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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatcatgtggtttcagtttagagtaacttcaactcatcatcttattgatgtgaacgctgcatcgtgcttatgtactctctggattttccatgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTTCGAGAAGGCGTACTCCATCAAAGGAGGCGTAGAAGGCCCCAAAGGATGG

Basic information

species Physcomitrella patens
transcript PP1S94_133V6.1
intron # 1
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|100404235|gb|BY955323.1|BY955323
EST:     TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCA                         ATTGGACGAAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCT
genomic: TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCT
EST: gi|208361962|gb|DC943445.1|DC943445
EST:     TTTGCCAAATACCGCGACGCCNAGAATACCACTGTCTACATTTTGGACCA                         ATTGGACGGAAATTCTCTTGCAGTTGCAAA
genomic: TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAA
EST: gi|67725469|gb|BJ975728.1|BJ975728
EST:     TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCA                         ATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
genomic: TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
EST: gi|100378304|gb|BY949784.1|BY949784
EST:     TTTGCCNAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCA                         -TTGNACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCNTAACA-TGGCT
genomic: TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGC-TAACAATGGCT
EST: gi|162217774|gb|FC394074.1|FC394074
EST:     TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCA                         ATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
genomic: TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
EST: gi|162170350|gb|FC346547.1|FC346547
EST:     TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCA                         ATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
genomic: TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
EST: gi|208397428|gb|DC916354.1|DC916354
EST:     TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCA                         ATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
genomic: TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
EST: gi|162233171|gb|FC408994.1|FC408994
EST:     GCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCA                         ATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
genomic: GCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
EST: gi|208388411|gb|DC945631.1|DC945631
EST:     TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCA                         ATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
genomic: TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
EST: gi|208368324|gb|DC955521.1|DC955521
EST:     TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCA                         ATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
genomic: TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
EST: gi|18338002|gb|BJ170026.1|BJ170026
EST:     TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCA                         ATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
genomic: TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
EST: gi|208350444|gb|DC926191.1|DC926191
EST:     TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCA                         ATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT
genomic: TTTGCCAAATACCGCGACGCCGAGAATACCACTGTCTACATTTTGGACCAgtaagtgctt ... atgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgtgaacgctgcatcgtgcttatgtactctctggattttccatgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTTCGAGAAGGCGTACTCCATCAAAGGAGGCGTAGAAGGCCCCAAAGGATGG
 tattgat  putative branch site (score: 3)
                                       ttttccat  putative PPT
                       ttatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatcatgtggtttcagtttagagtaacttcaactcatcatcttattgatgtgaacgctgcatcgtgcttatgtactctctggattttccatgggcatagATTGGACGGAAATTCTCTTGCAGTTGCAAAGATTCTCGCTAACAATGGCTTCGAGAAGGCGTACTCCATCAAAGGAGGCGTAGAAGGCCCCAAAGGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cgctgca