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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attctgacttggcgtgcttcatagaatggtcggcctcgaaaacaattgatttaaacacgagtttaagcaactctaatttccgtgttttcttttataccagGTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATGCTTACTCCATCAATTGCGGGTGCACTCATGGGTATAAGCTCTTTGGGTG

Basic information

species Physcomitrella patens
transcript PP1S19_275V6.1
intron # 17
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|18338648|gb|BJ170672.1|BJ170672
EST:     CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATT                         GTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
genomic: CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATTgtaagtcaat ... tttataccagGTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
EST: gi|162195237|gb|FC370810.1|FC370810
EST:     CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATT                         GTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
genomic: CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATTgtaagtcaat ... tttataccagGTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
EST: gi|162195238|gb|FC370811.1|FC370811
EST:     CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATT                         GTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
genomic: CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATTgtaagtcaat ... tttataccagGTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
EST: gi|37837888|gb|BJ595896.1|BJ595896
EST:     CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATT                         GTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
genomic: CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATTgtaagtcaat ... tttataccagGTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
EST: gi|37846733|gb|BJ604741.1|BJ604741
EST:     CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATT                         GTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
genomic: CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATTgtaagtcaat ... tttataccagGTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
EST: gi|37848987|gb|BJ606995.1|BJ606995
EST:     GCATTCATATACAACATT                         GTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
genomic: GCATTCATATACAACATTgtaagtcaat ... tttataccagGTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
EST: gi|162161864|gb|FC337953.1|FC337953
EST:     CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATT                         GTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
genomic: CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATTgtaagtcaat ... tttataccagGTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
EST: gi|162173383|gb|FC349554.1|FC349554
EST:     CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATT                         GTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG
genomic: CGCTTAAGAAAATCAAGCAGAATCTTTGGTGGGCATTCATATACAACATTgtaagtcaat ... tttataccagGTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatttaaacacgagtttaagcaactctaatttccgtgttttcttttataccagGTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATGCTTACTCCATCAATTGCGGGTGCACTCATGGGTATAAGCTCTTTGGGTG
                         ctctaat  putative branch site (score: 3)
                               tttccgtgttttcttt  CT-rich tract
                                     tgttttcttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attctgacttggcgtgcttcatagaatggtcggcctcgaaaacaattgatttaaacacgagtttaagcaactctaatttccgtgttttcttttataccagGTGGGACTACCACTCGCTGCAGGTGCTCTGCTGCCTTCAGCCAATATAATGCTTACTCCATCAATTGCGGGTGCACTCATGGGTATAAGCTCTTTGGGTG

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