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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgttggcttgctgcaagctacgactttgtagtactatcaggacattggaatcagttcagtatttgtcatgctagttatctccattactcctactaatgaatctaggggagtttttatgtacattatcttttaaaattcgaaatgacctaagtttctgatatttagattgatgtcacattctcagGTACTGGAGATCAATTTGGTCACATTTCCCAATGTGGCTGATGCAATTCTGGCGAATGGCATGTTCTCCCATTATGATCGTCCTCGCATTGCTCAACTCT

Basic information

species Physcomitrella patens
transcript PP1S452_30V6.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 8
gtgtgtgttggcttgctgcaagctacgactttgtagtactatcaggacattggaatcagttcagtatttgtcatgctagttatctccattactcctactaatgaatctaggggagtttttatgtacattatcttttaaaattcgaaatgacctaagtttctgatatttagattgatgtcacattctcagGTACTGGAGATCAATTTGGTCACATTTCCCAATGTGGCTGATGCAATTCTGGCGAATGGCATGTTCTCCCATTATGATCGTCCTCGCATTGCTCAACTCT-----------------------------------
                                                                                                                                                                                             |     || ||||  ||| |  | || || ||||| |||||||| ||||| || ||||| ||||||   ||||||||||| ||||| |||||||| || |                                   
------------------------------------------------------------------------------------------------------------------------------------------------------------nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcggatgaaatcagcttgatt-cgttcccgaatgttgctgatgccattcttgctaatggtatgttcagTCATTATGATCGCCCTCGTATTGCTCAGCTGTGTGAAAAGGCTGGGTTGTACTTGCGAGCCCTCCAG

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 16
gtgtgtgttggcttgctgcaagctacgactttgtagtactatcaggacattggaatcagttcagtatttgtcatgctagttatctccattactcctactaatgaatctaggggagtttttatgtacattatcttttaaaattcgaaatgacctaagtttctgatatttagattgatgtcacattctcagGTACTGGAGATCAATTTGGTCACATTTCCCAATGTGGCTGATGCAATTCTGGCGAATGGCATGTTCTCCCATTATGATCGTCCTCGCATTGCTCAACTCT
                                                                                | |  || ||  | ||  |  ||    || |||  ||||  | |  |   |||||     || ||| ||        ||  ||| ||  ||      |||| |  ||||||  ||||||| ||| |||| || || |||||||| |||||||||||  |||| ||||||||||||  ||||||||| |||||||| ||||| ||||| |
-------------------------------------------------------------------------------gtgtggcctttgtttctcatc-tg---ttatgggcattttactctgaaaattctttc----tttgaagtg--------ttacgatgttgtga-----atcac-tgttcagGTGTTGGAGATAAATCTGGTGACTTTCCCCAATGTTGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAACTTT

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 16
gtgtgtgttggcttgctgcaagctacgactttgtagtactatcaggacattggaatcagttcagtatttgtcatgctagttatctccattactcctactaatgaatctaggggagtttttatgtacattatcttttaaaattcgaaatgacctaagtttctgatatttagattgatgtcacattctcagGTACTGGAGATCAATTTGGTCACATTTCCCAATGTGGCTGATGCAATTCTGGCGAATGGCATGTTCTCCCATTATGATCGTCCTCGCATTGCTCAACTCT
                                                                          |   ||   ||   || ||| | |         || |||  || |  | |  |   |||||     || ||| ||     |  || |||       |||| |||       ||||||  ||||||| ||| |||| || || |||||||| |||||||||||  |||| ||||||||||||  ||||||||| |||||||| ||||| || || |
--------------------------------------------------------------------------gtgtgtggcctttgtttctcatccg-------ttatgggcattctactctgaaaattctttc----tttgaactgttacgatcttgtga-------attgctgt-------tcagGTGTTGGAGATAAATCTGGTGACTTTCCCCAATGTTGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAGCTTT

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 16
gtgtgtgttggcttgctgcaagctacgactttgtagtactatcaggacattggaatcagttcagtatttgtcatgctagttatctccattactcctactaatgaatctaggggagtttttatgtacattatcttttaaaattcgaaatgacctaagtttctga---tatttagattgatgtcacattctcagGTACTGGAGATCAATTTGGTCACATTTCCCAATGTGGCTGATGCAATTCTGGCGAATGGCATGTTCTCCCATTATGATCGTCCTCGCATTGCTCAACTCT
                                                                                                     ||||  |||  |     || | |   |    ||||    |    | | ||||   || |  |   | |||| ||   | |   |  | ||||| |||||||| |||||||| || ||||| ||||||||||||||  |  | || ||||| |||||| |||| ||||| || ||||||||||||||||| |
---------------------------------------------------------------------------------------------------gttgaaaatagttgccaccttgtatctctccgtttttt---tctctactcaccttctttccccagactgtttaaatcatttttcaa--cacagGTTCTGGAGATAAATTTGGTAACTTTTCCTAATGTGGCTGATGCGGTATTAGCAAATGGGATGTTCACCCACTATGACCGGCCTCGCATTGCTCAACTTT

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 16
gtgtgtgttggcttgctgcaagctacgactttgtagtactatcaggacattggaatcagttcagtatttgtcatgctagttatctccattactcctactaatgaatctaggggagtttttatgtac-attatcttttaaaattcgaaatgacctaagtttctgatat-ttagattgatgtcacattctcagGTACTGGAGATCAATTTGGTCACATTTCCCAATGTGGCTGATGCAATTCTGGCGAATGGCATGTTCTCCCATTATGATCGTCCTCGCATTGCTCAACTCT
                                                                                                         |  |   |||||   |  |   | |    | |    | |  | | ||||   ||||| | |  ||  | ||   || ||  | |||||  |||||||||||||||| || ||||| |||||||||||||||||  | || ||||| ||||||  ||||||||| || |||||  ||||||| || |
--------------------------------------------------------------------------------------------------------gttgaaaagagttgccaccttttacttctctgtgctttccctactcaccttcctttcttagaccttttagtgcactctcaa-cacagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT

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: 28 (upstream exon), 28 (downstream exon)
Score: 5

CGCAACATGATCAGGGAGGCAACCGCGTTTCTTTTGGATATTCTGAAGCCTAATTTACCGGAGCATGCCCTACTTCAAACCAAGgtgtgtgttg ... acattctcagGTACTGGAGATCAATTTGGTCACATTTCCCAATGTGGCTGATGCAATTCTGGCGAATGGCATGTTCTCCCATTATGATCGTCCTCGCATTGCTCAACTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaattcgaaatgacctaagtttctgatatttagattgatgtcacattctcagGTACTGGAGATCAATTTGGTCACATTTCCCAATGTGGCTGATGCAATTCTGGCGAATGGCATGTTCTCCCATTATGATCGTCCTCGCATTGCTCAACTCT
                                              cattctc  CT-rich tract
                            atatttagattgat  TA-rich tract