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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGGAACATGAGGTATCAGCTAGTTAACGGAGCGGAAAGGCTTATGCAAGATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctgtgcagtgttagctcactttgtagtgatcttgttttgaaccactctttgattattcattttattaacaacttgttagatcggaggattagt...

Basic information

species Physcomitrella patens
transcript PP1S4_62V6.2
intron # 7
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|162192880|gb|FC369874.1|FC369874
EST:     CTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: CTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162197210|gb|FC372523.1|FC372523
EST:     GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTA
genomic: GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTA
EST: gi|162185886|gb|FC360986.1|FC360986
EST:     CTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: CTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162158305|gb|FC334724.1|FC334724
EST:     CTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: CTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162274494|gb|FC450729.1|FC450729
EST:     CTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: CTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162255528|gb|FC431318.1|FC431318
EST:     GCAGCACTCAG                         GGCTCTGAATATTCACATNGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162235385|gb|FC411520.1|FC411520
EST:     GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162191494|gb|FC367185.1|FC367185
EST:     GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCA
genomic: GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCA
EST: gi|162173146|gb|FC349226.1|FC349226
EST:     GCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162224069|gb|FC400635.1|FC400635
EST:     GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162158306|gb|FC334725.1|FC334725
EST:     GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162173147|gb|FC349227.1|FC349227
EST:     GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162235384|gb|FC411519.1|FC411519
EST:     GCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162191493|gb|FC367184.1|FC367184
EST:     TCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: TCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162227026|gb|FC403370.1|FC403370
EST:     GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|18334105|gb|BJ166121.1|BJ166121
EST:     CTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: CTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162255529|gb|FC431319.1|FC431319
EST:     GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162166976|gb|FC343361.1|FC343361
EST:     GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162257914|gb|FC433800.1|FC433800
EST:     GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
EST: gi|162257913|gb|FC433799.1|FC433799
EST:     GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAG                         GGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA
genomic: GATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCA

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: 35 (upstream exon), 35 (downstream exon)
Score: 20

CAGGGAACATGAGGTATCAGCTAGTTAACGGAGCGGAAAGGCTTATGCAAGATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctg ... gtggatgcagGGCTCTGAATATTCACATTGGAGATGTGACAAGACTAGCATTTTTAGGTCAAGGGGAGTTGCCTGTCCACGCTGACGGAACTCTTTCACAAGCATATCGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGGAACATGAGGTATCAGCTAGTTAACGGAGCGGAAAGGCTTATGCAAGATCATTTTCAGCATTTGGGAGTTGTTATCTTCTTCTCTGCAGCACTCAGgtatgccctgtgcagtgttagctcactttgtagtgatcttgttttgaaccactctttgattattcattttattaacaacttgttagatcggaggattagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG