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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGTAGAGCAGCAGATGGTATCAGAAAAGAATGGTGGTACTGATTCAGTGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgatttatttcatacacctattgttttttttcaattatccacttggcacaattatgtttcactttctcttacgtccatcttcaccctttgcattccc...

Basic information

species Oryza sativa
transcript LOC_Os01g55170.1
intron # 8
splice site 5'
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|29643681|gb|CB648688.1|CB648688
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|109712028|gb|CI029198.1|CI029198
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|218505277|gb|FG951207.1|FG951207
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|33794161|gb|CF322971.1|CF322971
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|29673355|gb|CB669630.1|CB669630
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|86898803|gb|CI296092.1|CI296092
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|29682355|gb|CB678630.1|CB678630
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|29640595|gb|CB645604.1|CB645604
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|88661682|gb|CI458201.1|CI458201
EST:     CAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGGTAAAGGAGGACGAAAAGGTCGA
genomic: CAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|38480080|gb|CF964169.1|CF964169
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|7378454|gb|AU088725.1|AU088725
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|86897515|gb|CI294456.1|CI294456
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|86511851|gb|CI154484.1|CI154484
EST:     TTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|58686024|gb|CK074711.1|CK074711
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
EST: gi|58687646|gb|CK076333.1|CK076333
EST:     TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAG                         GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA
genomic: TGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGA

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), 48 (downstream exon)
Score: 38

AAAAGTAGAGCAGCAGATGGTATCAGAAAAGAATGGTGGTACTGATTCAGTGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgattta ... atatctttagGACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGTAGAGCAGCAGATGGTATCAGAAAAGAATGGTGGTACTGATTCAGTGGAGAGTGCTTTCGACAATGAGAATGTGAACTCTAATATTTCCCATGAGgtttgatttatttcatacacctattgttttttttcaattatccacttggcacaattatgtttcactttctcttacgtccatcttcaccctttgcattccc

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcaccc