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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgcaaagtttctcgtttacctcctcactacggatgtctattttgttgcagaacaagtggctctaatggatttgggaacagctctatgcagcttcatttacacttgtttttttttatgcag

Basic information

species Physcomitrella patens
transcript PP1S17_286V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os06g48300.1 (Oryza sativa), 5'ss of exon 6
GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgcaaagtttct--cgtttacctcctcactacggatgtctattttgttgca-gaaca-----agtggctctaatggatttgggaacagctctatgcagcttcatttacacttgtttttttttatgcag----------------------------
| || ||||| |||||||||||||||||||||||||| |||||||| |||   || |||||  ||||||| || ||||| ||||| ||  ||||    |   ||||||||  |  |  |    |||  |   |||    |  |   | | | | |     || |||  | |  |||||  | | |   | ||    | | || |||  |||    |    || |                              
GAACATGGCGCGTGGGTGGTGTTCTTGCTGTCTCTCGAGCATTTGGTGACAAACTCCTGAAGCAATATGTGGTTGCTGATCCAGAGATCAAGgt----cctcaagtttcttccaatctcaaattcataattcatgcagctcataaagaaagtatatgcatagaggccatgaacgatttcaggatacgaccatattacgttatgtactgttgcaaatcgaaattcgacatttatctgcttatttgatctgtacag

upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 5'ss of exon 6
GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgcaaagtttctcgtttacctcctcactacggatgtctattttgttgcagaacaagtggctctaatggatttgggaacagctctatgcagcttcatttacacttgtttttttttatgcag
| || |||||||| ||||||||||||||||| ||||| |||||||| ||    ||  ||||  | |||||||| ||||| ||||| ||  ||||    |  ||  ||  | | ||| |||   ||||  |   ||||| |    ||| || ||    |   |  | | ||||   ||   | |||||  ||  | || |                   
GGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgacttaat-ttgtttgcttagctctcaactaaagccttctatct----gcaaaataatattcatcatcgtaattgg---cattcccatgcatgttactctaaag------------------

upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM5G829894_T03 (Zea mays), 5'ss of exon 1
--------GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgcaaagtt---tctcgtt-tacctcctcactacggatgtctat-tttgttgcagaacaagtggctctaatggatttgggaaca-gctctatgcagcttcatttacacttgtttttttttatgcag-------------------------------------------------------------
        | || ||||| |||||||||||||||||||||||||| |||||||| ||    ||  ||||  | ||||| |||||||| || |||||  ||||    |    | ||   | |  ||     |  ||   |  | | |  |    | |    |    || |  | |  |||  |||  |||  |   || |   ||  |  |     |    |  |||| |||                                                              
ATTTGTAGGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAGgtttgtcatgcacttatgttttattacggattgtcgggatagtttttcagacctatcatggtttgagggaatatggtggggttgtaaacttgtaataagtgcctaaaaatggggattccatcattta-gcaatgtcatacatcacccacaccccctgtagccatctgaaaacgatttttgctgttacaatcag

upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM5G829894_T02 (Zea mays), 5'ss of exon 4
GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgcaaagtt---tctcgtt-tacctcctcactacggatgtctat-tttgttgcagaacaagtggctctaatggatttgggaaca-gctctatgcagcttcatttacacttgtttttttttatgcag-------------------------------------------------------------
| || ||||| |||||||||||||||||||||||||| |||||||| ||    ||  ||||  | ||||| |||||||| || |||||  ||||    |    | ||   | |  ||     |  ||   |  | | |  |    | |    |    || |  | |  |||  |||  |||  |   || |   ||  |  |     |    |  |||| |||                                                              
GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAGgtttgtcatgcacttatgttttattacggattgtcgggatagtttttcagacctatcatggtttgagggaatatggtggggttgtaaacttgtaataagtgcctaaaaatggggattccatcattta-gcaatgtcatacatcacccacaccccctgtagccatctgaaaacgatttttgctgttacaatcag

upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: Vv18s0001g15050.t01 (Vitis vinifera), 5'ss of exon 6
GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagc-gcaaagtttctcgtttacctcctcac-tacggatgtctattttgtt-gcagaacaagtggctctaatggatttgggaacagctctatgcagcttcatttacacttgtttttttttatgcag
| || ||||| || ||||||||||||||||| ||||| |||||||||||    ||||| ||   |||||| || ||||| ||||||||||||||        |  |  |   ||| |  | |  |  || |  ||    | | ||| |    |||||   || | ||   ||||  |||  |     |  |||   |                        
GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttatattgggtgctgttcaagtgcaaaaatatgattgctcctctcgtttgtctcacaagaatcttttat---tttgtaaac--cctggaggtgctctct------------------------

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|208365978|gb|DC955497.1|DC955497
EST:     TT-GGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|162184832|gb|FC361134.1|FC361134
EST:     TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|162195745|gb|FC371136.1|FC371136
EST:     TTGGGGACCGCCTTCTNNNNNNNTATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|208398836|gb|DC920784.1|DC920784
EST:     TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|162157032|gb|FC333394.1|FC333394
EST:     TGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: TGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|208381790|gb|DC928453.1|DC928453
EST:     TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|18334734|gb|BJ166751.1|BJ166751
EST:     AAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: AAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|162245393|gb|FC421295.1|FC421295
EST:     TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|19780877|gb|BQ039620.1|BQ039620
EST:     TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|208352662|gb|DC921396.1|DC921396
EST:     TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|162189230|gb|FC366739.1|FC366739
EST:     TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|37840856|gb|BJ598864.1|BJ598864
EST:     GAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: GAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
EST: gi|162229107|gb|FC405090.1|FC405090
EST:     TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG                         GAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC
genomic: TTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGC

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: 33 (upstream exon), 28 (downstream exon)
Score: 24

GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAGgtggagcgca ... ttttatgcagGAAAAATTAGTAACCAAGGAAGTCGAGTTTTTATTGCTCGCCAGTGATGGCCTGTGGGATGTTGTATCAAACCAG




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