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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGACGTCACCAAGATTGGTGTTACCAGTTTTGAGGGACCTGATGGCACCTTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattttttttctctttttttttcccctccgtttttctttttccttcacccatagaagatgcttgatatgattatactgtttcttgaatgtcttttcatatcaacagagcttgatttagcctgcttcagccttcctcctcaatgggctcgtaacaaagaatgattgaaattgatgttcag

Basic information

species Physcomitrella patens
transcript PP1S4_12V6.3
intron # 8
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|162178865|gb|FC354797.1|FC354797
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|208351568|gb|DC909998.1|DC909998
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATT-GATTACCANCCC-AAGTN
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|162159187|gb|FC334358.1|FC334358
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|100375450|gb|BY948872.1|BY948872
EST:     TTGATGTAGAGGTGTTTCGACTCA-CTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCCAGTT
genomic: TTGATGTAGAGGTGTT-CGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|162175775|gb|FC352077.1|FC352077
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|162198744|gb|FC374227.1|FC374227
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|162185024|gb|FC362470.1|FC362470
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|67568839|gb|BJ941663.1|BJ941663
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGAT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGAT
EST: gi|162257953|gb|FC433839.1|FC433839
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|162276463|gb|FC452466.1|FC452466
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT

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: 20 (upstream exon), 33 (downstream exon)
Score: 8

TTGACGTCACCAAGATTGGTGTTACCAGTTTTGAGGGACCTGATGGCACCTTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTTCAGCTTCTG




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