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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcgtgagtggatcaatttagcttttactttttcaggaatgttcacaagtagtatgttctgttcttcgtgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA

Basic information

species Physcomitrella patens
transcript PP1S408_23V6.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 17
tgtcgtgagtggatcaatttagct--tttactttttcaggaatgt-tcacaagtagtatgttctgttcttcg------tgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA
            ||    |||| |  ||||        | | ||| |   |  |  |  ||| | || ||        | ||  |||| |   |  | |     |  ||||| ||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    || ||  | ||||  |  |||
---------cacattttcttaggtaatttaagcccctggaactgtatttgatctgattagttttcttattaaataaattattaattgattgtgttttaatggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
-tgtcgtgagtggatcaatttagcttttactttttcaggaatgttcacaagtagtatgttctgttcttcgtgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA
 | |  |  |      | ||||  || | |   |  |    ||||       | ||  ||   |  |   | ||  ||||  || |  ||     |   ||||| ||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    || ||  | ||||| |  |||
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctca-agGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
tgtcgtgagtggatcaatttagcttttactttttcaggaatgttcac--aagtagt-atgttctgttcttcgtgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA
 ||  ||    ||  | ||    ||||   |  | |    ||||      | |||| |  || |  | |   |  |||||   ||| |  ||     ||| ||||| ||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    |||||  | || || |  |||
-gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttt-tcacttttc-tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 18
tgtcgtgagtggatcaatttagcttttactttttcaggaatgttcacaagtagtatgttctgttcttcgtgtttgttgagtcat--tcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA
     |||       | | |    | |||||| ||||     ||   ||    |    |   ||  ||  |  | || |   |   | | ||     |  |||||||||||||||||||||||||| ||||| ||||||||||| || |||||||| || ||||| |||       |    ||  |  | ||||| |   ||
--caatgacacccctagtatcctgtctactttctcagcccactttttaaaacattgactgaatttgtcaagcatattaatgaaagattaccattttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 18
tgtcgtgagtggatcaatttagcttttactttttcag----gaatgttcacaagtagtatgttctgttcttcgtgtttgttgagtcattcatcacac-attgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA
     |||       | ||     | |||||| ||||    |  | | ||  | |   ||  | |||    | | |   |  |  |  | | ||     ||| |||||||||||||||||||||||||| ||||| ||||||||||| || |||||||| || || || ||        |    ||  |  | || || |   ||
---aatgacacccctagttgcctgtgtactttctcagcccaggttttacagcattgacataatttgtcaggcatatgaatgaaagc--ttaccatgttgttgtagGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTA

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 18
-tgtcgtgagt-ggatcaatttagcttttactttttcaggaatgttcacaagtagtatgttctgttcttcgtgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA
 | |  | | |   | || | | | | || |||| |  |       |  ||| |  | |||          |||||||| |  | ||||     |||  |||||||||||| || ||||||||||| |||||||| || || || || ||||||||||| ||||| ||        || | ||| |  | ||||||| ||| 
gttttataaatcaaaacattcttgttatttctttctttg-------cggaagaaaaa-gttgaa------atgtttgttaaaac-ttcaatgtgcatgacagGAAGAAGAACATATTTAAGTTGGCGCAAGGAGAATATATAGCACCAGAGAAGATCGAAAATGTTTATACCAAATGTAGATTCGTTTCGCAGTGTTTCATT

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 18
-------------------------------------------------------------------------------------------tgtcgtgagtggatcaatttagcttttactttttcaggaatgttcacaagtagtatgttctgttc--ttcgtgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA
                                                                                           | || ||      | | |||    || |  |  ||    ||  | |||      ||   |||| |  ||| |   | |  | | |    |   | ||  |||||||||||| || ||||||||||| |||||||||||||| || || ||||| || |||||||| ||   |    |    ||  |  | ||||| |   ||
gtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTA

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|162171191|gb|FC346362.1|FC346362
EST:     GGTGATATTGGGTGTTGGTTGCCAGGTGGTCGGCTCAAAATCATCGACAG                         GAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAA
genomic: GGTGATATTGGGTGTTGGTTGCCAGGTGGTCGGCTCAAAATCATCGACAGgtactgtcgt ... cacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAA
EST: gi|19778765|gb|BQ039356.1|BQ039356
EST:     GGTGATATTGGGTGTTGGTTGCCAGGTGGTCGGCTCAAAATCATCGACAG                         GAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAA
genomic: GGTGATATTGGGTGTTGGTTGCCAGGTGGTCGGCTCAAAATCATCGACAGgtactgtcgt ... cacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAA
EST: gi|37848450|gb|BJ606458.1|BJ606458
EST:     TTGGTTGCCAGGTGGTCGGCTCAAAATCATCGACAG                         GAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAA
genomic: TTGGTTGCCAGGTGGTCGGCTCAAAATCATCGACAGgtactgtcgt ... cacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAA
EST: gi|162205653|gb|FC381881.1|FC381881
EST:     GGTGATATTGGGTGTTGGTTGCCAGGTGGTCGGCTCAAAATCATCGACAG                         GAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAA
genomic: GGTGATATTGGGTGTTGGTTGCCAGGTGGTCGGCTCAAAATCATCGACAGgtactgtcgt ... cacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAA
EST: gi|162163688|gb|FC340287.1|FC340287
EST:     GGTGATATTGGGTGTTGGTTGCCAGGTGGTCGGCTCAAAATCATCGACAG                         GAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAA
genomic: GGTGATATTGGGTGTTGGTTGCCAGGTGGTCGGCTCAAAATCATCGACAGgtactgtcgt ... cacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAA

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), 31 (downstream exon)
Score: 8

ACGGGAGATTTTTGATGAAGAGGGCTGGTTACATACTGGTGATATTGGGTGTTGGTTGCCAGGTGGTCGGCTCAAAATCATCGACAGgtactgtcgt ... cacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA




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