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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttattgcattttacatgaactcaatggattgatcacatggtcccaacagtttgtgttctcttagcagtattgaatcatgctctgggcttatctgtagacgcggattttctgtgtccacagGGAAGTCATTACAGAGCTGAAGGAAGCTGGTGCGTCGTGGATCCAACTGGACGAGCCAAAGTTAGTCATGGACCTTGAAGCTAGCCAATACGAAGCTTTT

Basic information

species Physcomitrella patens
transcript PP1S399_19V6.4
intron # 4
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|208392400|gb|DC904246.1|DC904246
EST:     AAGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTTCCCGTGTACAA                         GGAAGTCATTACAGAGCTGAAGGAAGCTGGTGCGTCGTGGATC
genomic: AAGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTTCCCGTGTACAAgtaagttatt ... gtgtccacagGGAAGTCATTACAGAGCTGAAGGAAGCTGGTGCGTCGTGGATC
EST: gi|67573928|gb|BJ946752.1|BJ946752
EST:     AGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTTTCCCGTGTACAA                         GGAAGTCATTACAGAGCTGAAGGAAGCTGGTGCGTCGTGG
genomic: AGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTT-CCCGTGTACAAgtaagttatt ... gtgtccacagGGAAGTCATTACAGAGCTGAAGGAAGCTGGTGCGTCGTGG
EST: gi|18368205|gb|BJ200290.1|BJ200290
EST:     AAGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTTCCCGTGTACAA                         GGAAGTCATTACAGAGTTGAAGGAAGCTGGTGCGTCGTGGATCCA
genomic: AAGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTTCCCGTGTACAAgtaagttatt ... gtgtccacagGGAAGTCATTACAGAGCTGAAGGAAGCTGGTGCGTCGTGGATCCA
EST: gi|100448742|gb|CJ973041.1|CJ973041
EST:     AAGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTTCCCGTGTACNA                         GGAAGTCATTACAGAGCTGAAGGAAGCTGGTGCGTC
genomic: AAGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTTCCCGTGTACAAgtaagttatt ... gtgtccacagGGAAGTCATTACAGAGCTGAAGGAAGCTGGTGCGTC
EST: gi|208353920|gb|DC930088.1|DC930088
EST:     AAGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTTCCCGTGTACAA                         GGAAGTCATTACAGAGCTGAAGNAA-CTGGTGCGTCNTGGATCNA-CTGGA
genomic: AAGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTTCCCGTGTACAAgtaagttatt ... gtgtccacagGGAAGTCATTACAGAGCTGAAGGAAGCTGGTGCGTCGTGGATCCAACTGGA
EST: gi|100369024|gb|BY984986.1|BY984986
EST:     AAGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTTCCCGTGTACAA                         GGAAGTCATTACAGAGC
genomic: AAGGGTTTCAATACTCTTTCACTTCTTGATGCCATACTTCCCGTGTACAAgtaagttatt ... gtgtccacagGGAAGTCATTACAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtattgaatcatgctctgggcttatctgtagacgcggattttctgtgtccacagGGAAGTCATTACAGAGCTGAAGGAAGCTGGTGCGTCGTGGATCCAACTGGACGAGCCAAAGTTAGTCATGGACCTTGAAGCTAGCCAATACGAAGCTTTT
                                       ttttctgt  CT-rich tract
                                      attttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttattgcattttacatgaactcaatggattgatcacatggtcccaacagtttgtgttctcttagcagtattgaatcatgctctgggcttatctgtagacgcggattttctgtgtccacagGGAAGTCATTACAGAGCTGAAGGAAGCTGGTGCGTCGTGGATCCAACTGGACGAGCCAAAGTTAGTCATGGACCTTGAAGCTAGCCAATACGAAGCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC