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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagcttcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG

Basic information

species Physcomitrella patens
transcript PP1S235_92V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
---tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagcttcttcaagcatgtta-catactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG
   || ||  |   | |   ||| ||   | |  |||   ||  | |     |      ||    |||||  ||  | | || ||| ||||    || |  |||||||||||||| ||||| || || |||||||| ||||||||||| || || || ||  | ||| | || ||||| |||| ||| |||||||||||||||
tagtataataattatttgttattgcatcttaagattcatttgtatcactgctt----attttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG

upper sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagct---tcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG
 |    |||||  |    |||     || || | | ||   |     | |   || |   | | || |||  |    |  | | | | |  || |   |  ||||||| ||||| |||||||| ||||| |||||||||||||| || || ||||||||| | ||| | || ||||| || |||||||||||||||||||||
-agctggaactattccagttaatccattgagat-gtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatat-tctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
----tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagcttcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG
    |  ||  ||  |   ||||| |   ||  | |||  ||  || |  | |  |||   | ||  |  |||    ||    |||| ||  |  |    | ||||  |  | || |||||||| |||||||  || |||||||| || || ||||||||  | ||| | || ||| |||||||||||||||||||||| |||
tacctggaaaaaaaatgccacattcccttctgtacttcatcttatttagtaaa--ataaaatatttgaa-atgaataatttctaactagtt-tctttttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
-----tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagcttcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG
        ||  ||  |   ||||| | | ||  |||||  ||  || |  | |  | |   | |  ||     | |  |  | |  || |  |       | ||||  |  | || |||||||| |||||||  || |||||||| || || ||||||||  | ||| | || ||| |||||||||||||||||||||| |||
tacctggaaaaaaaaatgccacattcccatctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttc-----cttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------------------------------------------------------------------tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagcttcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG
                                                                                         |    |   ||  ||  |||  |    |||     | ||    |||| |  | |             || | || ||    |  ||||   | |  | |||||||| | ||||||||||| ||||||||||| ||||| ||| |||| ||||||||  | ||| | || |||||||| ||||| || ||||||||||||
gtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattt-tatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattagGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAG

upper sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagcttcttcaagcatgttacatactga-acttgtcatgg---tggatt-cagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG
       ||||||    |  |  || |||| | |   || |  |    |  ||   ||   |||   ||||| | |   |   |||| |      |  ||| ||||||||| | || |||||||| || |||||||| |||||||| || || ||||||||  | ||| | || ||||| ||||||||||||||||||||||||
-----gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG

upper sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ11749 (Selaginella moellendorffii), 3'ss of exon 1
tacaacgaacttcttacattacaagcttaagttcgactgcttgaa-aatatcatagcttcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG
                                  |   ||| ||   | ||| |  ||||| | |   ||||| || |||   ||       |   | ||||||||| | |||||  ||||||| || ||||| || || ||| ||||||||||  |  | ||||| || ||||||||||| |||||||| |||||||||
----------------------------------gtacgctagagcgaaatcgt--cttctaccactctgttaaattctgggattcgtgcctt---tccagGTTGGCTTGCCTGCGAGAGGGAAAACGTTTACTGCCGCGAAGTTGACGAGATACTTACGTTGGCTGGGACATGATACCAAGCACTTCAACGTTGGAAAG

upper sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ22544 (Selaginella moellendorffii), 3'ss of exon 1
tacaacgaacttcttacattacaagcttaagttcgactgcttgaa-aatatcatagcttcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG
                                  |   ||| ||   | ||| |  ||||| | |   ||||| || |||   ||       |   | ||||||||| | |||||  ||||||| || ||||| || || ||| ||||||||||  |  | ||||| || ||||||||||| |||||||| |||||||||
----------------------------------gtacgctagagcgaaatctt--cttctaccactctgttaaattctgggattcgtgcctt---tccagGTTGGCTTGCCTGCGAGAGGGAAAACGTTTACTGCCGCGAAGTTGACGAGATACTTACGTTGGCTGGGACATGATACCAAGCACTTCAACGTTGGAAAG

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: 30 (upstream exon), 32 (downstream exon)
Score: 6

GCCATGCCAGAAGCCGCTGGTGCTGTAGCTGCTGGAGCTGTTGCCGACCATATGTTGGGGTCCAAGGAACGTGGCCAGCTAGCAATCATTCTGgtatgcatcc ... gtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatcatagcttcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG
                        ttacata  TA-rich tract