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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgttgccaatcctgtctactagaataatcgacagacggtaattgtcaccaattgtatgtctgtttgcggcctctggtgttcattattcgattgatcggtgcagGTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTGACCTCTTCAAGAAAGCCAAAGAGAATGCTCCTTGCATTGTCTTTGTGGA

Basic information

species Physcomitrella patens
transcript PP1S9_115V6.1
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|162276900|gb|FC452582.1|FC452582
EST:     GGCTAAGGCCATCGCCGGAGAGGCGGGAGTTCCGTTCTTCTCAATTTCAG                         GTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTG
genomic: GGCTAAGGCCATCGCCGGAGAGGCGGGAGTTCCGTTCTTCTCAATTTCAGgtccgttgcc ... atcggtgcagGTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTG
EST: gi|162268414|gb|FC444183.1|FC444183
EST:     GGCTAAGGCCATCGCCGGAGAGGCGGGAGTTCCGTTCTTCTCAATTTCAG                         GTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTG
genomic: GGCTAAGGCCATCGCCGGAGAGGCGGGAGTTCCGTTCTTCTCAATTTCAGgtccgttgcc ... atcggtgcagGTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTG
EST: gi|162273611|gb|FC449340.1|FC449340
EST:     GGCTAAGGCCATCGCCGGAGAGGCGGGAGTTCCGTTCTTCTCAATTTCAG                         GTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTG
genomic: GGCTAAGGCCATCGCCGGAGAGGCGGGAGTTCCGTTCTTCTCAATTTCAGgtccgttgcc ... atcggtgcagGTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTG
EST: gi|162199339|gb|FC374018.1|FC374018
EST:     GGCTAAGGCCATCGCCGGAGAGGCGGGAGTTCCGTTCTTCTCAATTTCAG                         GTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTG
genomic: GGCTAAGGCCATCGCCGGAGAGGCGGGAGTTCCGTTCTTCTCAATTTCAGgtccgttgcc ... atcggtgcagGTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTG
EST: gi|162194020|gb|FC370195.1|FC370195
EST:     GGCTAAGGCCATCGCCGGAGAGGCGGGAGTTCCGTTCTTCTCAATTTCAG                         GTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTG
genomic: GGCTAAGGCCATCGCCGGAGAGGCGGGAGTTCCGTTCTTCTCAATTTCAGgtccgttgcc ... atcggtgcagGTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattgtatgtctgtttgcggcctctggtgttcattattcgattgatcggtgcagGTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTGACCTCTTCAAGAAAGCCAAAGAGAATGCTCCTTGCATTGTCTTTGTGGA
                                        gattgat  putative branch site (score: 4)
                              ttcattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgttgccaatcctgtctactagaataatcgacagacggtaattgtcaccaattgtatgtctgtttgcggcctctggtgttcattattcgattgatcggtgcagGTTCTGAATTCGTTGAGATGTTCGTGGGAGTTGGTGCATCACGAGTGCGTGACCTCTTCAAGAAAGCCAAAGAGAATGCTCCTTGCATTGTCTTTGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA