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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttagatcttgtgctcgtcacgtaggaaaggctgttactgctgataacgaacttcaggtgtaaaccacgaattcctaacactttgtttgtgtaatgcagTGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCTCGGAGTGCTACATGCTGGACGTGGATAATCATTTTTATGACTTT

Basic information

species Physcomitrella patens
transcript PP1S83_251V6.1
intron # 2
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|100390663|gb|BY971418.1|BY971418
EST:     GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAG                         TGCTTGTATTTTCATTTTGC-TGTCATGCGACGTTATCTCTAAGCCCGCGC
genomic: GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAGgttagtgata ... tgtaatgcagTGCTTGTATTTTCATTT-GCCTGTCATGCGACGTTATCTCTAAGCCCGCGC
EST: gi|18354190|gb|BJ186246.1|BJ186246
EST:     GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAG                         TGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT
genomic: GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAGgttagtgata ... tgtaatgcagTGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT
EST: gi|208357963|gb|DC938834.1|DC938834
EST:     GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAG                         TGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT
genomic: GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAGgttagtgata ... tgtaatgcagTGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT
EST: gi|18354741|gb|BJ186799.1|BJ186799
EST:     GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAG                         TGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT
genomic: GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAGgttagtgata ... tgtaatgcagTGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT
EST: gi|18351529|gb|BJ183581.1|BJ183581
EST:     GTTTGCGATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAG                         TGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT
genomic: GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAGgttagtgata ... tgtaatgcagTGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT
EST: gi|67717787|gb|BJ968046.1|BJ968046
EST:     GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAG                         TGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT
genomic: GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAGgttagtgata ... tgtaatgcagTGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT
EST: gi|18356642|gb|BJ188701.1|BJ188701
EST:     GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAG                         TGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT
genomic: GTTTGCAATGGTGGGGAATAGATTCCAGCCATGCAGGCTACTCCTTGCAGgttagtgata ... tgtaatgcagTGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacgaacttcaggtgtaaaccacgaattcctaacactttgtttgtgtaatgcagTGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCTCGGAGTGCTACATGCTGGACGTGGATAATCATTTTTATGACTTT
                            tcctaac  putative branch site (score: 1)
                                     tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttagatcttgtgctcgtcacgtaggaaaggctgttactgctgataacgaacttcaggtgtaaaccacgaattcctaacactttgtttgtgtaatgcagTGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCTCGGAGTGCTACATGCTGGACGTGGATAATCATTTTTATGACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA