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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatggttgcactcttacttttgctcaggtctttgctttgcattactatttctcagtggtcactgtgatcagcaacctaatattcgtgccgtatttggcgacgtgcaaatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAATCATGCGGCAAATCGCCGCCAGTGTAACATTTCTTCCCAACATTGAGGAA

Basic information

species Physcomitrella patens
transcript PP1S219_74V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S219_74V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv01s0010g02430.t01 (Vitis vinifera), 3'ss of exon 4
gtaagatggttgcactcttacttttgctcaggtctttgctttgcattactatttctcagtggtcactgtgatcagcaacctaatattcgtgccgtatttggcgacgtgcaaatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAATCATGCGGCAAATCGCCGCCAGTGTAACATTTCTTCCCAACATTGAGGAA
|||| ||  ||      ||  || |   ||    ||| |      | |  |      |  |||  |||   |      | | || || ||  |  ||||||     ||   ||    ||||||  | || |||||||||||||| || ||||||| |||||| || ||||||||||| || || ||  ||||  | || | | | ||   ||| || |||
gtaatattattatctggttttttatctcca----ttttccaaatctcaaaaccctcgaaaggtttctggtttt-----cttcatgtttgtttc--atttggtt---tgtttatt---cagGGTGTCAAGGGAGAAGAGTGACAAAGAGATTATGAGAGAGATACAAGCAATCATGCGACAGATTGCTTCCAGCATCACTTATTTGCCATGCATCGATGAA

upper sequence: PP1S219_74V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ19104 (Selaginella moellendorffii), 3'ss of exon 3
gtaagatggttgcactcttacttttgctcaggtctttgctttgcattactatttctcagtggtcactgtgatcagcaacctaatattcgtgccgtatttggcgacgtgcaaatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAATCATGCGGCAAATCGCCGCCAGTGTAACATTTCTTCCCAACATTGAGGAA
                                                                       ||  |   | |   ||  |   |  | | |||   | |   |    ||| | ||| | ||| ||||| |||||||| || |||  ||||||||| || |||||||| |||||| || |||| || |||||||||||  || | || |||
----------------------------------------------------------------gtaaaattcttctctccaggcttgctcttgactgtagcg-ttttcttctttctcagTGCCACGAAAGAAAAGAGCGACAAGGAGATAATGCAAGAGATTCAAGCCATCATGCGACAAATCACCTCCAGCGTCACATTTCTTCCTCACCTCGAAGAA

upper sequence: PP1S219_74V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ10445 (Selaginella moellendorffii), 3'ss of exon 3
gtaagatggttgcactcttacttttgctcaggtctttgctttgcattactatttctcagtggtcactgtgatcagcaacctaatattcgtgccgtatttggcgacgtgcaaatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAATCATGCGGCAAATCGCCGCCAGTGTAACATTTCTTCCCAACATTGAGGAA
                                                                       ||  |   | ||  ||  |   |  | | |||   | |   |    ||| | ||| | ||| ||||| |||||||| || |||  ||||||||| || |||||||| |||||| || |||| || |||||||||||  || | || |||
----------------------------------------------------------------gtaaaattcttctctccaagcttgctcttgactatagcg-ttttcttctttctcagTGCCACGAAAGAAAAGAGCGACAAGGAGATAATGCAAGAGATTCAAGCCATCATGCGACAAATCACCTCCAGCGTCACATTTCTTCCTCACCTCGAAGAA

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|67571002|gb|BJ943826.1|BJ943826
EST:     GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGG                         GGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
genomic: GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
EST: gi|37836823|gb|BJ594831.1|BJ594831
EST:     GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGG                         GGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
genomic: GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
EST: gi|22133168|gb|BQ827585.1|BQ827585
EST:     GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGG                         GGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
genomic: GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
EST: gi|100407934|gb|BY955843.1|BY955843
EST:     GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAA-GG                         GGTCACTAGAGAGAAGAGTGAC
genomic: GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGAC
EST: gi|100432944|gb|BY978763.1|BY978763
EST:     AACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTTGAAAA-GG                         GGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTC
genomic: AACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATT-GAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTC
EST: gi|67694307|gb|BJ954540.1|BJ954540
EST:     GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGG                         GGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
genomic: GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
EST: gi|208359357|gb|DC954224.1|DC954224
EST:     GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGG                         GGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
genomic: GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
EST: gi|37836825|gb|BJ594833.1|BJ594833
EST:     GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGG                         GGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
genomic: GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
EST: gi|208390249|gb|DC949503.1|DC949503
EST:     GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGG                         GGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
genomic: GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
EST: gi|208387053|gb|DC941225.1|DC941225
EST:     GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGG                         GGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
genomic: GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
EST: gi|208368371|gb|DC935698.1|DC935698
EST:     GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGG                         GGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT
genomic: GAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAAT

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), 28 (downstream exon)
Score: 5

TTCAGAGAGTGGTCATGGTAATTGCCAGCATGTCCACGAAGGAAGTCCTGGAACGCTGGAACTTTAACATTGAGAATGACAACGAGGTTATTGAAAAAGGgtaagatggt ... aatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAATCATGCGGCAAATCGCCGCCAGTGTAACATTTCTTCCCAACATTGAGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgatcagcaacctaatattcgtgccgtatttggcgacgtgcaaatggaacagGGTCACTAGAGAGAAGAGTGACAAGGACATTATGACAGAGATTCAGGCAATCATGCGGCAAATCGCCGCCAGTGTAACATTTCTTCCCAACATTGAGGAA
            acctaat  putative branch site (score: 5)
               taatatt  TA-rich tract