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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctcttaaaacctagtggcaattaatggctttccttgccgggcagtgcctttacagtccatcaaacctacctttaattgattgcagcgtttcatgcagACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGCAGCGGACGCTTTGATGGATCTGGAGCGGCTGGCGCCAGGTGCTTGTGAAG

Basic information

species Physcomitrella patens
transcript PP1S59_173V6.1
intron # 16
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|37832630|gb|BJ590642.1|BJ590642
EST:     CTCTTAAAGAG                         ACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGCA
genomic: CTCTTAAAGAGgtaactattt ... tttcatgcagACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGCA
EST: gi|100369515|gb|BY948129.1|BY948129
EST:     TGGTGCATCGGCTGCCTTGACCCNTTCT-CTAATACCTGCTCT-AAAGAG                         ACTGCAGCTGAGCAGTCGGAAGGGGCTGCTTTNAGAGCTGCAGCTGATGC
genomic: TGGTGCATCGGCTGCCTTGACCC-TTCTTCTAATACCTGCTCTTAAAGAGgtaactattt ... tttcatgcagACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGC
EST: gi|162266710|gb|FC442863.1|FC442863
EST:     CTGGTGCATCGGCTGCCTTGACCCTTCTTCTAATACCTGCTCTTAAAGAG                         ACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGCA
genomic: CTGGTGCATCGGCTGCCTTGACCCTTCTTCTAATACCTGCTCTTAAAGAGgtaactattt ... tttcatgcagACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGCA
EST: gi|162266709|gb|FC442862.1|FC442862
EST:     CTGGTGCATCGGCTGCCTTGACCCTTCTTCTAATACCTGCTCTTAAAGAG                         ACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGCA
genomic: CTGGTGCATCGGCTGCCTTGACCCTTCTTCTAATACCTGCTCTTAAAGAGgtaactattt ... tttcatgcagACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGCA
EST: gi|67720706|gb|BJ970965.1|BJ970965
EST:     CTGGTGCATCGGCTGCCTTGACCCTTCTTCTAATACCTGCTCTTAAAGAG                         ACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGCA
genomic: CTGGTGCATCGGCTGCCTTGACCCTTCTTCTAATACCTGCTCTTAAAGAGgtaactattt ... tttcatgcagACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgcctttacagtccatcaaacctacctttaattgattgcagcgtttcatgcagACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGCAGCGGACGCTTTGATGGATCTGGAGCGGCTGGCGCCAGGTGCTTGTGAAG
                               aattgat  putative branch site (score: 4)
                            tttaattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctcttaaaacctagtggcaattaatggctttccttgccgggcagtgcctttacagtccatcaaacctacctttaattgattgcagcgtttcatgcagACTGCAGCTGAGCAGTCGGAAGGGCCTGCTTTAAGAGCTGCAGCTGATGCAGCGGACGCTTTGATGGATCTGGAGCGGCTGGCGCCAGGTGCTTGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA