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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcgacctaatgcgctcatacaagctttactttcaatttgtatgtttttttgatgacgtgcggatgtggtgcaagtttagctgtagtaaacggtatgaggagggttttgggagacatggaaatgttacgactatggcacttcctaattttttttttctaattctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTCCAAGTGTGAATACTGGAAATGCATTAGCTTGCGCCGAACATTGTATTTA

Basic information

species Physcomitrella patens
transcript PP1S93_138V6.1
intron # 2
splice site 3'
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|100442054|gb|BY962947.1|BY962947
EST:     CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAG                         GGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
genomic: CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAGgtaggcgacc ... ctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
EST: gi|100391012|gb|BY953022.1|BY953022
EST:     CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAG                         GGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
genomic: CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAGgtaggcgacc ... ctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
EST: gi|100447037|gb|CJ971336.1|CJ971336
EST:     CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAG                         GGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
genomic: CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAGgtaggcgacc ... ctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
EST: gi|18372772|gb|BJ204374.1|BJ204374
EST:     CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAG                         GGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
genomic: CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAGgtaggcgacc ... ctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
EST: gi|162228915|gb|FC404201.1|FC404201
EST:     CCGCGCCAAGCAGTTGCTACTCATTGTGCAGTTTGGTGTTGGGCTCGAAG                         GGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
genomic: CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAGgtaggcgacc ... ctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
EST: gi|208371164|gb|DC931596.1|DC931596
EST:     CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAG                         GGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
genomic: CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAGgtaggcgacc ... ctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
EST: gi|18367318|gb|BJ199400.1|BJ199400
EST:     CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAN                         GGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAANGTGGCTAGAATTC
genomic: CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAGgtaggcgacc ... ctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
EST: gi|100379739|gb|BY949920.1|BY949920
EST:     CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAG                         GGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAACTC
genomic: CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAGgtaggcgacc ... ctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
EST: gi|100411709|gb|BY992302.1|BY992302
EST:     CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAG                         GGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC
genomic: CCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAGgtaggcgacc ... ctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTC

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: 31 (upstream exon), 32 (downstream exon)
Score: 4

TATGACATCTGCGTACCTCGAATGATGCGTCTGGATGCCGAAGTGATTGCCCGCGCCAAGCAGTTGCAACTCATTGTGCAGTTTGGTGTTGGGCTCGAAGgtaggcgacc ... ctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTCCAAGTGTGAATACTGGAAATGCATTAGCTTGCGCCGAACATTGTATTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaatgttacgactatggcacttcctaattttttttttctaattctttctacagGGGTGGATATCGAAGCTGCGACAAGAGCGGGTATTAAGGTGGCTAGAATTCCAAGTGTGAATACTGGAAATGCATTAGCTTGCGCCGAACATTGTATTTA
                                     ttctaat  putative branch site (score: 4)
                     cttcctaatttttttt  CT-rich tract
                          taattttttttttcta  TA-rich tract