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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttctttcgaactcaaagtagttggtgtagcattttgaatgaacctcagtggaattcaggattgtgcttcatgtgtttcttcttcatgggacgatttatcctgcttcatttttctgctttctaaagcttgttggtttgagggttggcag

Basic information

species Physcomitrella patens
transcript PP1S35_94V6.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: LOC_Os01g23610.2 (Oryza sativa), 5'ss of exon 13
----------------------------GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttctttcgaactcaaagtagttggtgtagcattttgaatgaacctcagtggaattcaggattgtgcttcatgtgtttcttcttcatgggacgatttatcctgcttcatttttctgctttctaaagcttgttggtttgagggttggcag
                            ||||||||||||||||||||||| || || || || ||||| ||| |||| ||||| ||||| || || ||||||| |   |   | |     | |||| | |   |||    ||   |  || |   ||     | ||| | | || ||  |||| |                                                                  
TTTGCTCAACGCTGTTTACATCCCCCAGGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacatt--atttgtcattgttgttttgtaatt----atttgcaccaataatatagtcaactgtacgtgatatgcctcttttcag---------------------------------------------------------------

upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 14
GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttctttcgaactcaaagtagttggtgtagcattttgaatgaacctcagtggaattcaggattgtgcttcatgtgtttcttcttcatgggacgatttatcctgcttcatttttctgctttctaaagcttgttggtttgagggttggcag
||||||||||||||||||||||| || || || || ||||| ||| |||| ||||| ||||| || || ||||||| |   |   | |     | |||| | |   |||    ||   |  || |   ||     | ||| | | || ||  |||| |                                                                  
GACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacatt--atttgtcattgttgttttgtaatt----atttgcaccaataatatagtcaactgtacgtgatatgcctcttttcag---------------------------------------------------------------

upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 14
GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttctttcgaactcaaagtagttggtgtagcattt---tgaatgaacctcagtg--gaattcaggattgtgcttcatgtgtttcttcttcatgggacgatttatcctgcttcatttttctgctttctaaagcttgttggtttgagggttggcag
||||||||||||||||||||||| || || || || ||||||||| |||| || || |||||||| || ||||||  | |  | |  |     ||     | ||| || |   | |||||  ||  |||   ||   |  |      ||  ||    | | |   |   |   |   |   ||| |     || | ||   | ||                        
GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgc-cctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag---------------------

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|162239089|gb|FC416228.1|FC416228
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|7286407|gb|AW598836.1|AW598836
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|67692532|gb|BJ952765.1|BJ952765
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|162195482|gb|FC370899.1|FC370899
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|162185502|gb|FC362571.1|FC362571
EST:     CCCATCCCACCTTATTTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|162167618|gb|FC343750.1|FC343750
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|7584064|gb|AW699962.1|AW699962
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|162170368|gb|FC346773.1|FC346773
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|67694918|gb|BJ955151.1|BJ955151
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|208380575|gb|DC919361.1|DC919361
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|162166908|gb|FC343293.1|FC343293
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|162239088|gb|FC416227.1|FC416227
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|15728076|gb|BI740607.1|BI740607
EST:     CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
EST: gi|7582998|gb|AW699162.1|AW699162
EST:     CCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG                         CTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA
genomic: CCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCA

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: 26 (upstream exon), 34 (downstream exon)
Score: 11

GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttcttt ... gggttggcagCTTGACGAGGAGCATGCGGCAGTAGAAACCCCAAAGGAAGTACTTGAATCAGTGAGTGCTTGATGTCTCGGCTCAGTCGTTCTTGTCGAAGATTATTTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttctttcgaactcaaagtagttggtgtagcattttgaatgaacctcagtggaattcaggattgtgcttcatgtgtttcttcttcatgggacgatttatcctgcttcatttttctgctttctaaagcttgttggtttgagggttggcag

- - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT