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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcatgtggcataaagtgtcagtaaaagtaccagcatgtagtaagagtaagagatgactaaatttgcccgcagctcaagttggacgatggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACTACGGCCTGGACTTGTTTTTACTATCGATTGATGAAGGTATTGCTGGATA

Basic information

species Physcomitrella patens
transcript PP1S54_267V6.1
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|100385871|gb|BY951065.1|BY951065
EST:     ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAG                         ATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
genomic: ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAGgtgagtctga ... ggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
EST: gi|100385874|gb|BY951068.1|BY951068
EST:     ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAG                         ATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
genomic: ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAGgtgagtctga ... ggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
EST: gi|100425875|gb|BY977164.1|BY977164
EST:     ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAG                         ATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
genomic: ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAGgtgagtctga ... ggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
EST: gi|208386768|gb|DC937160.1|DC937160
EST:     ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAG                         ATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
genomic: ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAGgtgagtctga ... ggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
EST: gi|100379791|gb|BY949946.1|BY949946
EST:     ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAG                         ATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
genomic: ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAGgtgagtctga ... ggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
EST: gi|18342250|gb|BJ174285.1|BJ174285
EST:     ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAG                         ATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
genomic: ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAGgtgagtctga ... ggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
EST: gi|162160669|gb|FC337205.1|FC337205
EST:     ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAG                         ATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
genomic: ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAGgtgagtctga ... ggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
EST: gi|208354247|gb|DC957439.1|DC957439
EST:     TGCTGTCGCTGCTTCTGGTGGTAAAG                         ATTCANCAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
genomic: TGCTGTCGCTGCTTCTGGTGGTAAAGgtgagtctga ... ggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
EST: gi|208358391|gb|DC943222.1|DC943222
EST:     ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAG                         ATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT
genomic: ACTTTTTAATCGGGGTGACCGCGTTGCTGTCGCTGCTTCTGGTGGTAAAGgtgagtctga ... ggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagtaagagatgactaaatttgcccgcagctcaagttggacgatggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACTACGGCCTGGACTTGTTTTTACTATCGATTGATGAAGGTATTGCTGGATA
            gactaaa  putative branch site (score: 2)
             actaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcatgtggcataaagtgtcagtaaaagtaccagcatgtagtaagagtaagagatgactaaatttgcccgcagctcaagttggacgatggacttgcagATTCAACAGTGTTAGCACATGTTTTAACATTACTGAATAAGAGACACGACTACGGCCTGGACTTGTTTTTACTATCGATTGATGAAGGTATTGCTGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA