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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacccatctttaccgcttccacagaacttgaaaagctttcaccttcagttcattttcctcatttgtgaaacagctttccagtgaagtcacttccgagttctgaaagcggactggaatatgccgatctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGCTTGACCAATAAAATCTACGAAAACACCAAGAAAATCACGGCATATCATA

Basic information

species Physcomitrella patens
transcript PP1S4_12V6.1
intron # 6
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|162178865|gb|FC354797.1|FC354797
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|162159187|gb|FC334358.1|FC334358
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|67571702|gb|BJ944526.1|BJ944526
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAAC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAAC
EST: gi|100375450|gb|BY948872.1|BY948872
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|67568839|gb|BJ941663.1|BJ941663
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|162175775|gb|FC352077.1|FC352077
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|18354475|gb|BJ186531.1|BJ186531
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCA
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCA
EST: gi|162198744|gb|FC374227.1|FC374227
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|18348776|gb|BJ180825.1|BJ180825
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|208351568|gb|DC909998.1|DC909998
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|162257953|gb|FC433839.1|FC433839
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|162185024|gb|FC362470.1|FC362470
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|67717090|gb|BJ967349.1|BJ967349
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|100437911|gb|BY961558.1|BY961558
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|18363906|gb|BJ195978.1|BJ195978
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|18368891|gb|BJ200976.1|BJ200976
EST:     CGGTGCATTCATTCTGACCGCCAGCCACAACCCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGG
genomic: CGGTGCATTCATTCTGACCGCCAGCCACAACCCC-GGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGG
EST: gi|67570443|gb|BJ943267.1|BJ943267
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|18347743|gb|BJ179790.1|BJ179790
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
EST: gi|162276463|gb|FC452466.1|FC452466
EST:     ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG                         GACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC
genomic: ACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAGgtaacccatc ... atctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgaagtcacttccgagttctgaaagcggactggaatatgccgatctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGCTTGACCAATAAAATCTACGAAAACACCAAGAAAATCACGGCATATCATA
                                    aatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacccatctttaccgcttccacagaacttgaaaagctttcaccttcagttcattttcctcatttgtgaaacagctttccagtgaagtcacttccgagttctgaaagcggactggaatatgccgatctgcgcagGACTTTGGAATCAAGTACAATTGTGAAAACGGAGGCCCAGCTCCTGAAAGCTTGACCAATAAAATCTACGAAAACACCAAGAAAATCACGGCATATCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA