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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttgttgcggtgattttccttctactcgtagaaacataagaaaccttctctggctacgaattatcagtttaaagaatttatgtcatttgaaatgacaaggtttcattcaaacatgtctttgtgcttttggtaattagGTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCATTCCACACGGTGTCGAAGGGTTTCCTCGGAGAGTGTGGACAGCGAGGTG

Basic information

species Physcomitrella patens
transcript PP1S215_28V6.1
intron # 7
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|162176654|gb|FC352499.1|FC352499
EST:     ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAG                         GTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA
genomic: ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAGgtattttgtt ... tggtaattagGTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA
EST: gi|162178885|gb|FC354817.1|FC354817
EST:     ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAG                         GTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA
genomic: ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAGgtattttgtt ... tggtaattagGTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA
EST: gi|162186162|gb|FC361366.1|FC361366
EST:     ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAG                         GTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA
genomic: ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAGgtattttgtt ... tggtaattagGTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA
EST: gi|162178101|gb|FC354403.1|FC354403
EST:     ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAG                         GTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCT
genomic: ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAGgtattttgtt ... tggtaattagGTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCT
EST: gi|162269857|gb|FC445387.1|FC445387
EST:     ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAG                         GTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA
genomic: ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAGgtattttgtt ... tggtaattagGTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA
EST: gi|162217937|gb|FC393933.1|FC393933
EST:     ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAG                         GTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA
genomic: ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAGgtattttgtt ... tggtaattagGTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA
EST: gi|162151906|gb|FC328152.1|FC328152
EST:     ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAG                         GTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA
genomic: ACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAGgtattttgtt ... tggtaattagGTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCA

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: 69

TATCGAGTTCTGCATCAAGGAAAAGATTGTGCTGATGGCTGACGAGGTTTACCAGCAAAACGTTTATCAAGATGAGCGCCCCTTTATCAGCGCGAGGAAGgtattttgtt ... tggtaattagGTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCATTCCACACGGTGTCGAAGGGTTTCCTCGGAGAGTGTGGACAGCGAGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttgaaatgacaaggtttcattcaaacatgtctttgtgcttttggtaattagGTGCTGATGGGCATGGGACCCCCAGTCAGTGAAGCTCTGGAGTTGGTTTCATTCCACACGGTGTCGAAGGGTTTCCTCGGAGAGTGTGGACAGCGAGGTG
                                       tgctttt  CT-rich tract
                                                taatta  TA-rich tract