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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA

Basic information

species Physcomitrella patens
transcript PP1S316_34V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G042992_T01 (Zea mays), 3'ss of exon 4
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTA---ATGGGGCTCGA
                                                          ||| |||||  |        |        ||  ||||  ||  |  | |      ||||        | ||    | |     || ||||  |       | ||     || |||||| || ||||| |||||||||||||| ||||| || || || |||||||| ||||||||||||| ||||||| | || |   ||||||   |||| ||    
---------------------------------------------------------ctctacttgttat--------gcctacaa-atctaacaatgctttcagaagcacatttcgtgcatgtaaaagatgaggctaactgggttttctt-------tctaatgcctttcagTCTGAACTGGCAACATCAGCTTTGCAAGAACCCCAGACCAAACCCTGACATCAAGACACTCTTCACTGATCACTCTTGTGCTGCTCCTACCAATGGAGCA---

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 6
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA
                                                            |       | |  |||    ||       |||||   ||| ||     ||||| |    ||||        ||   |||  || |     | | || ||| || | ||  |||  | || |||||||| ||||||||||| ||||| || || ||||||||||| ||||| || ||  |||||||  |||| || |  || ||||| || || 
------------------------------------------------------------taaaaacggatttgcagctctgagtaggggcaaccatgcaattccccctttccat----ttcat-------tttgtatggtgggtaaccttat-tttgttcatgt-ttgacagCTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACATCAAGACCCTTTTTGTTGATCATTCATGTGGACAACCGAATGGTGCACGT

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 4
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA
                                                         |||   || ||  |||   ||||   |            || | ||| ||  || ||  |  ||  | |   | || |      | |||| | | ||  | || ||| ||  ||||||| || |||||||||||||| ||||||||||||||||| ||||| || ||||||||  | ||||  ||||||||||| |  |||||||||||  |||  
--------------------------------------------------------attccttttttaaatgattcttgtaaat-----------tcgaatttt-tagcttgctatgccttgcctat--tttttaatcagtgaatttatctatgcccatt-atcaat--gcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCTAATGGTCCTCTG

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 4
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA
                                                         |||   || || || |   ||||   |   |      | ||  || ||   || |||     || | ||| | ||| |           | ||||    |  ||||| ||  ||||||| || |||||||||||||| ||||||||||||||||| ||||| || ||||||||  | ||||  ||||||||||| |  ||||| |||||  |||  
--------------------------------------------------------gttccttttttaattcattcttgtaaatttgaatttttagcgtgctgtgc-cttgcctattttttaatcagtgaattta-----------tctatgc---cccttatcaat--gcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCCAATGGTCCTCTG

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 4
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA
                                                                     ||     || ||  |    |     |  | | ||  | |||  |||   ||   ||  |  ||||   | |   |    | ||||| |  | ||| ||  ||||| | |||||||| || ||||||||||||||||| ||||| ||||| || || |||||  | |||| ||| ||||||||    |||||||||||  ||| |
-------------------------------------------------------------------gattatatgttatttattat-taatttaatgtatttgatttttaacttgctat--gccttatcattgcttttattaaccgatttgtgtcc-ctaatcaat--gcagTTTAAATTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA
                                                                                        || |  |       |  || ||   | |   ||    |||| |||    | || |  | | |   ||  ||||      ||||||  | || |||||||||||||| || ||||| |||||||| ||||||||||| |||||| | ||| | |||||| | |||   ||  | || || ||||| 
---------------------------------------------------------------------------------------gtgaactaggaggagtcataattctttcctttttttatagag-attag--ttaaagtgtatgacaagtgtgtttgggacattgcagCTTAAACTGGCAGCATCAGCTATGTAAAAATCCAAGGCCTAATCCTGACATCAAGACATTGTTCTTGGATCACTCTTGCTCACCATCAAACGGTGCTCGT

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0002g07020.t01 (Vitis vinifera), 3'ss of exon 4
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgaca--tgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA
                                                                       |    | |     |  ||  |  |    | ||  | || | |   ||    |      |||||  |  | |   | | || |   |    || |    ||||||| | ||||||||||| |||||||||||||| || ||||| ||||||||||| || || ||||| |  || || || || ||||  || |||||  |||| 
-----------------------------------------------------------------------gtaattcgaacaggatattaagtatt-tatttacttttcttcaatgagaaaattgagctattgcaaacttagaaagtgttgttattcttcttgttgccttgcagTTTAAATTGGCAGCACCAGCTTTGCAAAAATCCCAGGCCAAATCCTGACATAAAAACTCTCTTTACAGACCATACTTGTGGGCAACCAAATGGATCTCGG

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatc-tatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA
                                                                      |   |||     |  |  ||  |||| |||     ||    |  || ||   |   ||    |   || ||    |  ||||  |  ||  ||  | | |||||| | ||||||||||| ||||||||||| |||||  |||| ||||| |||||||||||| | ||||  || || ||||| |  ||| | ||||||||||  
--------------------------------------------------------------------actttacatatactgctgtgtgttacac-gca-----tacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 5
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgc-actttgtattttccttcgaattcaccagagtattgacatgaaggattttt-atgtgttcgtttatctattt--gcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA
                                                                            ||    |   ||   |  |  |     |||  |||  | ||  |||||   || | |||   |      ||  | || | | |   | | |  ||   |||| | |||||||||||||||||||||||||| || |   | || |||||||| ||||| || ||  | ||||| || || ||||  || ||||| ||  | 
---------------------------------------------------------------------------tttcacagcaacaaaaaggattgttgagttgagtttgtcatcctattcat--gatttttggttttttcttttcctgatatttccccatgttttattcaacagTTTAAATTGGCAGCATCAGCTTTGCAAAAATCCGAAAGCTAACCCTGACATAAAGACCCTATTTGTAGATCATACTTGTGGGCAGCCAAATGGTGCAAGG

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: 33 (upstream exon), 34 (downstream exon)
Score: 13

TAGAACTCAAAAAACTAATAGAAGCCAATCCACTCTTTCGAGACAAGTTGGCTTTTCCATCATTAAAAGCATCTCGCCTGCGCACCCTTATTAATCAGAGgtaataaata ... ctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaccagagtattgacatgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA
           tattgac  putative branch site (score: 13)
                                        tttatct  putative PPT
                                        tttatctattt  TA-rich tract