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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatctatttggattttttatttcagtttttttcaacaaattatagttgctgtttggatagtgctagttcatctgttctgtgattgcgtaaaaatagtactgaagtctctaacatgttggtcattcctgctgtatacagAATCGCAATTCAGTGCCAAACCTCGTTTCTAAAGTGAAGCCAGCGGTCAACAGATCTGTTAGTCCAG

Basic information

species Physcomitrella patens
transcript PP1S28_184V6.2
intron # 12
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|162256738|gb|FC432632.1|FC432632
EST:     CTATCAGGACTAAGGAG                         AATCGCAATTCAGTGCCAAACCTCGTTTCTAAAGTGAAGCCAGCGGTCAAC
genomic: CTATCAGGACTAAGGAGgtacgtatct ... ctgtatacagAATCGCAATTCAGTGCCAAACCTCGTTTCTAAAGTGAAGCCAGCGGTCAAC
EST: gi|208398246|gb|DC912287.1|DC912287
EST:     GACATAAGCGCGGTAATACTATCAGGACTAAGGAG                         AATCGCAATTCAGTGCCAAACCTCGTTTCTAAAGTGAAGCCAGCGGTCAAC
genomic: GACATAAGCGCGGTAATACTATCAGGACTAAGGAGgtacgtatct ... ctgtatacagAATCGCAATTCAGTGCCAAACCTCGTTTCTAAAGTGAAGCCAGCGGTCAAC
EST: gi|100445020|gb|BY964319.1|BY964319
EST:     GACATAAGCGCGGTAATACTATCAGGACTAAGGAG                         AATCGCAATTCAGTGCCAAACCTCGTTTCTAAAGTGAA
genomic: GACATAAGCGCGGTAATACTATCAGGACTAAGGAGgtacgtatct ... ctgtatacagAATCGCAATTCAGTGCCAAACCTCGTTTCTAAAGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgtaaaaatagtactgaagtctctaacatgttggtcattcctgctgtatacagAATCGCAATTCAGTGCCAAACCTCGTTTCTAAAGTGAAGCCAGCGGTCAACAGATCTGTTAGTCCAG
                      ctctaac  putative branch site (score: 2)
                                       ttcctgct  putative PPT
     aaaaatagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtatctatttggattttttatttcagtttttttcaacaaattatagttgctgtttggatagtgctagttcatctgttctgtgattgcgtaaaaatagtactgaagtctctaacatgttggtcattcctgctgtatacagAATCGCAATTCAGTGCCAAACCTCGTTTCTAAAGTGAAGCCAGCGGTCAACAGATCTGTTAGTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC