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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctacttgcgcatgctcatcgctctgtggtttttccaagcgtgcgaaaagtgtcttttaagctctttttgctgtgctggtgttcgtttagagaaatgttggggttacttgggaagtgtgatgagatgtgaagcacatcgcttgactgcttcttcccctgagtttggcgttgttgctgtgctgtggcgtttttgtagATTGATTTCTGTGGCCAATTGGAGCGGTTTTGGCGAAGTTTGTGGGAGGTTTTTCTTGTGTAATT

Basic information

species Physcomitrella patens
transcript PP1S99_229V6.1
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|18346675|gb|BJ178720.1|BJ178720
EST:     GCTTTCCTTGTCAGCACCTATCAGCAGCACATTCTATGCAGAG                         ATTGATTTCTGTGGCCAATTGGAGCGGTTTTGGCGAAGTTTGTGGGAGGTT
genomic: GCTTTCCTTGTCAGCACCTATCAGCAGCACATTCTATGCAGAGgtgagctact ... gtttttgtagATTGATTTCTGTGGCCAATTGGAGCGGTTTTGGCGAAGTTTGTGGGAGGTT
EST: gi|208394362|gb|DC904182.1|DC904182
EST:     CTATCAGCAGCACATTCTATGCAGAG                         ATTGATTTCTGTGGCCAATTGGAGCGGTTTTGGCGAAGTTTGTGGGAGGTT
genomic: CTATCAGCAGCACATTCTATGCAGAGgtgagctact ... gtttttgtagATTGATTTCTGTGGCCAATTGGAGCGGTTTTGGCGAAGTTTGTGGGAGGTT
EST: gi|100422429|gb|BY976369.1|BY976369
EST:     ATCAGCAGCACATTCTATGCAGAG                         ATTGATTTCTGTGGCCAATTGGAGCGGTTTTGGCGAAGTTTGTGGGAGGTT
genomic: ATCAGCAGCACATTCTATGCAGAGgtgagctact ... gtttttgtagATTGATTTCTGTGGCCAATTGGAGCGGTTTTGGCGAAGTTTGTGGGAGGTT
EST: gi|100411668|gb|BY992279.1|BY992279
EST:     ATCAGCAGCACATTCTATGCAGAG                         ATTGATTTCTGTGGCCAATTGGAGCGGTTTTGGCGAAGTTTGTGGGAGGTT
genomic: ATCAGCAGCACATTCTATGCAGAGgtgagctact ... gtttttgtagATTGATTTCTGTGGCCAATTGGAGCGGTTTTGGCGAAGTTTGTGGGAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactgcttcttcccctgagtttggcgttgttgctgtgctgtggcgtttttgtagATTGATTTCTGTGGCCAATTGGAGCGGTTTTGGCGAAGTTTGTGGGAGGTTTTTCTTGTGTAATT
 gcttgac  putative branch site (score: 4)
                                            cgttttt  putative PPT
                                              tttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctacttgcgcatgctcatcgctctgtggtttttccaagcgtgcgaaaagtgtcttttaagctctttttgctgtgctggtgttcgtttagagaaatgttggggttacttgggaagtgtgatgagatgtgaagcacatcgcttgactgcttcttcccctgagtttggcgttgttgctgtgctgtggcgtttttgtagATTGATTTCTGTGGCCAATTGGAGCGGTTTTGGCGAAGTTTGTGGGAGGTTTTTCTTGTGTAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG