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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaccgtatatttgatgacttaatgttaagtgtttttcgttcactgacggtgaatcatcacttgacagtctttctcctacgctgattaaaaaaagtattacttcatggaattgtttcgttgcagtttactgacatgtatgagattgtttgtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGATTGGCTGCAGTTCACAAGAGCTTGCGTGTGGCTAAGGCTGGTGTCAGCA

Basic information

species Physcomitrella patens
transcript PP1S98_65V6.2
intron # 3
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|162223113|gb|FC399692.1|FC399692
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162209250|gb|FC385170.1|FC385170
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162266208|gb|FC441737.1|FC441737
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162273849|gb|FC449780.1|FC449780
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162219281|gb|FC395277.1|FC395277
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162266846|gb|FC441738.1|FC441738
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|18331139|gb|BJ163146.1|BJ163146
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162276138|gb|FC452830.1|FC452830
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|19785084|gb|BQ040267.1|BQ040267
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162274650|gb|FC450456.1|FC450456
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|67574153|gb|BJ946977.1|BJ946977
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162276139|gb|FC452831.1|FC452831
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|37823910|gb|BJ581976.1|BJ581976
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162262080|gb|FC436861.1|FC436861
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162223112|gb|FC399691.1|FC399691
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162277981|gb|FC454112.1|FC454112
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|18340983|gb|BJ173015.1|BJ173015
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162251344|gb|FC425516.1|FC425516
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
EST: gi|162219282|gb|FC395278.1|FC395278
EST:     CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAG                         GTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA
genomic: CCCTCTTGAAGAAGGATTTTCGCAAAATGGCTAAGACTGTAGTCAACCAGgtaataaccg ... gtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggaattgtttcgttgcagtttactgacatgtatgagattgtttgtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGATTGGCTGCAGTTCACAAGAGCTTGCGTGTGGCTAAGGCTGGTGTCAGCA
                      tactgac  putative branch site (score: 1)
     attgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataaccgtatatttgatgacttaatgttaagtgtttttcgttcactgacggtgaatcatcacttgacagtctttctcctacgctgattaaaaaaagtattacttcatggaattgtttcgttgcagtttactgacatgtatgagattgtttgtgggtctagGTCGCCACCAATGATTACAGGGCCGATTTGAAGTCTGCCGCTTTGGCCAGATTGGCTGCAGTTCACAAGAGCTTGCGTGTGGCTAAGGCTGGTGTCAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT