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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaatataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT

Basic information

species Glycine max
transcript GLYMA13G43680.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13
gtaagtactttgattaggtgacatttagttatctgctcttttccttct---tatt-cattgtttaatataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|| |||| |||  ||    ||  |  | || | |   | | || ||     ||||    || | ||||  || |  ||  | || ||||   |||| ||||| ||||| || ||||||||| |||| |||||||| || || || |||||||||||| |||||||||||
gtgagtaattttgttcctggatttaaatttttttttgcgtgtcatttggaatattatgatgctaaataggatctgctttcttat-ttgt---agAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4
gtaagtactttgattaggtgacatttagttatctgctcttttccttcttat-tcat--tgtttaatataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|| |||| |||  ||    ||     | |||| |    | |   ||   || | ||  || | ||||  ||    ||  | || ||||   |||| ||||| ||||| || ||||||||| |||| |||||||| || || || |||||||||||| |||||||||||
gtgagtaattttgttcatggattcaaatttattttgcgtgtcatttggaatattatgatgctaaataggatccgctttcttat-ttgt---agAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
gtaagt--actttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaata--taattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|| |||  | | | ||    ||| |||||   ||     |||||      | |||||  |  ||||  || |||||| | |    ||   | ||||||| || |||||||| || ||||| |||||  |||| || || ||||||||||||||||| ||||||||||| 
gtgagtcaaatattatctattgatatttatagattgatacttttaacgaat-ttcatactgaaataactagttttgtcactgtattt---ttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
gtaa-gtactttgattaggtgacattt-agttatctgctcttttccttcttattcattgtttaatataattttgttattaatcttgtgt-cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|||| | | |||| |    |   |||| |    | |  |    | | |   |||     | |  |   | |       |  |  | |||  |||| || ||||||||||||||||||||| ||||||||||||| || ||||| |||||||||||| |||| || |||
gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
gtaagtac-tttg--attaggtgacatttagtt----atctgctcttttccttcttat-------tcattg--tttaatat----aattttgt--tattaa--------tcttgtgt-cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
||||  || ||||  ||| | || | | || ||    | ||| | ||    |||  ||       | || |  ||| | ||    ||| ||||   | | |        |  | |||  |||| || ||||||||||||||||||||| ||||||||||||| || ||||| |||||||||||| |||| || |||
gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 14
----gtaagtacttt-gattaggtgacatttagttatctgctcttttccttcttattcattgtttaatataattttgtt--attaatcttgtgtc------agAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
    ||   |||||| | ||  |  |    ||   |||   | ||||   |||| ||      ||||    | |    |  |||| ||||||| |      ||||  | || |||||||||||||||||| | || ||||| || |||||| | |||||||||||| |||||||||||
gtgagtcgttacttttgcttcagcaatggatacccatcatgtgtttttactcttttttgcc--ttaacgccactggaattgattactcttgtgcctggtgtagAATGTATATTGGGCTGACAGTGGTGATTTGGTGACAATAGCAAGCGATTCGTCATTCTACATTTTGAAGTACAAT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 13
gtaagtactttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaatataattttgttattaatcttgtgtc---agAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
    ||   |  |     | |  |||  ||   ||    |||  |   |||     ||||||||| |   | || || ||| |||||    ||||  | ||||||||||| |||||||| |||||  |||| || || ||||||||||||||||| || |||||||||
----gtgagtcaaaagtattatttttccttgggtggaaattttgtatgtatga---gtttaatattaaccttttgtttatcatgtgtttatagAATGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
gtaagtactttgattaggtgacatttagttatctgc-----tcttttccttcttattcatt-gtttaatataattttgttattaatcttgtgt---cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
         |  || | ||   ||||  |  |  |      | || |   |   ||  ||  ||||| ||| |   | || || ||| ||  |    ||||| | ||||||||||| |||||||| |||||  |||| || || ||||||||||||||||| || |||||||||
--------gtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
--------------------------------------------------------------------------------------------gtaagtactttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaa--tataattttgttattaatct--tgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
                                                                                              ||     ||  |||  ||| |||||          |   |   |  |  ||  |  || |  | |||  || || || ||    ||| |||||| || || ||||| |||||||||||||||||  ||||||| || ||||||||||||||||| || |||| ||||
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
-------------------------------------------------------gtaagtactttgattaggtgacatttagtt--atctgctcttttcctt-cttattcattgtttaat--ataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
                                                          | || |   |     |  ||||   ||   | ||   |||||||   || ||  || | ||||   || | ||| ||   | | | || ||||| || || |||||||||||||||||| ||||| | |||||||| || ||||||||||||||  |||| | ||| 
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttg-cagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------------gtaagtacttt--gattaggtg---acatttagttatctgctcttttccttcttattcattgtttaatataattttgt-----tattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
                                          | | |  |||   |||  ||    ||||||  || || | |        ||  | | | ||| |    ||| | | |      || ||   | || ||||| || || |||||||| ||||||||| ||||| | |||||||| ||||| |||||||||||  |||||||||||
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttg-cagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
--------------gtaagtactttgattag-gtgacatt-tagttat-ctgctcttttccttcttattcattgtttaatataattttgttattaatct---tgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
              |   |    |||  ||  |||  ||| |  | || |  | ||        | ||| | ||||   | |   |||  | ||  | |   | | |||||||||||| |||||||| ||||| ||| | ||  | ||||| || ||||||||||| ||||| ||||||||||||
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttttccttcttattcattgtttaatataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
                                      tattaat  putative branch site (score: 2)
         ttcttattcattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtactttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaatataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG