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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTTAGCCAGGTAATGGGTAGCGGCTTCCGCATGGACCAAGTTGCACCTGCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttcacagaagtgcctgaagctttgaggcatactcctttggtatctgatcttgatttatctattttgtttcaagtggatttggaagagtagattgcgagtcctaacaacacgtcattgtctacgacag

Basic information

species Physcomitrella patens
transcript PP1S4_215V6.1
intron # 2
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|162264332|gb|FC440498.1|FC440498
EST:     TTCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
genomic: TTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
EST: gi|162235910|gb|FC411653.1|FC411653
EST:     GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAANAGA
genomic: GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
EST: gi|18333863|gb|BJ165879.1|BJ165879
EST:     GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
genomic: GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
EST: gi|208355802|gb|DC929983.1|DC929983
EST:     GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGANGCAGGATTTGATGCCCATAAACGAAAAGA
genomic: GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
EST: gi|162238939|gb|FC417703.1|FC417703
EST:     GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
genomic: GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
EST: gi|208371352|gb|DC944516.1|DC944516
EST:     GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
genomic: GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
EST: gi|100357608|gb|BY946481.1|BY946481
EST:     GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAG                         TCCAATCGGGTCGTTGTTGGAGGCAGGATTTGATGCCCCATAA-CGAAAAG
genomic: GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCC-ATAAACGAAAAG
EST: gi|162199675|gb|FC375914.1|FC375914
EST:     GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
genomic: GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
EST: gi|67696462|gb|BJ956695.1|BJ956695
EST:     GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
genomic: GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
EST: gi|162238938|gb|FC417702.1|FC417702
EST:     TCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
genomic: TCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
EST: gi|162264333|gb|FC440499.1|FC440499
EST:     GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
genomic: GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
EST: gi|162235909|gb|FC411652.1|FC411652
EST:     CCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
genomic: CCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
EST: gi|162199674|gb|FC375913.1|FC375913
EST:     GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAG                         TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA
genomic: GCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGA

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: 24 (upstream exon), 12 (downstream exon)
Score: 1

AGCTTAGCCAGGTAATGGGTAGCGGCTTCCGCATGGACCAAGTTGCACCTGCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttca ... tctacgacagTCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTTAGCCAGGTAATGGGTAGCGGCTTCCGCATGGACCAAGTTGCACCTGCGGAAGACTACTCCACGATTCTGCTCTTCGCCACTGGTTCTGGAATTAGgtgggtttcacagaagtgcctgaagctttgaggcatactcctttggtatctgatcttgatttatctattttgtttcaagtggatttggaagagtagattgcgagtcctaacaacacgtcattgtctacgacag

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