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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttctttttctgaacatcacaccattatttctaaatgtgtggcgtgtgctgtcgtgaaagttcgctttctgttggtttcttcatttctacaaatccttatcgtcaaatatttggcag

Basic information

species Physcomitrella patens
transcript PP1S8_288V6.1
intron # 30
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|162189371|gb|FC366529.1|FC366529
EST:     TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG                         GCCATCTTCCAAGTAGTGGTACTTTTGACCTTGAATTTTGCGGGGAACAAA
genomic: GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA
EST: gi|162259197|gb|FC435217.1|FC435217
EST:     GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG                         GCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA
genomic: GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA
EST: gi|162153113|gb|FC329519.1|FC329519
EST:     TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG                         GCCATCTTCCAAGTAG
genomic: GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAG
EST: gi|162189370|gb|FC366528.1|FC366528
EST:     TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG                         GCCATCTTCCAAGTAGTGGTACTTTTGACCTTGAATTTTGCGGGGAACAAA
genomic: GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA
EST: gi|162155067|gb|FC330861.1|FC330861
EST:     TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAN                         GCCATCTTCCAAGTAGTGGTACTTTTGACCTTGAATTTTGCGG
genomic: GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGG
EST: gi|100367439|gb|BY984706.1|BY984706
EST:     GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG                         GCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA
genomic: GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA
EST: gi|162153021|gb|FC330051.1|FC330051
EST:     TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG                         GCCATCTTCCAAGTAGTGGTACTTTTGACCTTGAATTTTGCGGGGAACAAA
genomic: GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA
EST: gi|162245992|gb|FC421881.1|FC421881
EST:     TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG                         GCCATCTTCCAAGTAGTGGTACTTTTGACCTTGAATTTTGCGGGGAACAAA
genomic: GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA
EST: gi|162186821|gb|FC363065.1|FC363065
EST:     TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG                         GCCATCTTCCAAGTAGTGGTACTTTTGACCTTGAATTTTGCGGGGAACAAA
genomic: GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA
EST: gi|162272382|gb|FC449034.1|FC449034
EST:     GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG                         GCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA
genomic: GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA
EST: gi|162256676|gb|FC433194.1|FC433194
EST:     GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG                         GCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTNTGCGGGGAACAAA
genomic: GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAA

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: 34 (upstream exon), 35 (downstream exon)
Score: 48

GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttct ... tatttggcagGCCATCTTCCAAGTAGTGGTTCTTTTGACCTTGAATTTTGCGGGGAACAAAATCTTAGGTCTTACTGGACCCGATAAAGAAAGGGACTTGTTAAGAACCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAGgtattgttctttttctgaacatcacaccattatttctaaatgtgtggcgtgtgctgtcgtgaaagttcgctttctgttggtttcttcatttctacaaatccttatcgtcaaatatttggcag

- - - - - - - - - - - - GTGGAG
- - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - GGAGAA