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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcttctctatttagtttgtgttaattgcaataggatgatattgtgatggtgatggaaatatcattggtagacttttgacacactattgtgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAATTTGCAAACTGAGAATATT

Basic information

species Oryza sativa
transcript LOC_Os02g27950.1
intron # 8
splice site 3'
intron type U2

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|33657023|gb|CF279637.1|CF279637
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|33658414|gb|CF281027.1|CF281027
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|33797329|gb|CF324527.1|CF324527
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|58674525|gb|CK063212.1|CK063212
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTCGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|58677564|gb|CK066251.1|CK066251
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTCGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|218478232|gb|FG962363.1|FG962363
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTCGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|58689025|gb|CK077712.1|CK077712
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTCGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|56157273|gb|D39206.2|D39206
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGGCACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|218494729|gb|FG965196.1|FG965196
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTCGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|33675902|gb|CF304141.1|CF304141
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|33658429|gb|CF281042.1|CF281042
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|2310139|gb|C26294.1|C26294
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACA
EST: gi|218504451|gb|FG953021.1|FG953021
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTCGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
EST: gi|218498152|gb|FG965352.1|FG965352
EST:     TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAG                         GTCGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA
genomic: TTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAA

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: 72 (upstream exon), 67 (downstream exon)
Score: 28

CTTCCCATTTATTTGGCACTGATTTGCCTGTCACTAACAATGTTAGCCAGTTAGTATCTCAGTCCCAGCTGAATAAACTTTTGCCCATTGATGAAAGCAGgtatatatac ... tgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAATTTGCAAACTGAGAATATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatggtgatggaaatatcattggtagacttttgacacactattgtgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAATTTGCAAACTGAGAATATT
                             ttttgac  putative branch site (score: 28)
            aaatatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcttctctatttagtttgtgttaattgcaataggatgatattgtgatggtgatggaaatatcattggtagacttttgacacactattgtgaaccacagGTTGGATGACAAACTGACCAAAGATAGCAGTGGTAATAGGGACACAAGCAATTTGCAAACTGAGAATATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
-agcttct
- - - - - - - - -ttgtgtt
- - - - - - - - - - - - aattgca
- - - - - - - - - - - - - - - - - -gatgata
- - - - - - - - - - - - - - - - - - - - - ttgtgat
- - - - - - - - - - - - - - - - - - - - - - - - -ggtgatg