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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaccgttgcaagagattatattttgaaaagaaaaaaaaaaaacaattgtattttggtcttcaaggattaaattctatgttgggcatgaactcagatagTCAAGTTAGATGCTGTGATGAAGGCTCGCCAAGCCAAGGAGCTCGCTTCTATGGGTTTTCAAGGTGATGAAAAGGAGCAGGTTGCCAGTATAGACACTTT

Basic information

species Physcomitrella patens
transcript PP1S83_64V6.3
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|67577807|gb|BJ949974.1|BJ949974
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGATAG                      
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGAT--G--AGgtgagaagct ... actcaga
EST: gi|18344622|gb|BJ176663.1|BJ176663
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAG                         A
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGgtgagaagct ... actcagatag-
EST: gi|18344622|gb|BJ176663.1|BJ176663
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAG                         A
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGgtgagaagct ... actcagatag-
EST: gi|100438950|gb|BY961885.1|BY961885
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAG                         A
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGgtgagaagct ... actcagatag-
EST: gi|100438950|gb|BY961885.1|BY961885
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAG                         A
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGgtgagaagct ... actcagatag-
EST: gi|18356009|gb|BJ188068.1|BJ188068
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGATAG                      
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGAT--G--AGgtgagaagct ... actcaga
EST: gi|208346768|gb|DC913049.1|DC913049
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGATAG                      
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGAT--G--AGgtgagaagct ... actcaga
EST: gi|67573188|gb|BJ946012.1|BJ946012
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGATAG                      
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGAT--G--AGgtgagaagct ... actcaga
EST: gi|100383938|gb|BY987195.1|BY987195
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGATAG                      
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGAT--G--AGgtgagaagct ... actcaga
EST: gi|208380477|gb|DC914901.1|DC914901
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGATAG                      
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGAT--G--AGgtgagaagct ... actcaga
EST: gi|208353947|gb|DC930101.1|DC930101
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGATAG                      
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGAT--G--AGgtgagaagct ... actcaga
EST: gi|100411537|gb|BY974685.1|BY974685
EST:     AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGATGAGATAG                      
genomic: AAGGTAGCAAGGCCGAGCAAAAGGCCAAGAAGAAAGCTGCCGAAGAT--G--AGgtgagaagct ... actcaga


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgtattttggtcttcaaggattaaattctatgttgggcatgaactcagatagTCAAGTTAGATGCTGTGATGAAGGCTCGCCAAGCCAAGGAGCTCGCTTCTATGGGTTTTCAAGGTGATGAAAAGGAGCAGGTTGCCAGTATAGACACTTT
                      attaaattctatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaccgttgcaagagattatattttgaaaagaaaaaaaaaaaacaattgtattttggtcttcaaggattaaattctatgttgggcatgaactcagatagTCAAGTTAGATGCTGTGATGAAGGCTCGCCAAGCCAAGGAGCTCGCTTCTATGGGTTTTCAAGGTGATGAAAAGGAGCAGGTTGCCAGTATAGACACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG