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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttttatttgtgttattttgccctaatattctattttactgcaaattcaaaggctatttacccttgactctgttcctatccttaaaattaaattgcagCAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAG

Basic information

species Glycine max
transcript GLYMA10G35140.1
intron # 51
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 51
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 48
-tgtttttatttgtgttattttgccctaatattc-tattttactg----caaattca-aaggctatttacccttgactctgttcctatccttaaaattaaattgcagCAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAG
 |  | ||| |  |  |    |  | ||| |||  ||  ||||||    ||||||   |  || ||| |   |  | | |||   | |  | |  ||      | ||||||||||||||||| |||| ||||| ||||| || || ||||| || ||||||||||| |||||||| || ||||| |||||| ||||||| |||
gtagtattactgattcttaactaacataacatttgtaaattactgcttgcaaatttgtacagcaattgatgttctattttgtctttcttttgattatgg----gtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG

upper sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 51
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 49
----tgtttttatttgtgttattttgccctaatattctattttactgcaaattcaaaggctatttacccttgactctgttcctatccttaaaattaaattgcagCAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAG
     | | || |||  ||  ||    | |  |  |  |  |  ||  | ||| | |   |  || | | ||    | ||  | || ||       |    |||||||||||||||||||| || ||||| ||||| || |||||||| || || ||||| || |||||||| |||||||| || ||  | |||||||||
gtacagctgttcttttagtcgttcatgctttgtggtgcaaat-gcttaagattaatacagtgatttcacatgctatttttgttctcttttgtggctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG

upper sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 51
lower sequence: PP1S66_170V6.1 (Physcomitrella patens), 3'ss of exon 49
---------------------------------------tgtttttatttgtgttattttgcc-ctaatattctatttta-ctgcaaattcaaaggc-tatttac---ccttgactctgttcctatccttaaaattaaattgcagCAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAG
                                       ||| |    ||     || | |    ||  | |||  || | || ||  | || |    |  ||||   | ||| ||  |||  | |   |    ||   ||| ||||||||||||||||  | || |||||||| || || ||||| ||||||||||||||||| || || || ||||| || || ||  | || ||  ||
gtaagttatgcacttttcttctttacaactttttttctgtgtgtacgcttaatcaatctggtaattagaagtcttcttcagcttcatttgcatatatgtgattacaatctttggctgagtttttgttgatctcgttg--ttgtagCAAGAGCTTGCTGCAGTGTTCAAGAAGATCGGTGATAAGCAGACTTGCACAATTGGTCTTTACGAGCTTTATCGTATCACACAGCTTTATCCTCAG

upper sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 51
lower sequence: PP1S131_18V6.1 (Physcomitrella patens), 3'ss of exon 49
---------------------tgtttttatttgtgttatt--ttgccctaata---ttctattttactgcaaattcaaaggc--tattt--acccttgactctgttcctatccttaaaattaaattg-cagCAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAG
                     || | ||||  |    |||  | |    | ||   || |  ||||| |||  |||     |  || |   | |||||||| |||     || || |  |  | ||| |||||||||||||||||  | ||||||||||| || || ||||| ||||| ||||||||||| ||||| |||||||| || |||||  | || ||  ||
gtaagttttgcgctccttctatggtattatacgctgaattcatcgggtcagtagacttattgtttacagcaccttcgtgttcattactgcaatccttgactgtgtat---tctttgacctccacttggcagCAAGAGCTTGCTGCAGTGTTTAAGAAGATCGGTGATAAGCAGACTTGTACAATTGGTCTCTATGAGCTATATCGTATCACCCAGCTATATCCTCAG

upper sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 51
lower sequence: EFJ11209 (Selaginella moellendorffii), 3'ss of exon 46
-----------------------------------------tgtttttatttgtgttattttgccc-taatat--tctattttactgcaaattcaaaggctatttacccttgact-ctgttcctatccttaaaattaaattgca--gCAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAG
                                         |   |  |||| | |   | ||  | |||||     ||  | |  | ||   |     || |  |   |   |  ||| ||    | ||    ||   |||||  ||||||| | || ||  | ||||||||||||||||| |||||||| ||||| |||||  | || ||  | ||||| || || || || || ||  ||
gtaagcagagtgcgattgcacgaggagagtgcacgacatcctacgtaaatttctctagctctgtgcataatagaacttacatcagcg-aagcccgttctctttccagtttcatccgctgatcggtactttcgtttttgtttgcacagCAAGAGTTAGCAGCGGTTTTTAAGAAGATTGGAGACAAGCAAACGTGCACGATTGGGTTGTACGAGTTGTATCGTATAACTCAGTTATATCCTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcaaaggctatttacccttgactctgttcctatccttaaaattaaattgcagCAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAG
                  ccttgac  putative branch site (score: 4)
                                 tatccttaaaattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttttatttgtgttattttgccctaatattctattttactgcaaattcaaaggctatttacccttgactctgttcctatccttaaaattaaattgcagCAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAG

- - - - tttgtgt
- - - - - - - - - -ttgccct
- - - - - - - - - - - - - - - - - - - tactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccttga