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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accttggttgtttagatacatgaggagtttctacaaatcatgatccatctgttaagttgaagttacatagtctgaccatatttcgtcctgatttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAGCCCCACTGCGGAGGATTTGACAACGATTCTGGAGTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g09510.1
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|427157|gb|D23239.1|D23239
EST:     CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAG                         GATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
genomic: CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAGgtaaacggca ... atttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
EST: gi|33821538|gb|CF336581.1|CF336581
EST:     CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAG                         GATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
genomic: CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAGgtaaacggca ... atttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
EST: gi|33810146|gb|CF330962.1|CF330962
EST:     CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAG                         GATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
genomic: CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAGgtaaacggca ... atttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
EST: gi|33662441|gb|CF293408.1|CF293408
EST:     CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAG                         GATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
genomic: CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAGgtaaacggca ... atttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
EST: gi|33686251|gb|CF314490.1|CF314490
EST:     CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAG                         GATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
genomic: CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAGgtaaacggca ... atttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
EST: gi|86897498|gb|CI294448.1|CI294448
EST:     CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAG                         GATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
genomic: CGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAGgtaaacggca ... atttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
EST: gi|7645997|gb|AU090561.1|AU090561
EST:     GCAGCCAATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAG                         GATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
genomic: GCAGCC-ATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAGgtaaacggca ... atttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAG
EST: gi|163925772|gb|EG714608.1|EG714608
EST:     CGTCGGGCTCTCTCCATCTCCCATCCAG                         GATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGG
genomic: CGTCGGGCTCTCTCCATCTCCCATCCAGgtaaacggca ... atttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGG

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: 72 (upstream exon), 72 (downstream exon)
Score: 151

CCTTCACCGCAGAAACCCTAGAGCTCACCCTAGCGCGCCGCCGCCGCAGCCATCTCCGCCGCCGCTCGTCGGGCTCTCTCCATCTCCCATCCAGgtaaacggca ... atttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAGCCCCACTGCGGAGGATTTGACAACGATTCTGGAGTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctgttaagttgaagttacatagtctgaccatatttcgtcctgatttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAGCCCCACTGCGGAGGATTTGACAACGATTCTGGAGTCAG
                                        tcctgat  putative branch site (score: 151)
                                              tttgttc  CT-rich tract
                                atattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accttggttgtttagatacatgaggagtttctacaaatcatgatccatctgttaagttgaagttacatagtctgaccatatttcgtcctgatttgttcagGATGAAGTTCATTTCTGCCTATCTGATGGCCTATCTGGCTGGCAACTCCAGCCCCACTGCGGAGGATTTGACAACGATTCTGGAGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - gttgttt
- - - - - - - -atacatg
- - - - - - - - - - - - - - - ctacaaa
- - - - - - - - - - - - - - - - - - -tcatgat
- - - - - - - - - - - - - - - - - - - - - - -catctgt