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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG

Basic information

species Glycine max
transcript GLYMA02G43540.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
                                         || | | | | | |||     || || |||      ||||  | |  || || || ||   | ||   |||||| | ||         |  | |||    ||||| | ||||| |||||||| ||||||||| | ||||||||||| || |||||  ||||||| ||||| ||||| |||||||| || ||||| || |||
---------------------------------------gtatttcttgctctgttccacagttcattttgcac-acttgtgttat--tttctgaacttggattcatgatatttatgtat---------tcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG

upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G126795_T01 (Zea mays), 3'ss of exon 9
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgc-ttgcttaagttttctacagattatttacgcatggctatcat---tttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
                                                    | | || ||  |  ||  |||     ||  |||  | |||||  | | |  | || | |     |   ||| | |  |   ||      ||  ||||| | |||||||||||||||||||| ||  | ||||||||||| || |||||  ||||||| || || ||||| |||||||| || || || || |||
---------------------------------------------------gtatccactctattttacagttcattctgcaatggccattgctgtattataattcaaactgag-gcatgtggtttttgtgtattgtgacatgctagAGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAG

upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
                                  |||||   ||| |       |||     || ||  ||   ||  |||  |||  ||     |   |    || ||  |||  |  |         ||   |  ||  ||||| | |||||||||||||||||||| ||| | ||||||||||| || |||||  | |||||  | || ||||| |||||||| || ||||| || |||
----------------------------------gtatccactctcta------ttcgacagttcattctgcaatggctgtattgtaattc----aaactgaggcatatggtttctgtgta--------ttgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG

upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
                                     | ||  ||||    | |   | |   ||| || |     ||    || | | | || | |  |||| |||  |||||         | | || | ||||  |||||||| | ||||| ||||||||||| ||||| ||||| |||||||| ||||||||| ||||||| || || ||||||||||||||||| || ||||| |||
------------------------------------gtgagtacttt----acccaaagtatctaacatcgcacctataag-atattcat-ctcatgaattctgcagcgtatttg-----aatttttatgtaaactgaggcagAGTCTTATGGAGTATGAAGAGCACGAAAAACGTGCCTGGAGTGTTGACTTTTCACGAACAGAACCATCAATGCTTGTATCTGGTAGTGACGACTGCAAG

upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 8
gtaaatgttgaattcaaatggtcagtttgttctt-gtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
                            || ||| | || | |  ||  ||  ||  || | | ||        | ||||    ||| ||||  ||   | | || | || || ||   ||| |||  |  |    |||  |||||| | ||||||||||||||||||||||| || ||||||||||| || |||||| | ||||| ||||| | |||||||||||| || ||||| ||||||
---------------------------ggtcctttgaatgaaaaattctgggctcgccactgacta--------tagatt----tgtccttgtata---tatatatatat-atatatatatg-ctaataaatgttttttatcagAGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAG

upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgct-taagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
||   |     |||   |||  |  |  |||   ||  |    | |||  | | ||  ||  |  || ||| | || |||   |   |||    | | | | |     ||       |  | |   |||  ||   |||  |||||  | ||||||||||| |||||||||||| | || |||||||| || |||||| |||| |||||  | ||||| || || || || |||||  | |||
gtctgtccctcattttgatga-cgttaagttgaagttaccaccccttgaat-tatttttttgtgtatgttggtctgtttgaagttcacttctagttaatgtgcggtgaatggccagggatttgacttcaaattt-tttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG

upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S180_148V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
                                   ||  ||||    |||     || |  |  || |||  |  |   || | ||  || |||  |||   ||    |||| | |  | |      | |||   |   ||||||| | ||||||||||| || |||||||||||||| |||||  | || |||||  | |||||||| || ||||| || ||||| || || ||  | |||
----------------------------------atacaagatgagggggagcaatcctagagaaaaattagtacgtgagtaaggt--ttacttgtgttacttat--gttatcttcctaag-----taatttgtttcgtgcagAGTGTGATGGAATATGAGGAACATGAAAAGCGTGCTTGGAGCATCGATTTTTCTCGTACAGATCCATCAATGCTGGTTTCTGGAAGTGACGATGGAAAG

upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 8
---------------gtaaatgttgaattcaaatggtcagtttgttcttgta---tcagatctttgggtatctt---cattcatta-atattgttttgattgtcatgtgcttgcttaa-gttttctacagatt-atttacgcatggctatcattttaactttg--------gcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
               |   |||  ||| ||| |        ||| |  ||||   || |  |||| |||| ||    |   ||| | |       |||||     |  |  ||  | | || |  | | | || |   | |||  | | ||| || |  | |         ||||||  ||| ||| |||||||||||||||||| | ||||||||||| || |||||| |||| |||||| ||||| | || || || ||||||||  | |||
gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgtgtctgacgtgtctttctggttcacacaggca-agttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
                                        ttttaac  putative branch site (score: 2)
                                   tatcattttaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC