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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgccttatttggatgatatatcagtattgtagaacgcgttgcgtgtaatccaaacttccagtttctgattctagcttgaattttggtgttatttgcagAATGATGGTCTGGTTAAGATAGTTGTGGGGAAGACTGTCGAGAAGATCGTGATGGATGACACGAAGGATGTTTTTCTTTTT

Basic information

species Physcomitrella patens
transcript PP1S77_54V6.1
intron # 9
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|162180317|gb|FC355322.1|FC355322
EST:     AGAAAGCTTCCTCTATACTATAAGTCTGATCCTGTTCCTGCTCAG                         AATGATGGTCTGGTTAAGATAGTTGTGGGGAAGACTGTCGAGAAGATCGTG
genomic: AGAAAGCTTCCTCTATACTATAAGTCTGATCCTGTTCCTGCTCAGgtgcatcttg ... ttatttgcagAATGATGGTCTGGTTAAGATAGTTGTGGGGAAGACTGTCGAGAAGATCGTG
EST: gi|67726315|gb|BJ976574.1|BJ976574
EST:     ACGCTAGAAAGCTTCCTCTATACTATAAGTCTGATCCTGTTCCTGCTCAG                         AATGATGGTCTGGTTAAGATAGTTGTGGGGAAGACTGTCGAGAAGATCGTG
genomic: ACGCTAGAAAGCTTCCTCTATACTATAAGTCTGATCCTGTTCCTGCTCAGgtgcatcttg ... ttatttgcagAATGATGGTCTGGTTAAGATAGTTGTGGGGAAGACTGTCGAGAAGATCGTG
EST: gi|162256397|gb|FC432407.1|FC432407
EST:     ACGCTAGAAAGCTTCCTCTATACTATAAGTCTGATCCTGTTCCTGCTCAG                         AATGATGGTCTGGTTAAGATAGTTGTGGGGAAGACTGTCGAGAAGATCGTG
genomic: ACGCTAGAAAGCTTCCTCTATACTATAAGTCTGATCCTGTTCCTGCTCAGgtgcatcttg ... ttatttgcagAATGATGGTCTGGTTAAGATAGTTGTGGGGAAGACTGTCGAGAAGATCGTG
EST: gi|162256398|gb|FC432408.1|FC432408
EST:     ACGCTAGAAAGCTTCCTCTATACTATAAGTCTGATCCTGTTCCTGCTCAG                         AATGATGGTCT
genomic: ACGCTAGAAAGCTTCCTCTATACTATAAGTCTGATCCTGTTCCTGCTCAGgtgcatcttg ... ttatttgcagAATGATGGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaatccaaacttccagtttctgattctagcttgaattttggtgttatttgcagAATGATGGTCTGGTTAAGATAGTTGTGGGGAAGACTGTCGAGAAGATCGTGATGGATGACACGAAGGATGTTTTTCTTTTT
                   ttctgat  putative branch site (score: 3)
                                ttgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgccttatttggatgatatatcagtattgtagaacgcgttgcgtgtaatccaaacttccagtttctgattctagcttgaattttggtgttatttgcagAATGATGGTCTGGTTAAGATAGTTGTGGGGAAGACTGTCGAGAAGATCGTGATGGATGACACGAAGGATGTTTTTCTTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG