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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttttttattctgtcacttcgaacagtcgttttaaattcaggttgaggtagtgattgagtgttcttacgttctggagaagtgtttgttttgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAACAGGTTCTTGGTGAAGAGAAATGGAAATAATAACAACAGTGTTCAGTTC

Basic information

species Physcomitrella patens
transcript PP1S98_65V6.1
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|162277980|gb|FC454111.1|FC454111
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162277981|gb|FC454112.1|FC454112
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|18359055|gb|BJ191115.1|BJ191115
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162276139|gb|FC452831.1|FC452831
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162209251|gb|FC385171.1|FC385171
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162261514|gb|FC437531.1|FC437531
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162273848|gb|FC449779.1|FC449779
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|18344706|gb|BJ176747.1|BJ176747
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162215347|gb|FC391115.1|FC391115
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162213765|gb|FC390380.1|FC390380
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162213766|gb|FC390381.1|FC390381
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|37852452|gb|BJ610460.1|BJ610460
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162261513|gb|FC437530.1|FC437530
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162273849|gb|FC449780.1|FC449780
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|19777228|gb|BQ039161.1|BQ039161
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|18340471|gb|BJ172499.1|BJ172499
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|7147930|gb|AW509852.1|AW509852
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162262080|gb|FC436861.1|FC436861
EST:     CACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162209250|gb|FC385170.1|FC385170
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162274650|gb|FC450456.1|FC450456
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|162241490|gb|FC414664.1|FC414664
EST:     CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
EST: gi|19785084|gb|BQ040267.1|BQ040267
EST:     CATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAG                         AATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA
genomic: CATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 35 (downstream exon)
Score: 69

GAGAGCTCTCTCTCTCTTCGCAATTGTGCACCTGCTGCGTTGCACGCACGCGCTCCATCGCTGCCTTGCCGCAGTACTCACGCCTCCCTTGAACCTTCAGgtacttcccc ... tgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAACAGGTTCTTGGTGAAGAGAAATGGAAATAATAACAACAGTGTTCAGTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggtagtgattgagtgttcttacgttctggagaagtgtttgttttgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAACAGGTTCTTGGTGAAGAGAAATGGAAATAATAACAACAGTGTTCAGTTC
                 ttcttac  putative branch site (score: 69)
                                      tttgtttt  putative PPT
                                      tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttttttattctgtcacttcgaacagtcgttttaaattcaggttgaggtagtgattgagtgttcttacgttctggagaagtgtttgttttgtgcatcagAATGGCGTCTGTATCAGATGACTTGATCTGGTTGTTGGTCAAGGACAGCAACAGGTTCTTGGTGAAGAGAAATGGAAATAATAACAACAGTGTTCAGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA