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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatttatttgattttcacaatattgtttcggattgaaacttacgaatttatttttaaaatatcgcactctgaatgaacaactgtgatttggtgtttcagGTCCGAGATTACATTCATGTCATGGATTTGGCAAGTGGTCATACGAAGGCTCTGGACAAACTCTTCACAACTCCCGACATAG

Basic information

species Physcomitrella patens
transcript PP1S101_67V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_67V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------taatttatttgattttcacaatattgtttcggattgaaacttacgaatttatttttaaaatatcgcactctgaatgaa-caactgtgatttggtg-tttcagGTCCGAGATTACATTCATGTCATGGATTTGGCAAGTGGTCATACGAAGGCTCTGGACAAACTCTTCACAACTCCCGACATAG
                                                   | |     || | ||     ||||| |   | || | |  | |   |   | || | || |||   |      || |  || || || | || |  ||||||||  ||||||||||||||||||||||||| |||  ||| || |     ||||||   || ||    |  | || | | ||  
gtatgtgacttatgatgtcttatagacaacaaaccatttgacagatttacattacaatcttaaattgtgatatattatggagtatgggagataatacaacgaattgtgaattatattaacagatattattcatctttgttgtgtttctttcagGTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAG--ATGA-TCTCAAAATCA
















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|208351996|gb|DC925805.1|DC925805
EST:     AAATGCTCACTGTCTTCGGCAAAGATTACAAAACCCGTGATGGAACTGGGGTTAG                     
genomic: AAATGCTCACTGTCTTCGGCAAAGATTACAAAACCCGTGATGGAACT--GG---Ggttaggtttt ... ggtgtt
EST: gi|208388227|gb|DC956977.1|DC956977
EST:     AAATGCTCACTGTCTTCGGCAAAGATTACAAAACCCGTGATGGAACTGGG                         GTCCGAGATTACATTCATGTCATGGATTTGGCAAGTGGTCATACGAAGGCT
genomic: AAATGCTCACTGTCTTCGGCAAAGATTACAAAACCCGTGATGGAACTGGGgttaggtttt ... ggtgtttcagGTCCGAGATTACATTCATGTCATGGATTTGGCAAGTGGTCATACGAAGGCT
EST: gi|208382034|gb|DC919921.1|DC919921
EST:     TACAAAACCCGTGA-NGAACTGGG                         GTCCGAGATTACATTCATGTCATGGATTTGGCAAGTGGTCATACGAAGGCT
genomic: TACAAAACCCGTGATGGAACTGGGgttaggtttt ... ggtgtttcagGTCCGAGATTACATTCATGTCATGGATTTGGCAAGTGGTCATACGAAGGCT

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: 15

TCCCAACAATTTGATGCCCTTCGTGCAACAAGTTGCAGTGGGTCGTAGAGAAATGCTCACTGTCTTCGGCAAAGATTACAAAACCCGTGATGGAACTGGGgttaggtttt ... ggtgtttcagGTCCGAGATTACATTCATGTCATGGATTTGGCAAGTGGTCATACGAAGGCTCTGGACAAACTCTTCACAACTCCCGACATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttatttttaaaatatcgcactctgaatgaacaactgtgatttggtgtttcagGTCCGAGATTACATTCATGTCATGGATTTGGCAAGTGGTCATACGAAGGCTCTGGACAAACTCTTCACAACTCCCGACATAG
     atttttaaaatat  TA-rich tract