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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttatctaaccataccatgaaatttcttccaaatgcactctttaaaactgctgaaaatgatttgcgtgtcattagcgaaggttttttgaggtgtgaaatctgatcaatcgtcccatcacgtagccacaatctaaaacctgaaaacatttttcatttgaattcctgtagGTTATATGGTTGCGAGGACACTAGCTGCAGCACCCCTGTTGGCAGAGTCTGTTATAAAGAGCTTGGGGGGTTCCACAAGCACCCATGTTTCCAGTAGACC

Basic information

species Physcomitrella patens
transcript PP1S55_202V6.1
intron # 6
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|162149863|gb|FC326186.1|FC326186
EST:     AAGAGTGCTTGGTATTGGTGGAACCGCANGCATGGGTCATCCATCAACTG                         GTTATATGGGTGCGAGGACACTAGCTG
genomic: AAGAGTGCTTGGTATTGGTGGAACCGCAGGCATGGTTCATCCATCAACTGgtactttatc ... attcctgtagGTTATATGGTTGCGAGGACACTAGCTG
EST: gi|162193792|gb|FC368706.1|FC368706
EST:     AAGAGTGCTTGGTATTGGTGGAACCGCAGGCATGGTTCATCCATCAACTG                         GTTATATGGTTGCGAGGACACTAGCTGCAGCACCCCTGTTGGCAGAGTCTG
genomic: AAGAGTGCTTGGTATTGGTGGAACCGCAGGCATGGTTCATCCATCAACTGgtactttatc ... attcctgtagGTTATATGGTTGCGAGGACACTAGCTGCAGCACCCCTGTTGGCAGAGTCTG
EST: gi|162158482|gb|FC334485.1|FC334485
EST:     AAGAGTGCTTGGTATTGGTGGAACCGCAGGCATGGTTCATCCATCAACTG                         GTTATATGGTTGCGAGGACACTAGCTGCAGCACCCCTGTTGGCAGAGTCTG
genomic: AAGAGTGCTTGGTATTGGTGGAACCGCAGGCATGGTTCATCCATCAACTGgtactttatc ... attcctgtagGTTATATGGTTGCGAGGACACTAGCTGCAGCACCCCTGTTGGCAGAGTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcacgtagccacaatctaaaacctgaaaacatttttcatttgaattcctgtagGTTATATGGTTGCGAGGACACTAGCTGCAGCACCCCTGTTGGCAGAGTCTGTTATAAAGAGCTTGGGGGGTTCCACAAGCACCCATGTTTCCAGTAGACC
               atctaaa  putative branch site (score: 3)
                                              ttcctgt  putative PPT
                           aaaacatttttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttatctaaccataccatgaaatttcttccaaatgcactctttaaaactgctgaaaatgatttgcgtgtcattagcgaaggttttttgaggtgtgaaatctgatcaatcgtcccatcacgtagccacaatctaaaacctgaaaacatttttcatttgaattcctgtagGTTATATGGTTGCGAGGACACTAGCTGCAGCACCCCTGTTGGCAGAGTCTGTTATAAAGAGCTTGGGGGGTTCCACAAGCACCCATGTTTCCAGTAGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT