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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCTCTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaatcagataaccttgccagaaatttgcagtttttggtccaagtagaatgatctgtagcgttcaggaacgctggaatgtgtgcgcgtctggaa...

Basic information

species Physcomitrella patens
transcript PP1S58_38V6.1
intron # 1
splice site 5'
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|162278221|gb|FC454456.1|FC454456
EST:     AGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: AGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162229091|gb|FC404775.1|FC404775
EST:     AGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: AGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162212016|gb|FC388126.1|FC388126
EST:     GTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: GTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|67569177|gb|BJ942001.1|BJ942001
EST:     TAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: TAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162230248|gb|FC406604.1|FC406604
EST:     AGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCNCAATGGTCACTTCAA
genomic: AGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|19788486|gb|BQ040777.1|BQ040777
EST:     TAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: TAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162214883|gb|FC391018.1|FC391018
EST:     GGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: GGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162184451|gb|FC359197.1|FC359197
EST:     CGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|18366625|gb|BJ198704.1|BJ198704
EST:     CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|18374966|gb|BJ206544.1|BJ206544
EST:     CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|208346451|gb|DC917404.1|DC917404
EST:     CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCCAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|208349479|gb|DC905617.1|DC905617
EST:     CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162209537|gb|FC385633.1|FC385633
EST:     GCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: GCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|18327512|gb|BJ159515.1|BJ159515
EST:     CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|67692422|gb|BJ952655.1|BJ952655
EST:     CGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162271775|gb|FC448908.1|FC448908
EST:     CGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162212397|gb|FC388125.1|FC388125
EST:     GTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: GTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162217291|gb|FC392031.1|FC392031
EST:     CGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|208381498|gb|DC919500.1|DC919500
EST:     AGATCGTGCGTCGCTGCCTCGCCAGCTCCTCAA-                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: AGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162222665|gb|FC397477.1|FC397477
EST:     CGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|18355339|gb|BJ187398.1|BJ187398
EST:     CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162278222|gb|FC454457.1|FC454457
EST:     GTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: GTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|208384998|gb|DC903505.1|DC903505
EST:     CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162229991|gb|FC407353.1|FC407353
EST:     CGCAAGCTCNTCAAG                         GGTGGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|18374111|gb|BJ205689.1|BJ205689
EST:     CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|67703647|gb|BJ963880.1|BJ963880
EST:     TCTCCTGGTCCCGCTAGTATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: TCTCCTGGTCCCGCTAG-ATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162229992|gb|FC407354.1|FC407354
EST:     CGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
EST: gi|162230249|gb|FC406605.1|FC406605
EST:     CTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAG                         GGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA
genomic: CTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAA

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: 31 (upstream exon), 32 (downstream exon)
Score: 12

CCTCTCTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaa ... ctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACCTGGTTCAACCAGCCCGCCCGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCTCTCTCCTGGTCCCGCTAGATCGTGCGTCGCTGCCTCGCAAGCTCCTCAAGgtacatcgaatcagataaccttgccagaaatttgcagtttttggtccaagtagaatgatctgtagcgttcaggaacgctggaatgtgtgcgcgtctggaa

- - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - CTCCTC