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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttgccctaacgttgcaagttctaagaaataaacactaaggactttgcatgacatgactgagaaatgaccttaccttattgctaacaattcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCTAAATCAACAAAGATTACGTTTGGTGATTCTGATGAGGACTAGCAACATT

Basic information

species Oryza sativa
transcript LOC_Os07g20580.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g20580.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G076484_T01 (Zea mays), 3'ss of exon 11
ccttgccctaacgttgcaagttctaagaaataaacactaagg-actttgcat----gacatgactgagaaatgacctt-accttattgctaacaattcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCTAAATCAACAAAGATTACGTTTGGTGATTCTGATGAGGACTAGCAACATT
    | |  ||  | | || |   |   ||| |||| ||| | | |||||||    || ||   ||| || || | || |  |||      || ||   ||||||||||||  | ||||| |||||||||||||| ||| | | |||||||||||||||||| || ||||| || ||||| ||||||||||||||||      || 
----ggctcaatttagtaa-tcgaacataatgaacattaaagtagtttgcatatgggagatttatgataagtgtcttttaatttagcagctaccatat-tttgcagGAATCTAAGATATACGGATCTCATTTCAAGGAACTTACAGCAGATGCTCCTAAATCCACGAAGATCACATTTGGCGATTCTGATGAGGACTGATGTGATG
















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|88382124|gb|CI533328.1|CI533328
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|86429166|gb|CI075847.1|CI075847
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|87031255|gb|CI259835.1|CI259835
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|88380526|gb|CI521095.1|CI521095
EST:     GCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: GCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|88472115|gb|CI409386.1|CI409386
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|163926476|gb|EG712344.1|EG712344
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACTCACGTCAAGAAAAAG                         GAATCGCAAATATATG
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATG
EST: gi|89173588|gb|CI041481.1|CI041481
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|29673123|gb|CB669398.1|CB669398
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|88533053|gb|CI460586.1|CI460586
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|88958834|gb|CI381637.1|CI381637
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|88835556|gb|CI370661.1|CI370661
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCGTTTCAAAGAAATCAAACCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|86593359|gb|CI257999.1|CI257999
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|86431877|gb|CI085488.1|CI085488
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
EST: gi|88283651|gb|CI405097.1|CI405097
EST:     AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAG                         GAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT
genomic: AGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCT

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: 61 (upstream exon), 75 (downstream exon)
Score: 14

GGACTTGCTGGTGAACTTGTCAATGTTTTGCGGGAGGCTGGTCAGGTCGTTCCTCCTGCACTTACAAAATTTGGCACACACGTCAAGAAAAAGgtttgtgtta ... tcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCTAAATCAACAAAGATTACGTTTGGTGATTCTGATGAGGACTAGCAACATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatgacatgactgagaaatgaccttaccttattgctaacaattcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCTAAATCAACAAAGATTACGTTTGGTGATTCTGATGAGGACTAGCAACATT
                                   tgctaac  putative branch site (score: 14)
                                            ttcattt  putative PPT
                                          aattcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttgccctaacgttgcaagttctaagaaataaacactaaggactttgcatgacatgactgagaaatgaccttaccttattgctaacaattcatttgcagGAATCGCAAATATATGGATCTCATTTCAAAGAAATCAAAGCAGATGCTCCTAAATCAACAAAGATTACGTTTGGTGATTCTGATGAGGACTAGCAACATT

-cttgccc
- - - - - - -ttgcaag
- - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - atgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctaa