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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtttttgtttagtttggatgttcacagctatgctgtacagtacttgtgagcttgtttacagttaattggatgtataaccatttcttgtattctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAGGACAGAGCGGCGATGGGCAAGAACTAGCGAAAGACCTCAGGCAATTTCG

Basic information

species Oryza sativa
transcript LOC_Os06g03514.1
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|88370495|gb|CI590073.1|CI590073
EST:     GCGGTGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAATGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|86417923|gb|CI032132.1|CI032132
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|2428795|gb|C73258.1|C73258
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|87004318|gb|CI298850.1|CI298850
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|15848507|gb|BI796783.1|BI796783
EST:     GCGGC-CCGCCACCGCCGGCCTCTCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCATAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|3767335|gb|AU031445.1|AU031445
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|163926140|gb|EG712838.1|EG712838
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|58659827|gb|CK048507.1|CK048507
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|325494283|gb|JG458807.1|JG458807
EST:     GCGGCGCCGCCACCGCCGGTCTCGCCGGGGTCTTCCTCTTCAACGCCCAG                         GAGAAGTTCCAGAAGTATCTTT
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTT
EST: gi|7206587|gb|D15612.2|D15612
EST:     GCGGCGCCGCCACCGCCGGCCTCGCC-GGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|55411004|gb|CV723380.1|CV723380
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|88241665|gb|CI241514.1|CI241514
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|88559138|gb|CI489691.1|CI489691
EST:     GCGGCGCCGCCACCNCCGGCCTCGCCGGGGTCTTCCTCTTCAACNCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|88591530|gb|CI709567.1|CI709567
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|5038608|gb|AU070718.1|AU070718
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|88765359|gb|CI774453.1|CI774453
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|88512890|gb|CI440396.1|CI440396
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|88240802|gb|CI238653.1|CI238653
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|87014565|gb|CI284077.1|CI284077
EST:     CTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: CTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|66917380|gb|CX104228.1|CX104228
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|88253794|gb|CI352420.1|CI352420
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|86863226|gb|CI344922.1|CI344922
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|38475944|gb|CF960077.1|CF960077
EST:     GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: GCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
EST: gi|6782753|gb|AU082163.1|AU082163
EST:     CGGCGCCGCCACCGCCGGCCTTCGCCGGGGTCTTCCTCTTCAACGCCAAG                         GAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG
genomic: CGGCGCCGCCACCGCCGGCC-TCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAG

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: 60 (upstream exon), 64 (downstream exon)
Score: 43

GATGATCTACCGCAAGTGGTCGCTGCTCTCCTCCACCATCCTCATCTGGGGCGGCGCCGCCACCGCCGGCCTCGCCGGGGTCTTCCTCTTCAACGCCAAGgtttacccgc ... attctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAGGACAGAGCGGCGATGGGCAAGAACTAGCGAAAGACCTCAGGCAATTTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgagcttgtttacagttaattggatgtataaccatttcttgtattctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAGGACAGAGCGGCGATGGGCAAGAACTAGCGAAAGACCTCAGGCAATTTCG
                            gtataac  putative branch site (score: 43)
                agttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtttttgtttagtttggatgttcacagctatgctgtacagtacttgtgagcttgtttacagttaattggatgtataaccatttcttgtattctggcagGAGAAGTTCCAGAAGTATCTTTCCGGTGAAGGCCAGAGGCTCAGGCAGCAGGACAGAGCGGCGATGGGCAAGAACTAGCGAAAGACCTCAGGCAATTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- gtttttg
- - - - - - - -ttggatg
- - - - - - - - - - - - - - - tatgctg
- - - - - - - - - - - - - - - - - - - - -gtacttg
- - - - - - - - - - - - - - - - - - - - - - - - -gagcttg