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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctcattgcgatcaagtgcaatcatcatgtgtgagaatgatgttccagctgatatggtttttgtggatttgatgattgatttctccgacggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGTCTCAAAACTCGAAAGTTTTGGCGGGAAAGGCTACTGCAACAGCTGTAGT

Basic information

species Physcomitrella patens
transcript PP1S99_42V6.2
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|100440899|gb|BY962387.1|BY962387
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
EST: gi|100379974|gb|BY968783.1|BY968783
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
EST: gi|162195534|gb|FC371835.1|FC371835
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
EST: gi|208386797|gb|DC937189.1|DC937189
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
EST: gi|162257183|gb|FC433059.1|FC433059
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
EST: gi|100437064|gb|BY961333.1|BY961333
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
EST: gi|100427559|gb|BY977558.1|BY977558
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
EST: gi|100386075|gb|BY970014.1|BY970014
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
EST: gi|162159901|gb|FC336154.1|FC336154
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
EST: gi|162227790|gb|FC402705.1|FC402705
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
EST: gi|67508225|gb|BJ941096.1|BJ941096
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
EST: gi|100440507|gb|BY962234.1|BY962234
EST:     TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTG                         TGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT
genomic: TGCTGGGATCCGCCGACGGGCGACTAAGGCGTCGGTTGCGTCCAGTCTTGgtatatcctg ... ggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagctgatatggtttttgtggatttgatgattgatttctccgacggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGTCTCAAAACTCGAAAGTTTTGGCGGGAAAGGCTACTGCAACAGCTGTAGT
                             gattgat  putative branch site (score: 4)
                              attgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggctcattgcgatcaagtgcaatcatcatgtgtgagaatgatgttccagctgatatggtttttgtggatttgatgattgatttctccgacggtggtgcagTGTCACGTTTTTATGGATTGCAATTAGCAGCTGAAGGGAAAGTTGTGAGGTCTCAAAACTCGAAAGTTTTGGCGGGAAAGGCTACTGCAACAGCTGTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG