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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgctctcttgatgtgaaactatgaacattgttaccgaaccgttaagcatatttttcttactcgttttatttatacctgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAGGAAGGAGAAACTAACCAAAAAAAATACTGGACTAACAAGCTTCTTGTAT

Basic information

species Oryza sativa
transcript LOC_Os05g34650.1
intron # 13
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|29645587|gb|CB650594.1|CB650594
EST:     GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTG                         GAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
genomic: GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
EST: gi|117223389|gb|CT846265.1|CT846265
EST:     GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTG                         GAGCGATGTGCAACA
genomic: GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACA
EST: gi|88502051|gb|CI429557.1|CI429557
EST:     GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTG                         GAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
genomic: GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
EST: gi|218496920|gb|FG952344.1|FG952344
EST:     GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTG                         GAGCGATGTCCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
genomic: GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
EST: gi|88472792|gb|CI410063.1|CI410063
EST:     GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTG                         GAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
genomic: GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
EST: gi|88539793|gb|CI469780.1|CI469780
EST:     GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCCACTTTG                         GAGCGATGTGCAACATCATGGGGTATGCTTACTCATTGAAAGACGGGGAAG
genomic: GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
EST: gi|88979302|gb|CI025804.1|CI025804
EST:     GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTG                         GAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
genomic: GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
EST: gi|12622951|gb|AU173164.1|AU173164
EST:     GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTG                         GAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
genomic: GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
EST: gi|88536102|gb|CI465826.1|CI465826
EST:     GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTG                         GAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
genomic: GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
EST: gi|88545613|gb|CI475182.1|CI475182
EST:     GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTG                         GAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
genomic: GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
EST: gi|88446473|gb|CI536504.1|CI536504
EST:     GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTG                         GAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG
genomic: GTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAG

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: 65 (upstream exon), 42 (downstream exon)
Score: 19

CTATGTGAGTCAGCGAACTTCTTTAACTAAATCAACCATATCGAAGTGAAGTACCTGGCATGCACCGCGCGAGACAGGATGGATGGGTACTTCAACTTTGgttagtgctc ... tgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAGGAAGGAGAAACTAACCAAAAAAAATACTGGACTAACAAGCTTCTTGTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccgaaccgttaagcatatttttcttactcgttttatttatacctgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAGGAAGGAGAAACTAACCAAAAAAAATACTGGACTAACAAGCTTCTTGTAT
                      ttcttac  putative branch site (score: 19)
                                           cctgttct  putative PPT
                atatttttcttactcg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgctctcttgatgtgaaactatgaacattgttaccgaaccgttaagcatatttttcttactcgttttatttatacctgttctgcagGAGCGATGTGCAACATCATGGGGTATGCTGACTCATGGAAAGACGGGGAAGGAAGGAGAAACTAACCAAAAAAAATACTGGACTAACAAGCTTCTTGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT