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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaataagtagataataaattctctgttgtaactactcaaaatttactcgactatcatattcccatgatttgaagttatcgttgctgaattggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG

Basic information

species Physcomitrella patens
transcript PP1S41_177V6.1
intron # 15
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|162249296|gb|FC423979.1|FC423979
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|37825115|gb|BJ583181.1|BJ583181
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|162192524|gb|FC368634.1|FC368634
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|162263738|gb|FC439637.1|FC439637
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|162278733|gb|FC454843.1|FC454843
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|18334344|gb|BJ166361.1|BJ166361
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|208394915|gb|DC924134.1|DC924134
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|162230101|gb|FC406249.1|FC406249
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|162278732|gb|FC454842.1|FC454842
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|162214450|gb|FC391209.1|FC391209
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|37823906|gb|BJ581972.1|BJ581972
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|67692630|gb|BJ952863.1|BJ952863
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
EST: gi|208397350|gb|DC916318.1|DC916318
EST:     ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAG                         GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT
genomic: ATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCT

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: 30 (upstream exon), 21 (downstream exon)
Score: 3

ATACAAACATGAAGACCTTCCGCTGGTTTTTGAGGCTTGTGAACGAATGCATGCACATCTTACTGCTGCGGTTGTTTCTAACGATGTTCATTTCTTACAGgttaatatac ... tggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcgactatcatattcccatgatttgaagttatcgttgctgaattggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG
       tatcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaataagtagataataaattctctgttgtaactactcaaaatttactcgactatcatattcccatgatttgaagttatcgttgctgaattggtttacagGAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgaa