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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaatccatggattgtaatataattatacttaatatttttttcgactttcaaaggaaagcttcttgtctacagaatttcataaggtctacaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC

Basic information

species Vitis vinifera
transcript Vv00s0239g00110.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
-----------gtttgaatccatggattgtaatataattatacttaatatttttttcgactttcaaaggaaagcttcttgtctacagaattt---cataaggtctacaactgatatggactgagaactgctaatcagaat-gtatcat-atatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC
            ||  |||  | | | ||  |    |||  |  |||  || |   | |   |      ||    | |    | |  |||||   | |       | | | |   || ||   ||  |||||  | ||    | |  | || |||  ||| | || ||||| ||||||||||||||||| || ||||||||||||||||| ||||| ||||||  |||  |||| ||||| ||||| | |||||||||||
gtcagaaaattattccaattgacgaagtgctactgcattg-atgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC

upper sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 3
-------------gtttgaatccatgg-attgta--atataattatacttaatatttttttcgactttcaaaggaaagcttcttgtctacagaatttcataaggtctacaactg--atatggac-tgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC
               || |||   ||  | ||||   |  | ||||   || | |   ||| ||    |  |  |  ||||      |    | ||  ||||  | | || |||  | |||||  || |   | || | |  | | | ||||   |||  |||   || ||||| ||||||||||||||||| || ||||||||||||||||| ||||| |||||   |||  |||| ||||| || || | |||||||||||
gtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgatcaacttat-atggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagct-attttttcat-cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC

upper sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
gtttgaatccatggattgtaatataattatacttaatat-ttttttcgactttcaaaggaaagcttcttgtctacagaatttcataaggtctacaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC
                                    ||| ||  |  | |  |     || | ||    ||      || |  ||   || ||   |    || |  || ||   | | | |   |  |   |  | | |  ||| ||||||| || || || ||||||||||||||||||||||| |||||||| ||||| || ||   |||  | ||||  |  ||| | | |||||||||||
-----------------------------------gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgt-gcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC

upper sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
gtttgaatccatggattgtaatataattatacttaatatttttttcgactttcaaagg-aaagcttcttgtctacaga-atttcataaggtctacaactgatatggac-tgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC
                                              || | | || |  ||| ||||   |  |   |   |||||||    || || ||  | |    | | ||     ||    ||   ||| | | | |  ||| ||||  |||| |||| ||||||||| ||||| |||||||| ||||| || ||||| ||||||  |||  |||||||| | |||||   |||||||||||
-------------------------------------------aaagattatgaaggctaaatcttcgaatgcatgcacgcttcataaa---tagaaatggaaggagtataaaaatgaagaactttaacacatc-tgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC

upper sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
gtttgaatccatggattgtaatataattatacttaatatttttttcgactttcaaaggaaagcttcttgtctacagaatttcataaggtctacaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC
                                                                                       || |   || | | |   ||  |   |||  ||        ||  |  || | |||| | ||||||||||| ||||||||||||||||| || |||||||| || ||||| || || |||| |||  |||| ||   ||| ||    || |||||||
---------------------------------------------------------------------------------------gtttgacaccgttgttttcttcg---tgcgcatt----ctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC

upper sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
gtttgaatccatggattgtaatataattatacttaatatttttttcgactttcaaaggaaagcttcttgtctacagaatttcataaggtctacaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC
                                                             | |   |||  | | |     |  || | | |    ||  |||    | ||||  | ||         || |   |||||||| | |||||||| || || ||||||||||| || || |||||||||||||| || || || || |  ||  |||| ||  | || || |  || || ||||
-------------------------------------------------------------gttctctgtgaa-aaagagagaggagattttcctacgacttggttctaaaacttgtcat---------tctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC

upper sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ29693 (Selaginella moellendorffii), 3'ss of exon 10
gtttgaatccatggattgtaatataattatacttaatatttttttcgactttcaaaggaaagcttcttgtctacagaatttcataaggtctacaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC
                                                                                       || |   || | | |   ||  |   |||  ||        ||  |  || | |||| | ||||||||||| ||||||||||| ||||| || |||||||| || ||||| || || |||| |||  |||| ||   ||| ||    || |||||||
---------------------------------------------------------------------------------------gtttgacaccgttgttttcttcg---tgcgcatt----ctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAATTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC
                        tgctaat  putative branch site (score: 2)
                                  aatgtatcatatattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaatccatggattgtaatataattatacttaatatttttttcgactttcaaaggaaagcttcttgtctacagaatttcataaggtctacaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA