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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTGTACTTGCCTTGATGGACCGTAGCGAGGCTGAACTTGGAGAACCTTTAGCCCGCTTTCTATGTCTTGGTCTTGGTCTTCTCTACCTTGGGAAGCAGgtacttcttttgctacctctctaatttgttcttgaaacacacgtagctcagctccattgtagatttaagatggatactgtagattttaattttgttctga...

Basic information

species Physcomitrella patens
transcript PP1S414_22V6.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S414_22V6.1 (Physcomitrella patens), 5'ss of exon 17
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 17
TATTGTACTTGCCTTGATGGACCGTAGCGAGGCTGAACTTGGAGAACCTTTAGCCCGCTTTCTATGTCTTGGTCTTGGTCTTCTCTACCTTGGGAAGCAGgtacttcttttgctacctctctaatttgttcttgaaacacacgtagctcagctccattgt---agatttaagatggatactgtagattttaattttgttctga----
 ||| || |||||||||||||||| || ||  | ||| | || || ||| |  |  |  || |   |||||||||||||||||| |||||||||||||||||| | |||     |  ||| |   || | | || ||  |||    || | ||| ||  |   ||| | | | ||  | |  | || ||   || |||| |      
AATTATATTTGCCTTGATGGACCGAAGTGATTCAGAATTGGGGGAGCCTCTCACAAGACTTTTGCCTCTTGGTCTTGGTCTTCTTTACCTTGGGAAGCAGgtaatcctt-----atttcttttggtt-tccatggaattcactatccttacctctatgatttgagaatcatgttgtgttcctttgaattcc-ttgtgttttaccttt
















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|162196104|gb|FC372743.1|FC372743
EST:     TAGCCCGCTTTCTATGTCTTGGTCTTGGTCTTCTCTACCTTGGGAAGCAG                         GAAGCTGCGGATGCAACCATGGAGGTGGCCAAGACTTTGAATGAGAAAATT
genomic: TAGCCCGCTTTCTATGTCTTGGTCTTGGTCTTCTCTACCTTGGGAAGCAGgtacttcttt ... tggtgctcagGAAGCTGCGGATGCAACCATGGAGGTGGCCAAGACTTTGAATGAGAAAATT
EST: gi|162198496|gb|FC375331.1|FC375331
EST:     TAGCCCGCTTTCTATGTCTTGGTCTTGGGCTTCTCTACCTTGGGAAGCAG                         GAAGCTGCGGAT
genomic: TAGCCCGCTTTCTATGTCTTGGTCTTGGTCTTCTCTACCTTGGGAAGCAGgtacttcttt ... tggtgctcagGAAGCTGCGGAT

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: 35 (upstream exon), 11 (downstream exon)
Score: 6

TATTGTACTTGCCTTGATGGACCGTAGCGAGGCTGAACTTGGAGAACCTTTAGCCCGCTTTCTATGTCTTGGTCTTGGTCTTCTCTACCTTGGGAAGCAGgtacttcttt ... tggtgctcagGAAGCTGCGGATGCAACCATGGAGGTGGCCAAGACTTTGAATGAGAAAATTTCCAAGTATTGTCTTGTTACCATAGAAACTTGTGCGTACGCAGGCACTG




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