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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatcaatgttcttccattccctctttctttttcctcgaacaatttctgtggtaagtcttatatttagaatttaagttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC

Basic information

species Physcomitrella patens
transcript PP1S425_12V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 8
------------------------------------------------------------------aaatcaatgttcttccattccctctttctttttcctcgaacaatttctgtggtaagtc----------ttatatttagaatttaagttcgaatctc----tcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC
                                                                   | |  || |      |||  || | |  || |    | |  |||| |     ||||           ||| |  |||||  ||  ||| ||   |    |  |  | || ||||| |||||||| || |||||||| || ||||| |||||||| || || || ||||| ||||| |  || ||||||||||||||||| || || |||||| 
gtacatatagcagacttttgaagttctgattcataccaatttgttatgcatggaaactaattctgctagtgtatatgtgcttattttctgtatggttatatatgcatcatttttaacagaagttgacctgattgttaaaggtagaacatattttctaacaccaggctactctgtttacagGCAAATGATCCCACCATTGAACGTATCATCACCCCTCGAATTGCACTGACAACTGCAGAATATTTGGCATATGAATGTGGGAAGCACGTGCTTGTCATCT

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 8
aaatcaatgttcttccattccctctttctttttcctcgaacaatttct----gtggtaagtcttatatttag---aatttaagttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC
          || ||    ||  | |     |    | || |  ||||    |||  |       | | |||   |   ||  ||  |  |  |  |   ||| |||||||||||||| || |||||||| |||||||| ||||| || || || || || || ||||| |  || |||||||||||||||||||| || |||||| 
-------ctatcctctggccctgcataacgatgagccaaatatattctacatgtgacataatcagtgtatagcacagcatatttttaacaccttgatcctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCAGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTCATCT

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 8
aaatcaatgttcttccattccctctt--tctttttcctcgaacaatttctgtggtaagtcttatatttagaatttaagttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC
||| |||  ||         | | ||  | |  |  || | |  |  |   |  |   |   || ||       ||| |  |||| | |  |   || |||||| |||||||| || |||||||| |||||||||||||| || || ||||||||||||||||| |  |||||||||||||| |||||||| || || || |
aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaagtagctaatccctaaaatgttctcttgctaa-tgtgaatatgtgatttact-gcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 9
aaatcaatgttcttccattccctctttctttttcctcgaacaatttctgtggtaagtcttatatttagaattta--agttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC
||| |||  ||         | | ||  |||     |   || |    | | |||  | || | |      ||   | |  |||| | |  |   || |||||| |||||||| || ||||| || |||||||||||||| || || ||||||||||||||||| |  |||||||||||||| ||||| || || || || |
aaagcaaaatttaaatgaggctttttgatttcctgacttgca-tgaaggagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttact-gcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 8
--aaatcaatgttcttccattccctctttctttttcctcgaacaatttctgtggtaagtcttatatttagaatttaagttcgaatctctcttgggc-ttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC-
    || |   || | | |||  |   || |  || |    |  |  | | ||      || ||  ||| |||      ||   |  || |      || ||||| |||||||| |||||||| || || ||||||||||| || || ||||||||||||||||| |  || ||||||||||| |||||||| || || || | 
gtggatgatcattgtgctatttgcaaattttgatttc----atgacctgtatgaaggagctgatcattaaaatcctgtctcttgttgctgtgatttattacaggCAAATGATCCTACGATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATACT

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 8
---aaatcaatgttcttccattccctctttctttttcctcgaacaatttctgtggtaagtcttatatttagaatttaagttcgaatctctcttgggc-ttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC
     || |   || |   |||  |   || |  || |    |  |  | | ||      || ||  ||| ||||     |    |  || |    | ||  |||| |||||||| || ||||| || || ||||||||||| || || ||||||||||||||||| |  || ||||||||||| |||||||| || || || |
tgtggattatcattgtgttattttcaaattttgatttc----atgacctgtatgaaggaactgatcattaaaattctctcttttgttgctgtgattcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------aaatcaatgtt--cttccattccctctttctttttcctcgaacaatttctgtggtaagtcttatatttagaatttaagttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC
                    |  | |  |   ||| || |   |  ||||  | || | |  | |    |  ||  ||     |   ||||| |  ||   ||   |      |   ||||| ||||||||||| |||||  | ||||||||||||||||| ||||| || || |||||||| |  |||||||||||||| |||||||| || || ||  
gtaatttactagttactagtactactagtaatttctatgcttccaatcttacttcttgtagtactatcatattatatca---gtgaggaattgaccttattatgcattccactcgaacagGCCAATGATCCAACCATTGAGAGAATTATCACTCCTCGAATTGCCCTAACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGCATGTGCTTGTTATAT

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
aaatcaatgttcttccattccctctttctttttcctcgaacaatttctgtggtaagtcttatatttagaatttaagttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC
          |||  || || | ||       || |  | ||| || |      | | || |  | |   |||       | ||| | ||  ||   ||||| || || || || ||||| || || ||||||||||| ||||| ||||| |||||||| ||||  || ||||||||||| ||||||||||| ||||| |
-----gcaagtctcgcaatcacactacagacatcttgaagcaaattttagttccaatgtttttctgaaggttt----ctcattctgttttccgc--acagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 8
aaatcaatgtt-cttccattccctctttctttttcctcgaacaatttctgtggtaagtcttatatttagaatt---taagttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC
   | ||| |  |||| ||  |   || |  | || | ||    ||||     |     |  |  ||||  ||    |  ||  |   ||  ||   |   ||||| ||||| ||||| |||||  | || |||||||||||||| ||||| || || ||||||||    ||||||||||||||||| || ||||| || ||  
--gtaaatttgacttctatagctgattgccatatcatggagttttttcaagtatttagatgtttcttagctttaaacagatttaaccttcctttattccaacagGCCAATGACCCAACCATTGAGAGAATCATCACTCCTCGAATTGCCCTCACAACAGCTGAATATCTGGCTTATGAATGTGGGAAACACGTCCTTGTTATAT

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 8
------------aaatcaatgttcttccattccctctttcttt---------ttcctcgaacaatttctgtggtaag------tcttatatttagaatttaagttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC
            || | ||| |  |  | |       || |||         |  |||     ||||  |||| | |      | ||   ||||  ||||    |    |  |||||  ||   ||||| |||||||| || || ||||| ||||||||||||||||| || || || ||||| ||||| |  |||||||| |||||||||||||| || || ||  
gtatcaattaataatttaatctcttatcctaattatgttgtttaggatgatctctctcatttcatttaggtggaagggtgttttttttcttttaatatttgtaatgatgtggctcttttgc--acagGCCAATGATCCCACCATAGAACGCATTATCACTCCTCGAATTGCTCTCACAACTGCAGAATATTTGGCTTATGAGTGTGGGAAGCATGTTCTAGTTATAT

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 8
-----------aaatcaatgttcttccattccctctttctttttcctcgaa---caatttctgtggtaagtctt---atatttagaattta--agttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC
           |||| ||| |  |   |||   | ||  || |      ||    || || |     | |  |    ||| || |  || |  ||||         ||   |    ||||| || || || || |||||||| || |||||||||||||| || || || ||||||||||| |  || ||||||||||| || ||||| || ||||| |
gtatttatattaaattaatatagtggtatttattattgtttgtggtgtaaattctaaattttaaaccaggcttcagaatagttggctttgaatagtttctgatatgctcaagtggacagGCCAACGACCCCACCATTGAACGCATCATCACTCCTCGAATTGCTCTCACCACTGCTGAATATTTAGCATATGAATGTGGCAAACATGTTCTTGTCATAC

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: 11 (upstream exon), 35 (downstream exon)
Score: 5

TTAACATGGAGACAGCTACTTTCTTCAAACGTGATTTCGAAGAAAATGGATCTATGGAGAGAGTGACACTTTTTCTCAACTTGgtatgtttca ... gggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtggtaagtcttatatttagaatttaagttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC
                                     tctctcttg  CT-rich tract
       taagtcttatatttag  TA-rich tract