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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcctttgattgctatcttattactagtattttagttgttatcttacaaaaggtcttataagaactttccttcaataaatcaagGCTAGAATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA

Basic information

species Glycine max
transcript GLYMA20G34340.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os12g16650.1 (Oryza sativa), 3'ss of exon 17
---------------------------------------------------------------------gtaagtgcctttgattgctatct--tattactagtattttag----ttgttatct-tacaaaaggtcttataa------gaacttt----ccttcaataaatcaa-gGCTAGAATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
                                                                       |  || ||| ||| | ||| |  ||| |  |  |          || |||||| || | | ||||| ||         | ||||      | || | ||| || ||||| | | |   ||    ||||| |||||||||||||  |||| ||||| ||||| || || ||||| || || ||||| ||||||||||| || ||  
gtgataattctatcatatagtagtttttgtgtttccacctatctctctctcaccacataatgagagagaacatatgtctt-gatcgatatttactatgaagatgaacccgaccctttcttatctatatacatggtctgatgttccttcaatcttttacatgtccacttaatgaaagGCTAAAGTGGGACAGGATGATGAAGTTCTTGAGATTGGTAGTGGTTGGGGCAGTTTGGCTATGGAAGTGGTGAAGCAAACTGGCTGCAAATATACAGGAG

upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G23480.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtgcctttgattgctatcttat-tactagtatttt-agttgttatcttacaaaaggtcttataagaactttccttcaataaatcaagGCTAGAATAGATAAGA--CACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
|||||  |  | |      || || | || |  ||     |     | | ||      | | || ||   |      ||    || |  |||| || ||| | ||||  || ||||  || | ||||| ||||| |||||||||| ||||||||| |||||||| |||  ||| || ||||||||||||||  
gtaagatctataggagatcattttctatatttttaacaagaaccactgttttttctttg-ttttttagtgatcaaaatttggaaatttcagGCGAGGATAAAGAAGAACCATATGAGGTTTTAGAGATAGGATGCGGATGGGGAACTTTAGCCATAGAAGTTGTGAAAAGAACTGGATGCAAATACACTGG--

upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G23530.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaagtgcctttgattgctatcttattactagtatt--ttagttgttatcttacaaaaggtcttataagaactttccttcaataaatcaagGCTAGAATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
||||  || |||  ||| | |   |  || | |  |  ||  || |    |    ||    |  | | | || || |            |||| |||||||| |||   || ||  || | ||||| |||||||||||||||| ||| ||||| |||||||| | |  ||| || ||||||||||| || |
gtaaa-gcattttcttgatttagaacaacaacttgtggttttttatctcttcttgaataaccgaagagggacatttc------------agGCGAGAATAGAGAAGGACCACGAGGTTTTAGAGATAGGATGTGGATGGGGAACTTTGGCCATAGAAGTTGTGAGAAGAACTGGATGCAAATACACCGGGA

upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G23470.1 (Arabidopsis thaliana), 3'ss of exon 8
---------gtaagtgcctttgattgctatcttattactagtattttag----ttgttatcttacaaaaggtcttataagaactttccttcaataaatcaagGCTAGAATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
           | | | | ||  ||  |   |||| || || | |  ||        ||| ||  |   | |||| |||  |       |    || |  |||| || ||||| ||||  |||||  |  | ||||| ||||| |||||||||| ||| ||||| |||||||| |||  ||| || |||||||||||||| |
gtaaggtctacaggagacatt--ttcttgatttataacaagaagtcaagagtacacgtattttttatttgttctt-taatgatcaattgtgggaaatttcagGCGAGGATAGAGAAGAACCATGAGGTCTTAGAGATGGGATGCGGATGGGGAACTTTTGCCATAGAAGTTGTGAAAAGAACTGGATGCAAATACACTGGCA

upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G23480.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtgcctttgattgctatcttat-tactagtatttt-agttgttatcttacaaaaggtcttataagaactttccttcaataaatcaagGCTAGAATAGATAAGA--CACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA---
|||||  |  | |      || || | || |  ||     |     | | ||      | | || ||   |      ||    || |  |||| || ||| | ||||  || ||||  || | ||||| ||||| |||||||||| ||||||||| |||||||| |||  ||| || ||||||||||||||     
gtaagatctataggagatcattttctatatttttaacaagaaccactgttttttctttg-ttttttagtgatcaaaatttggaaatttcaggcgagGATAAAGAAGAACCATATGAGGTTTTAGAGATAGGATGCGGATGGGGAACTTTAGCCATAGAAGTTGTGAAAAGAACTGGATGCAAATACACTGGCTTTA

upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G23510.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaagtgcctttgattgctatcttattactagtattttagttgttatcttacaaaaggtcttataagaactttccttcaataaatcaagGCTAGAATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
||||  || |||  ||| |   |||  || |    ||  ||  || | ||        |||   || |||         | |  ||| ||| |||||||| |||   |||||  || | ||||| |||||||||||||||| ||| ||||| |||||||| | |  ||| || ||||||||||| || |
gtaaa-gcattttcttgat---ttagaacaacagctt--gtgatttttttgtttctcttctcg-aataaccgaagagggacatttca-gGCGAGAATAGAGAAGGACCATGAGGTTTTAGAGATAGGATGTGGATGGGGAACTTTGGCCATAGAAGTTGTGAGAAGAACTGGATGCAAATACACCGGCA

upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv05s0049g01620.t01 (Vitis vinifera), 3'ss of exon 14
gtaagtgcctttgattgctatcttattactagtattttagttgt--tatcttacaaaa--ggtcttataagaactttccttcaataaatcaagGCTAGAATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
|| |||   ||      | |    || | |  |   ||  || |  |  | | | |||  | | || |  |   |  | |  ||  || | |||| ||||| |||||||  |||||| || | |||||||| ||||| |||||||||||||| |||||||| || |||||||| || || ||||||||||| |
gtgagtcttttctgcaacaactacatgaattttgaattgattttcttgccatgctaaattgattttctgtgttttcccatctaaccaacctagGCAAGAATTGATAAGAAGCATGAAGTTTTAGAGATTGGTTGTGGTTGGGGAAGTTTAGCTATTGAAGTCGTGAAACAAACTGGATGTAAATACACTGGCA

upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 18
gtaagtgcctttgattgctat--cttattactagtattttagttgttatcttacaaaa--ggtcttataagaactttcc--ttcaataaatcaagGCTAGAATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
|| |||   ||      | |   |||     | | |||    || ||  | | |||||    | || || |   |||||  |  ||  || | |||   |||| |||||||  |||||| || | |||||||| ||||| |||||||||||||| ||||||||||| |||| ||| || |||||||||||||| |
gtgagtcttttctgcaacaactgcttgaattttgaattgattttcttgccatgcaaaattaattttctatgtgttttcccatctaaccaacctagGTACGAATTGATAAGAAGCATGAAGTTTTAGAGATTGGTTGTGGTTGGGGAAGTTTAGCTATTGAAGTTGTGAAACGAACTGGATGCAAATACACTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagttgttatcttacaaaaggtcttataagaactttccttcaataaatcaagGCTAGAATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
           atcttac  putative branch site (score: 3)
                                         ttcaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcctttgattgctatcttattactagtattttagttgttatcttacaaaaggtcttataagaactttccttcaataaatcaagGCTAGAATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG