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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgccttttctccctatctctttctctttctctatatgttattatacgattcgtcgttttgacacgtgtgtttaaatggaacgcagGGGAAGGGAACAGGGAGCTTCGGTAAGAGGAGGAACAAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCG

Basic information

species Glycine max
transcript GLYMA13G43450.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43450.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g56990.1 (Oryza sativa), 3'ss of exon 1
----------------------gtaat-gccttttctccctatctctttctctttctctatatgttattatacgattcg-tcgttttgacacgtgtgtttaaatggaacgcagGGGAAGGGAACAGGGAGCTTCGGTAAGAGGAGGAACAAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCG
                      |  || |     |||        || ||      |  || ||  |      |||  | | | ||||     |||  ||   ||   ||||||| ||||| || ||||||||||| ||| |  |||||||||| ||||| ||||| ||| | || |||||||||||||||||||| ||||||||   |||| 
gtgaggagaatcgcggcgagcggcgatcgatgcatcttgtagcgcctctcctcgcgtggatctgacagggattgatctggttgctttgtgttttgttcttctttg---cgcagGGCAAGGGCACGGGGAGCTTCGGGAAGCGCCGGAACAAGACGCACACGCTCTGCGTGCGCTGCGGCCGCCGCAGCTTCCACCTGCAGAAGAGCACCTGCT

upper sequence: GLYMA13G43450.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g02130.1 (Oryza sativa), 3'ss of exon 1
gtaatgccttttctccctatctctttctctttctctatatgttattatacgattcgtcgttttgacacgt--gtgtttaaatggaacgcagGGGAAGGGAACAGGGAGCTTCGGTAAGAGGAGGAACAAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCG
||||      ||| | |   | |   ||| ||   | |   |  |    | | || | | | | ||| |    | ||    |||  ||||||||||||| || || |||||||| ||| |  |||||||||| ||||| ||||| ||  | || |||||||||||||||||||||||||||||   |||| 
gtaac----cttcgcgccgccgccgcctcattgcttcttcctcgt----ctactcctagctctaacatggtgatcttcttgtggctcgcagGGGAAGGGTACGGGCAGCTTCGGCAAGCGCCGGAACAAGACGCACACGCTCTGCGTCCGCTGCGGCCGCCGCAGCTTCCACCTCCAGAAGAGCACCTGCT

upper sequence: GLYMA13G43450.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g03450.1 (Oryza sativa), 3'ss of exon 1
gtaatgccttttctccctatctctttctctttctctatatgttattatacgattcgtcgttttgacacgt--gtgtttaaatggaacgcagGGGAAGGGAACAGGGAGCTTCGGTAAGAGGAGGAACAAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCG
||||  |       | |   | |   | |   |||   |||   |       | | | | | | ||  |    | ||    |||  ||||||| ||||| || || |||||||| ||| |  |||||||||| ||||| ||||| ||  | || |||||||||||||||||||||||||||||   |||| 
gtaaacctcgcagccgccgccgccgccgcggcctcctcatggcttc------tccatagctctaacgtggtgatcttgttgtggctcgcagGGTAAGGGTACGGGCAGCTTCGGCAAGCGCCGGAACAAGACGCACACGCTCTGCGTCCGCTGCGGCCGCCGCAGCTTCCACCTCCAGAAGAGCACCTGCT

upper sequence: GLYMA13G43450.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G077991_T02 (Zea mays), 3'ss of exon 1
gtaatgccttttctccctatctctttctctttctctatatgttattatacgattcgtcgttttgacacgtgtgtttaaatggaacgcagGGGAAGGGAACAGGGAGCTTCGGTAAGAGGAGGAACAAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCG
     |    ||| | |   | ||  | | | | |   | |      | ||     ||| |   |  |   ||||    |||   |||||| ||||| || || |||||||| ||| |  |||||||||| ||||| |||||  |  | || ||||||||||||||||||||||||||||||  |||| 
-----gtacgttcgcgccgccgctgccgcctccccggca-gcccccgtccgcccgctcgctaacatgcagttgtt---gtggcttgcagGGTAAGGGTACGGGCAGCTTCGGCAAGCGCCGGAACAAGACGCACACGCTCTGCATCCGCTGCGGCCGCCGCAGCTTCCACCTCCAGAAGAGTACCTGCT

upper sequence: GLYMA13G43450.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G168674_T01 (Zea mays), 3'ss of exon 1
------------------------gtaatgccttttctccctatctctttctctttctctatatgttattatacgattcgtcgttttgacacgtgtgtttaaatggaacgcagGGGAAGGGAACAGGGAGCTTCGGTAAGAGGAGGAACAAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCG
                        |  | ||   | | | |||  |||   |   ||  |   |  | |     ||   |  | | ||   |   ||||    |||  ||||||||||||| || || |||||||| ||| |  ||||||| || ||||| || ||  |  | || ||||||||||||||||||||||||||||||  |||| 
gtacgtgtcgccgccgtcgccgttgccacgcagctcccctctacgtctccgttcgtccgtgcgt-ctgtccgctgacgtggtgctatggtgctgttgtt---gtggctcgcagGGGAAGGGTACGGGCAGCTTCGGCAAGCGCCGGAACAAAACGCACACGCTGTGCATCCGCTGCGGCCGCCGCAGCTTCCACCTCCAGAAGAGTACCTGCT

upper sequence: GLYMA13G43450.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G52300.1 (Arabidopsis thaliana), 3'ss of exon 1
----gtaatgccttttctccctatctctttctctt-tctctat---------atgttattatacgattcgtcgttttgacacgtgtgtttaaatggaacgcagGGGAAGGGAACAGGGAGCTTCGGTAAGAGGAGGAACAAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCG
       | |  | | ||| |||||| | | | |  |||||||         || | ||||  |   |    |||||  | | | |||||    |   | |||   |||||||| || || ||||| ||||| || |||||||  ||||| |||||||| || |||||||| ||||| |||||| ||||||||||||| ||| 
gtgatctacgattctcctctctatctttctatttcatctctatgcttcgttgatttcattactctgatatctgttttatcgctt-tgtttttgagattctcagACTAAGGGAACGGGAAGTTTCGGAAAGAGAAGAAACAAGAGTCACACACTCTGTGTCAGATGTGGCCGTCGCAGTTTCCACATCCAGAAGAGTCGTTGCT

upper sequence: GLYMA13G43450.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G16080.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaatgccttttctccctatctctttctctttctctatatgttattatacgattcgtcgttttgacacgtgtgtttaaatggaacgcagGGGAAGGGAACAGGGAGCTTCGGTAAGAGGAGGAACAAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCG
|| ||  ||  ||| ||| | || |    |  |  |  |    ||        |  |  || ||  || |   ||| | |  |  |||||| |||||||||||||| ||||||||||||||||||||||  ||||| ||||||||||| ||||| || || || |||||| ||||||||||||| ||| 
gtgatctctcctcttcctctttcgtcgattgaccatgaaaaccatctctgatattattattgtggaactt---tttgagt--attgcagGGAAAGGGAACAGGGAGTTTCGGTAAGAGGAGGAACAAGAGTCACACACTCTGTGTGAGATGTGGTCGTCGTAGTTTCCACATCCAGAAGAGTCGTTGCT

upper sequence: GLYMA13G43450.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G15250.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaatgccttttctccctatctctttctctttctctatatgttattatacgattcgtcgttttgacacgtgtgtttaaatggaacgcagGGGAAGGGAACAGGGAGCTTCGGTAAGAGGAGGAACAAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCG
           |   |   |  | || | ||||  | || | |  | |  || |  |   | | ||  |||  ||  ||  ||   ||||| || |||||||||||||| |||||||||||||||||| | ||||| ||||||||||| ||||| ||||| ||||| ||| ||||||||||||| ||| 
----------gtaatctattggcattttttttccatgtaagctcatgtgtgacttatg--tgtaaccggtgctttggaaatga---cagGGTAAAGGAACAGGGAGCTTTGGTAAGAGGAGGAACAAGTCACACACGCTCTGTGTGAGATGTGGTCGCCGGAGCTTTCACATCCAGAAGAGTCGTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatatgttattatacgattcgtcgttttgacacgtgtgtttaaatggaacgcagGGGAAGGGAACAGGGAGCTTCGGTAAGAGGAGGAACAAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCG
                         ttttgac  putative branch site (score: 3)
     tgttattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgccttttctccctatctctttctctttctctatatgttattatacgattcgtcgttttgacacgtgtgtttaaatggaacgcagGGGAAGGGAACAGGGAGCTTCGGTAAGAGGAGGAACAAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT