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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcacgtatctcgtctgtaccgaagattacttaagaagctcgaagtatttgggatttgaagcaaattttgtaaaatttgttccgtatgagtattcatcgcctcaccttggtgttcgctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG

Basic information

species Physcomitrella patens
transcript PP1S17_286V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 5
gtgagtcacgtatctcgtctgt--accgaagattacttaagaagctcgaagtatt-tgggatttgaagcaaattttgtaaaatttgttccgtatgagtattcatcgcctcaccttggtgttcgctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG
         |||| ||  || |  | | |    |  |   || |||  |  ||   |    || ||     |      |    ||  ||  ||  | |  | |    ||    |||| |     | ||| ||| || ||||| |||||||||||||||||||||||||| |||||||| |||   || |||||  ||||||| || ||||| ||||| ||  ||
---------gtatttcaactcttgatctattcattgtgctgatgctacatttaccctttttttcgacattgaacaccaagtccttaatctataaaaatgctaaaattctg---ttggcggaaatt-ttgtagGAACATGGCGCGTGGGTGGTGTTCTTGCTGTCTCTCGAGCATTTGGTGACAAACTCCTGAAGCAATATGTGGTTGCTGATCCAGAGATCAAG

upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 5
gtgagtcacgtatctcgtctgtaccgaagattacttaagaagctcgaagtatttgggatttgaagcaaattttgtaaaatttgttccgtatgagtattcatcgcctcaccttggtgttcgctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG
                                       ||  ||    |   |  ||  | |   |  ||   |   | ||||     ||||  |||  |    ||     | ||  ||   ||||||| || |||||||| ||||||||||||||||| ||||| |||||||| ||    ||  ||||  | |||||||| ||||| ||||| ||  ||
-------------------------------------gtaatttcatgattcctttgaaattatctattttgctttgtacttgta----atgatcattggttctttctaacggttgaacgactttgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG

upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g05630.3 (Oryza sativa), 3'ss of exon 5
gtgagtcacgtatctcgtctgtaccgaagattacttaagaagctcgaagtatttgggatttgaagcaaattttgtaaaatttgttccgtatgagtattcatcgcctcaccttggtgttcgctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG--------
                                       ||  ||    |   |  ||  | |   |  ||   |   | ||||     ||||  |||  |    ||     | ||  ||   ||||||| || |||||||| ||||||||||||||||| ||||| |||||||| ||    ||  ||||  | |||||||| ||||| ||||| ||  ||        
-------------------------------------gtaatttcatgattcctttgaaattatctattttgctttgtacttgta----atgatcattggttctttctaacggttgaacgactttgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGGTTTGACT

upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
gtgagtcacgtatctcgtctgtaccgaagattacttaagaagctcgaagtatttgggatttgaagcaaattttgtaaaatttgttccgtatgagtattcatcgcctcaccttggtgttcgctgtt-gcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG
                               || | |     ||     ||| |   |   ||| | |  ||     ||| ||| ||  || | | ||  |       | |   | ||||   || | ||| || ||||| |||||||||||||||||||||||||| |||||||| ||    ||  ||||  | ||||| |||||||| || |||||  ||
------------------------------gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgcc--attactgttgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG

upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv18s0001g15050.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtcacgtatctcgtctgtaccgaagattacttaagaagctcgaagtatttgggatttgaagcaaattttgtaaaatttgttccgtatgagtattcatcgcctcacct-tggtgttcgctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG
                          | |||||      |||||| ||  ||    | | | |     ||||   | | |    |     |||   |||           | ||   ||| ||     ||| || ||||| || ||||||||||||||||| ||||| |||||||||||    ||||| ||   |||||| || ||||| ||||||||||||
-----------------------gttatgattatcccc-aagctccaatgatacaag-tctaacatggatttcagatagtaaactgtacctgaaatttctctaaaatgtttctgaacttcact-----agGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG

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:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTT-GGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|162184832|gb|FC361134.1|FC361134
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|162195745|gb|FC371136.1|FC371136
EST:     ATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: ATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|208378728|gb|DC914702.1|DC914702
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTANTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTNGGG-ACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|208398836|gb|DC920784.1|DC920784
EST:     GAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: GAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|162243725|gb|FC421846.1|FC421846
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|208381790|gb|DC928453.1|DC928453
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|162245393|gb|FC421295.1|FC421295
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|19780877|gb|BQ039620.1|BQ039620
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|100401328|gb|BY990947.1|BY990947
EST:     GATGAACGGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGGTCTTGCTGTCTC
genomic: GATGAACGGG-AACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTC
EST: gi|208352662|gb|DC921396.1|DC921396
EST:     TGATGAACNGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|162229107|gb|FC405090.1|FC405090
EST:     GGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: GGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC

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), 31 (downstream exon)
Score: 28

CCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatttgttccgtatgagtattcatcgcctcaccttggtgttcgctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG
                            gcctcac  putative branch site (score: 28)
                    tattcat  TA-rich tract