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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatggccaatatgcagccgatgttttttggatgggaattttgacagttaggctaatcacaggaccaattaattattttatgatttcactgtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTGTAATGCCAAATATACACGTGTATGGATTCTCCAAAGCAGAAGATCCTGA

Basic information

species Oryza sativa
transcript LOC_Os01g29409.1
intron # 7
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|88517790|gb|CI445444.1|CI445444
EST:     AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAG                         ATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
genomic: AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
EST: gi|86260139|gb|CI066012.1|CI066012
EST:     AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAG                         ATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
genomic: AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
EST: gi|88199516|gb|CI199366.1|CI199366
EST:     AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAG                         ATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
genomic: AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
EST: gi|29617638|gb|CB622650.1|CB622650
EST:     AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAG                         ATGTGTTCAGAGGAATCTCATGGAACCACCAGTTGGCTGTGCCTTCTTGTG
genomic: AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
EST: gi|29618956|gb|CB623968.1|CB623968
EST:     AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAG                         ATGTGTTCAGAGGAATCTCATGGAACCACCAGTTGGCTGTGCCTTCTTGTG
genomic: AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
EST: gi|88485196|gb|CI422467.1|CI422467
EST:     AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAG                         ATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
genomic: AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
EST: gi|86882808|gb|CI327409.1|CI327409
EST:     AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAG                         ATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
genomic: AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
EST: gi|86890133|gb|CI321310.1|CI321310
EST:     AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAG                         ATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
genomic: AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
EST: gi|86482719|gb|CI125352.1|CI125352
EST:     TAATGAATTTGCCCAATGATGCTGCAGAATTGTTAG                         ATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
genomic: TAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
EST: gi|29689147|gb|CB685422.1|CB685422
EST:     AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAG                         ATGTGTTCAGAGGAATCTCATGGAACCATCATTTGGCTGTGCCTTCTTGTG
genomic: AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
EST: gi|88544195|gb|CI474269.1|CI474269
EST:     AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAG                         ATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG
genomic: AGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTG

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: 71 (upstream exon), 61 (downstream exon)
Score: 18

GACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAACATGTGCATCCAGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTGCAGAATTTTTAGgtgggttttc ... gtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTGTAATGCCAAATATACACGTGTATGGATTCTCCAAAGCAGAAGATCCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttaggctaatcacaggaccaattaattattttatgatttcactgtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTGTAATGCCAAATATACACGTGTATGGATTCTCCAAAGCAGAAGATCCTGA
                     aattaat  putative branch site (score: 18)
                                      tttcactgtttcccc  putative PPT
                     aattaattattttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatggccaatatgcagccgatgttttttggatgggaattttgacagttaggctaatcacaggaccaattaattattttatgatttcactgtttccccagATGTGTTCAGAGGAATCTCATGGAACCACCATTTGGCTGTGCCTTCTTGTGTAATGCCAAATATACACGTGTATGGATTCTCCAAAGCAGAAGATCCTGA

- - - - - - tgcagcc
- - - - - - - - - - - - - - tggatgg