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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggatgtgtctatgagtacaagcggcatattataatgttcttttgatgatgttgtatataaacatcagttctgattttgcaacgtccttgctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCAATGAAGGG

Basic information

species Physcomitrella patens
transcript PP1S180_67V6.1
intron # 6
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|162254586|gb|FC429436.1|FC429436
EST:     ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAG                         ATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
genomic: ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctatttt ... ctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
EST: gi|208393130|gb|DC929625.1|DC929625
EST:     ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAG                         ATTTGCAGGGATAAA-CTGCAGTACCCCAGGTT-GGGA
genomic: ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctatttt ... ctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGA
EST: gi|208365735|gb|DC944163.1|DC944163
EST:     ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAG                         ATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
genomic: ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctatttt ... ctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
EST: gi|162220966|gb|FC396151.1|FC396151
EST:     ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAG                         ATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
genomic: ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctatttt ... ctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
EST: gi|67698972|gb|BJ959205.1|BJ959205
EST:     ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAG                         ATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
genomic: ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctatttt ... ctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
EST: gi|18340553|gb|BJ172581.1|BJ172581
EST:     ATTATGGCNTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAG                         ATTTGCAGGGATAAAACTGCAGTACCCCAGGTTAGGGAGGATGTCCCACCA
genomic: ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctatttt ... ctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
EST: gi|208364966|gb|DC947108.1|DC947108
EST:     ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAG                         ATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
genomic: ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctatttt ... ctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
EST: gi|162220965|gb|FC396150.1|FC396150
EST:     ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAG                         ATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
genomic: ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctatttt ... ctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
EST: gi|100417046|gb|BY993217.1|BY993217
EST:     ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAG                         ATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
genomic: ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctatttt ... ctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
EST: gi|37821493|gb|BJ579559.1|BJ579559
EST:     ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAG                         ATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
genomic: ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctatttt ... ctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA
EST: gi|18340752|gb|BJ172783.1|BJ172783
EST:     ATTATGGCNTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAG                         ATTTGCAGGGATAAAACTGCAGTACCCCAGGTTAGGGAGGATGTCCCACCA
genomic: ATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctatttt ... ctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatgttgtatataaacatcagttctgattttgcaacgtccttgctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCAATGAAGGG
                       ttctgat  putative branch site (score: 3)
                                       tccttgct  putative PPT
      ttgtatataaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggatgtgtctatgagtacaagcggcatattataatgttcttttgatgatgttgtatataaacatcagttctgattttgcaacgtccttgctgttaacagATTTGCAGGGATAAAACTGCAGTACCCCAGGTTTGGGAGGATGTCCCACCAATGAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG