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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCAGTTCCCCGGAAGGGTCCTTCAACGTGTTTTCGAATTTACCCTACAGCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgttactccccactttcttcattttcttcttcctgcgtctgtttgtttgacatgtgattggaaatttaagccatttagacgtttctggagcttcg...

Basic information

species Physcomitrella patens
transcript PP1S62_170V6.1
intron # 1
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|208349421|gb|DC910438.1|DC910438
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|208380363|gb|DC907688.1|DC907688
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|208349538|gb|DC905648.1|DC905648
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|208397156|gb|DC908170.1|DC908170
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCANAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|67717007|gb|BJ967266.1|BJ967266
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAACTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|100396279|gb|BY990051.1|BY990051
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|208368648|gb|DC940027.1|DC940027
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|100408335|gb|BY974121.1|BY974121
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|100385897|gb|BY951091.1|BY951091
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|208391613|gb|DC938226.1|DC938226
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|100427623|gb|BY977590.1|BY977590
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|100358621|gb|BY965739.1|BY965739
EST:     TTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: TTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|100389578|gb|BY952384.1|BY952384
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|100409219|gb|BY991905.1|BY991905
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|18345646|gb|BJ177689.1|BJ177689
EST:     GCGGAATCTATTTATTTTTCTTC-TTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|100440839|gb|BY962327.1|BY962327
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGGTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|100412790|gb|BY992437.1|BY992437
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|100447563|gb|CJ971862.1|CJ971862
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|208399457|gb|DC908454.1|DC908454
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|208370343|gb|DC931755.1|DC931755
EST:     GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
EST: gi|208352428|gb|DC906197.1|DC906197
EST:     GTGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAG                         GCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT
genomic: GCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCT

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: 32 (upstream exon), 16 (downstream exon)
Score: 3

CCGCAGTTCCCCGGAAGGGTCCTTCAACGTGTTTTCGAATTTACCCTACAGCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgtta ... actgatacagGCCAGAACAAGCCTCTTTGATTTCGCACCCCTAGCTGTAAACTTCAGAGCTCGGTATGGATGACATGGACAATATCTCGGGGAGTGCCATCCAAGTCGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCAGTTCCCCGGAAGGGTCCTTCAACGTGTTTTCGAATTTACCCTACAGCGGAATCTATTTATTTTTCTTCTTTTTAGTTCCATTTTTCCTGCTGGAGgtgtgtgttactccccactttcttcattttcttcttcctgcgtctgtttgtttgacatgtgattggaaatttaagccatttagacgtttctggagcttcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA