCTTTGGGATGTTGTGGAAAATGAG

upper sequence: LOC_Os02g15594.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G442404_T01 (Zea mays), 3'ss of exon 6
------agttcaacttgtctc--tttgtatgactcctctgctgtataattctgatcatgaccatatagcttgtgtgtgaagcttgattaatgtcttaagaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG
        ||| |     |||  ||| ||| |  |   | ||  | ||  |||       ||| ||||    |   ||||| |       | |  ||| ||| | ||||||||||   ||| ||| ||  |||||||||| ||||| ||||| || || ||||||||||| ||||||||||||
tagtatgtttcgaaccacctcggtttttataaaccagtttcttaaaaa--ctgggtgcttccaaataggcctttaatgaagttc------ttttctaataaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG
















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|86428595|gb|CI075276.1|CI075276
EST:     TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAG                         GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
genomic: TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAGgtatcttatt ... gaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
EST: gi|89198338|gb|CI007398.1|CI007398
EST:     TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAG                         GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
genomic: TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAGgtatcttatt ... gaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
EST: gi|29639155|gb|CB644164.1|CB644164
EST:     TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAG                         GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
genomic: TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAGgtatcttatt ... gaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
EST: gi|25797747|gb|CA753700.1|CA753700
EST:     TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAG                         GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
genomic: TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAGgtatcttatt ... gaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
EST: gi|87010644|gb|CI278346.1|CI278346
EST:     TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAG                         GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
genomic: TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAGgtatcttatt ... gaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
EST: gi|325493254|gb|JG457778.1|JG457778
EST:     TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAG                         GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
genomic: TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAGgtatcttatt ... gaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
EST: gi|38477230|gb|CF961363.1|CF961363
EST:     TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAG                         GAAGAACTTGTCCATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
genomic: TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAGgtatcttatt ... gaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
EST: gi|86539934|gb|CI180140.1|CI180140
EST:     TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAG                         GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA
genomic: TTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAGgtatcttatt ... gaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGA

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: 68 (upstream exon), 70 (downstream exon)
Score: 25

GTACTTGGAGGGTAGGAGGTGTACTGGCAATGTCGCGTGCATTTGGCAATCGTCTACTGAAGCCATTTGTGGTGGCAGAGCCTGAAATTCAGgtatcttatt ... gaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatgaccatatagcttgtgtgtgaagcttgattaatgtcttaagaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG
                               gattaat  putative branch site (score: 25)
                                         ttaagaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttcaacttgtctctttgtatgactcctctgctgtataattctgatcatgaccatatagcttgtgtgtgaagcttgattaatgtcttaagaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - ttgtatg
- - - - - - - - - - - - - - tctgctg
- - - - - - - - - - - - - - - - - - - - ttctgat
- - - - - - - - - - - - - - - - - - - - - - - -catgacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaagct