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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttatacatcatgtcttactctaaattacacaatctggttatgtggaaaaaagaaagtaactgatgtgttctgacctaaattttcatttttttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTGGTTCATATTGAAGGACTGTTGACATTTTTGAGGGAAAATGAGTGGTGCA

Basic information

species Oryza sativa
transcript LOC_Os07g29450.1
intron # 1
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|88695779|gb|CI737356.1|CI737356
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|88415231|gb|CI584054.1|CI584054
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|58671063|gb|CK059749.1|CK059749
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|88430580|gb|CI569603.1|CI569603
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|88696078|gb|CI739653.1|CI739653
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|88355787|gb|CI626228.1|CI626228
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|88727233|gb|CI750888.1|CI750888
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|88372740|gb|CI612668.1|CI612668
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|117216881|gb|CT845247.1|CT845247
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|88431756|gb|CI579725.1|CI579725
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|29628070|gb|CB633081.1|CB633081
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|88355816|gb|CI626257.1|CI626257
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTAAAAGGCATTGGGCTATATCCTTTCGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
EST: gi|25797154|gb|CA753115.1|CA753115
EST:     GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTG                         TGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG
genomic: GTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTG

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: 64 (upstream exon), 72 (downstream exon)
Score: 7

ATCCCCATCCATCCATCCACCCAGCGACCGACCGACCGAGCAGGGTCGCCGTCGTTCGTACGGCTGCTTCCTCGCCGCATCCATCCATCCATCCATCCTGgtgaggaacc ... tttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTGGTTCATATTGAAGGACTGTTGACATTTTTGAGGGAAAATGAGTGGTGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaaaagaaagtaactgatgtgttctgacctaaattttcatttttttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTGGTTCATATTGAAGGACTGTTGACATTTTTGAGGGAAAATGAGTGGTGCA
                                   ttttcattttttttt  CT-rich tract
                            acctaaattttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttatacatcatgtcttactctaaattacacaatctggttatgtggaaaaaagaaagtaactgatgtgttctgacctaaattttcatttttttttggcagTGCATTGTGTCAAAGGCATTGGGCTATATCCTTTTGTATTTGTGTTTCTTGGTTCATATTGAAGGACTGTTGACATTTTTGAGGGAAAATGAGTGGTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - -atcatgt
- - - - - - - - - - - - - -acacaat
- - - - - - - - - - - - - - - - - - - - - - -gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - gaaagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctaaa