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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgttacgaaatttaagctctggttagatgccgttttttttgttaaaaaagtcctgtagggaattctgatcatcatcaatacatgtacttgtcattgtagGCAGCAGCAGCTAAGGAACTTGCAGCGAAAGGTATTGCAGACCTTCAGCATACTGTAACGGATGCAGTGCAGGTGGTGGATGATGAGGAGGTGGATGCTC

Basic information

species Physcomitrella patens
transcript PP1S480_2V6.1
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|162182457|gb|FC358056.1|FC358056
EST:     ACGAGATCCAGCAGGCAGCGGCCGAGGCTGCTGAAGAGATTCAGAGAAAT                         GCAGCAGCAGCTAAGGAACTTGCAGCGAAAGGTATTGCAGACCTTCAGCAT
genomic: ACGAGATCCAGCAGGCAGCGGCCGAGGCTGCTGAAGAGATTCAGAGAAATgtgagtgaga ... gtcattgtagGCAGCAGCAGCTAAGGAACTTGCAGCGAAAGGTATTGCAGACCTTCAGCAT
EST: gi|162265245|gb|FC440168.1|FC440168
EST:     ACGAGATCCAGCAGGCAGCGGCCGAGGCTGCTGAAGAGATTCAGAGAAAT                         GCAGCAGCAGCTAAGGAACTTGCAGCGAAAGGTATTGCAGACCTTCAGCAT
genomic: ACGAGATCCAGCAGGCAGCGGCCGAGGCTGCTGAAGAGATTCAGAGAAATgtgagtgaga ... gtcattgtagGCAGCAGCAGCTAAGGAACTTGCAGCGAAAGGTATTGCAGACCTTCAGCAT
EST: gi|100417890|gb|BY993235.1|BY993235
EST:     ACGAGATCCAGCAGGCAGCGGCCGAGGCTGCTGAAGAGATTCAGAGAAAT                         GCAGCCGCAGCTAAGGAACTTGCAGCGAAAGGTATTGCAGACCTTCAGCAT
genomic: ACGAGATCCAGCAGGCAGCGGCCGAGGCTGCTGAAGAGATTCAGAGAAATgtgagtgaga ... gtcattgtagGCAGCAGCAGCTAAGGAACTTGCAGCGAAAGGTATTGCAGACCTTCAGCAT
EST: gi|162186993|gb|FC363399.1|FC363399
EST:     ACGAGATCCAGCAGGCAGCGGCCGAGGCTGCTGAAGAGATTCAGAGAAAT                         GCAGCAGCAGCTAAGGAACTTGCAGCGAAAGGTATTGCAGACCTTCAGCAT
genomic: ACGAGATCCAGCAGGCAGCGGCCGAGGCTGCTGAAGAGATTCAGAGAAATgtgagtgaga ... gtcattgtagGCAGCAGCAGCTAAGGAACTTGCAGCGAAAGGTATTGCAGACCTTCAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaagtcctgtagggaattctgatcatcatcaatacatgtacttgtcattgtagGCAGCAGCAGCTAAGGAACTTGCAGCGAAAGGTATTGCAGACCTTCAGCATACTGTAACGGATGCAGTGCAGGTGGTGGATGATGAGGAGGTGGATGCTC
                  ttctgat  putative branch site (score: 3)
                             atcaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgttacgaaatttaagctctggttagatgccgttttttttgttaaaaaagtcctgtagggaattctgatcatcatcaatacatgtacttgtcattgtagGCAGCAGCAGCTAAGGAACTTGCAGCGAAAGGTATTGCAGACCTTCAGCATACTGTAACGGATGCAGTGCAGGTGGTGGATGATGAGGAGGTGGATGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA