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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgtcttgtcttgttcccaattaggtcatctgatatatgataaaaatatttggcatgtcctgcaagcctcttaattactctttgtgttattattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCAAAACTGCCAAATGGCCGTCCGTTTCCGCCTCTGTTCAACTTTAAGCAAG

Basic information

species Oryza sativa
transcript LOC_Os06g35530.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g35530.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G043350_T01 (Zea mays), 3'ss of exon 10
ctttgtcttgtcttgttcccaattaggtcatctgatatatgataaaaatatttggcatgtcctgcaagcctc--ttaattactctttgtgttattattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCAAAACTGCCAAATGGCCGTCCGTTTCCGCCTCTGTTCAACTTTAAGCAAG
     | | ||| | |   ||  || || |    |  | |     | ||      |   |  |||   | |   || ||| || ||||  ||||| ||  |||| ||||| |||||||||||||| ||||| || ||||||||| ||||||||| ||| || ||||| || || ||||| || || |||||||||||||| |
--acttttagtcatatgttcatatatgtgaatatacttgtacggtatattaacctcgctttttgctgacttgagttcattgctgtttgaattattgttctagCTTGAGGCGTGTGCTCATTCATTCTTTGACGAATTACGAGAATCACATGCAAGACTCCCTAATGGACGCCCATTTCCTCCACTATTCAACTTTAAGCAGG
















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|29672897|gb|CB669172.1|CB669172
EST:     ATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCG                         CTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA
genomic: ATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCGgtaagttttt ... attattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA
EST: gi|33801683|gb|CF326713.1|CF326713
EST:     ATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCG                         CTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA
genomic: ATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCGgtaagttttt ... attattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA
EST: gi|38473115|gb|CF957247.1|CF957247
EST:     ATCTTGTGTCCCGTCTCCTTCAGTATTCACCAAATCTGCGATGTACTGCG                         CTGGAGGCATGTGCTCATTCATTTTTTGATGAGCTACGAGAACCACATGCA
genomic: ATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCGgtaagttttt ... attattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA
EST: gi|87018925|gb|CI256810.1|CI256810
EST:     ATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCG                         CTGGAGGCATGTGCTCATTCAGTTTTTGATGAGTTACGAGAACCACATGCA
genomic: ATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCGgtaagttttt ... attattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA
EST: gi|29689143|gb|CB685418.1|CB685418
EST:     ATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCG                         CTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA
genomic: ATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCGgtaagttttt ... attattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA
EST: gi|29660850|gb|CB657125.1|CB657125
EST:     ATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCG                         CTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA
genomic: ATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCGgtaagttttt ... attattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA
EST: gi|86478870|gb|CI121503.1|CI121503
EST:     CCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCG                         CTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA
genomic: CCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCGgtaagttttt ... attattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCA

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: 74 (upstream exon), 71 (downstream exon)
Score: 28

ATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCGgtaagttttt ... attattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCAAAACTGCCAAATGGCCGTCCGTTTCCGCCTCTGTTCAACTTTAAGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatttggcatgtcctgcaagcctcttaattactctttgtgttattattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCAAAACTGCCAAATGGCCGTCCGTTTCCGCCTCTGTTCAACTTTAAGCAAG
                         tcttaat  putative branch site (score: 28)
                                     tttgtgttattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgtcttgtcttgttcccaattaggtcatctgatatatgataaaaatatttggcatgtcctgcaagcctcttaattactctttgtgttattattacagCTGGAGGCATGTGCTCATTCATTTTTTGATGAGTTACGAGAACCACATGCAAAACTGCCAAATGGCCGTCCGTTTCCGCCTCTGTTCAACTTTAAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- -tgtcttg
- - - - - - - - - - - - - - catctga
- - - - - - - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaagc