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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcatatattttcgaaggattttggtattcccggagaaaggttttttgtatggctttgttttctctaccttcaccacatagacacttctgtgattgcagGATTCTGGATGCCCATGCTTTAAAGGAGGTCCTCGTACAGTGCAAAATTTGAGGAAGCGTTTCCATCTAAGCTTGACTGAGGAA

Basic information

species Physcomitrella patens
transcript PP1S113_110V6.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S113_110V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: EFJ06373 (Selaginella moellendorffii), 3'ss of exon 16
attcatatattttcgaaggattttggtattcccggagaaaggttttttgtatggctttgttttctctaccttcaccacatagacacttctgtgattgcagGATTCTGGATGCCCATGCTTTAAAGGAGGTCCTCGTACAGTGCAAAATTTGAGGAAGCGTTTCCATCTAAGCTTGACTGAGGAA
                            |   ||   ||| ||| | |   | | || || ||    ||     ||     ||   ||   ||   | ||||||| ||||| || ||||||   ||||||||    ||  | |  |||||||| |||||||||||||| |||||||||||||| 
---------------------------gtagacgactaaaagttctat---tcgattcgtcttgcgaactaatgcc-----gattttttcttg--cgtagGATTCGGGATGTCCTTGCTTTCGTGGAGGTCCCAAAACGATCCTGAATTTGAGAAAGCGTTTCCATCTTAGCTTGACTGAGGAG

upper sequence: PP1S113_110V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: EFJ26597 (Selaginella moellendorffii), 3'ss of exon 14
attcatatattttcgaaggattttggtattcccggagaaaggttttttgtatggctttgttttctctaccttcaccacatagacacttctgtgattgcagGATTCTGGATGCCCATGCTTTAAAGGAGGTCCTCGTACAGTGCAAAATTTGAGGAAGCGTTTCCATCTAAGCTTGACTGAGGAA
                            |   ||   ||| ||| | |   | | || || ||  | | | | |  |    ||   ||   ||   ||||||||| ||||| || ||||||   ||||||||    ||  | |  |||||||| |||||||||||||| |||||||||||||| 
---------------------------gtagacgactaaaagttctat---tcgattcgtcttg-cgaacattataatgccgattttttcttg--cgcagGATTCGGGATGTCCTTGCTTTCGTGGAGGTCCCAAAACGATCCTGAATTTGAGAAAGCGTTTCCATCTTAGCTTGACTGAGGAG
















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|18341350|gb|BJ173385.1|BJ173385
EST:     TATTCTACTGGTGGAGATGATGCAG                         GATTCTGGATGCCCATGCTTTAAAGNAGGTCNTCGTACAGTGCAAAATTTG
genomic: TATTCTACTGGTGGAGATGATGCAGgtgtggtttc ... gtgattgcagGATTCTGGATGCCCATGCTTTAAAGGAGGTCCTCGTACAGTGCAAAATTTG
EST: gi|161982255|gb|EE296241.1|EE296241
EST:     TGNCCGGAAACATGNCTGAGTGCATTATTCTACTGGTGGAGATGATGCAG                         GATTCTGGATGCCCATGCTTTAAAGGAGGTCCTCGT
genomic: TG-CCGGAAACATG-CTGAGCGCATTATTCTACTGGTGGAGATGATGCAGgtgtggtttc ... gtgattgcagGATTCTGGATGCCCATGCTTTAAAGGAGGTCCTCGT

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: 11 (upstream exon), 25 (downstream exon)
Score: 1

GTTCTGTGTATTCAGGGTTTCTTGACATGCCGGAAACATGCTGAGCGCATTATTCTACTGGTGGAGATGATGCAGgtgtggtttc ... gtgattgcagGATTCTGGATGCCCATGCTTTAAAGGAGGTCCTCGTACAGTGCAAAATTTGAGGAAGCGTTTCCATCTAAGCTTGACTGAGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtatggctttgttttctctaccttcaccacatagacacttctgtgattgcagGATTCTGGATGCCCATGCTTTAAAGGAGGTCCTCGTACAGTGCAAAATTTGAGGAAGCGTTTCCATCTAAGCTTGACTGAGGAA
                                        cttctgt  CT-rich tract
          tttgtttt  TA-rich tract