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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgattttatacacgaacttatgactgtttaatgtgttatattgactctggcataaaccattctaagtttatatatactttggatattttgtgttttcagGAGAGAAAAAGTATTCGGCCTACTTTCTCCGCTGAAGCCATCTATGGCGGAACTTTGCTTGCAGTGCGAACAAATGAGTTCATATGTTTCTATGATTGGG

Basic information

species Physcomitrella patens
transcript PP1S61_1V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 12
------------------------------atgattttat----acacgaacttatgactgtttaatgtgtt-atattgactctggcataaaccattctaagtttatatatactttggatattttgtgttttcagGAGAGAAAAAGTATTCGGCCTACTTTCTCCGCTGAAGCCATCTATGGCGGAACTTTGCTTGCAGTGCGAACAAATGAGTTCATATGTTTCTATGATTGGG
                              |  ||||| |      | ||   || |  ||   ||  ||   ||  |  |  | |    | | |||    | |||| |||| |    | |  | |||||||||||| || || ||||| |||||||||||||| |||||    || | ||| ||||| ||| | ||| || |  | ||||| ||||| || |||||||||||||
gtttgctattctcattatggccttactcatactattttgttggagtatgattctagggttgaagaaattgcagatgcttgcaatagagacagctattactggcttat-tatattaataaaaggtggtgttttcagGAAAGGAAGAGTATCCGGCCTACTTTCTCAGCTGAGAAGATTTTTGGAGGAACCTTGTTAGCAATGTGTTCGAATGATTTCATCTGCTTCTATGATTGGG
















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|162254476|gb|FC430676.1|FC430676
EST:     GTGCGAGAGAGTACTTCTAAAATTAAAATATTCAATAAGACTTTGCAG                         GAGAGAAAAAGTATTCGGCCTACTTTCTCCGCTGAAGCCATCTATGGCGGA
genomic: GTGCGAGAGAGTACTTCTAAAATTAAAATATTCAATAAGACTTTGCAGgtttgttttc ... gtgttttcagGAGAGAAAAAGTATTCGGCCTACTTTCTCCGCTGAAGCCATCTATGGCGGA
EST: gi|100443456|gb|BY981883.1|BY981883
EST:     CTGTGCGAGAGAGTACTTCTAAAATTAAAATATTCAATAAGACTTTGCAG                         GAGAGAAAAAGTATTCGGCCTACTTTCTCCGCTGAAGCCATCTATGGCGGA
genomic: CTGTGCGAGAGAGTACTTCTAAAATTAAAATATTCAATAAGACTTTGCAGgtttgttttc ... gtgttttcagGAGAGAAAAAGTATTCGGCCTACTTTCTCCGCTGAAGCCATCTATGGCGGA
EST: gi|162186953|gb|FC363359.1|FC363359
EST:     CTGTGCGAGAGAGTACTTCTAAAATTAAAATATTCAATAAGACTTTGCAG                         GAGAGAAAAAGTATTCGGCCTACTTTCTCCGCTGAAGCCATCTATGGCGGA
genomic: CTGTGCGAGAGAGTACTTCTAAAATTAAAATATTCAATAAGACTTTGCAGgtttgttttc ... gtgttttcagGAGAGAAAAAGTATTCGGCCTACTTTCTCCGCTGAAGCCATCTATGGCGGA

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), 32 (downstream exon)
Score: 5

ATCTTTTGGCTCTGCTTTGGAGTTTGTTTGGTCCAATGATGGTGAATATGCTGTGCGAGAGAGTACTTCTAAAATTAAAATATTCAATAAGACTTTGCAGgtttgttttc ... gtgttttcagGAGAGAAAAAGTATTCGGCCTACTTTCTCCGCTGAAGCCATCTATGGCGGAACTTTGCTTGCAGTGCGAACAAATGAGTTCATATGTTTCTATGATTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctggcataaaccattctaagtttatatatactttggatattttgtgttttcagGAGAGAAAAAGTATTCGGCCTACTTTCTCCGCTGAAGCCATCTATGGCGGAACTTTGCTTGCAGTGCGAACAAATGAGTTCATATGTTTCTATGATTGGG
                                              tgttttc  CT-rich tract
                  taagtttatatatact  TA-rich tract