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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGTACTTAACAGGGTTTACCAAAGTTGATGATAATAGATACTCCATGAAAATATTCTTTGAAATCAGGAAGCAAAAATATCTAGAAGCACTTGATGGgtatctattaatttgaatctatttgggattttctaattgtttttgtgcttatggtggtacttcacatgttttatctttggtgctcttctattttag

Basic information

species Glycine max
transcript GLYMA03G39290.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39290.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os01g15020.1 (Oryza sativa), 5'ss of exon 2
AGAAGTACTTAACAGGGTTTACCAAAGTTGATGATAATAGATACTCCATGAAAATATTCTTTGAAATCAGGAAGCAAAAATATCTAGAAGCACTTGATGGgtat--ctattaatttgaa---------tctatttgggattttctaattgtttttgtgc--ttatggtggtacttcacatgttttatctttggtgctcttctattttag-----------------------
|||| ||  |  |||| || ||||| || ||||| ||||| || || ||||| ||||||||||| ||||| ||||| || ||| | |||||||||||  |||||   |    || ||||          | ||||          ||    || ||| |  |  |  ||| |||      | | || |||        ||  || ||                         
AGAAATATCTTTCAGGTTTCACCAAGGTGGATGACAATAGGTATTCTATGAAGATATTCTTTGAGATCAGAAAGCAGAAGTATTTGGAAGCACTTGACAGgtataatttcatatctgaagggaaagttcccatttcaaccaaaaaaaggacttgtgttccatccttttggcactgggtgagatataacttctactaattttcatattcatttatatattttttttgtaacag

upper sequence: GLYMA03G39290.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 5'ss of exon 2
AGAAGTACTTAACAGGGTTTACCAAAGTTGATGATAATAGATACTCCATGAAAATATTCTTTGAAATCAGGAAGCAAAAATATCTAGAAGCACTTGATGGgtatctattaatttgaatctatttgggattttctaattgtttttgtgcttatggtggtacttcacatgttttatctttggtgctcttctattttag--
||| ||| ||  |||| ||||| || ||||||||||| |||||||| ||||| || ||||||||||| |||||||| || ||||| || || |||||| |||||      |||  || || | |         || |||||||| | ||  ||  | |   |      |||    |||| || |||    | |||   
AGACGTATTTGTCAGGTTTTACTAAGGTTGATGATAACAGATACTCTATGAAGATTTTCTTTGAAATTAGGAAGCAGAAGTATCTCGAGGCTCTTGATCGgtat-----gattataagctgtct---------tatttgtttttttactcttgaagat---ttgtggttttagagtttgatgttctctgttgttacag

upper sequence: GLYMA03G39290.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 2
AGAAGTACTTAACAGGGTTTACCAAAGTTGATGATAATAGATACTCCATGAAAATATTCTTTGAAATCAGGAAGCAAAAATATCTAGAAGCACTTGATGGgtatctattaatttgaatctatttgggattttctaattgtttttgtgcttatggtggtacttcacatgttttatctttg-gtgctcttctattttag
||||||| ||| | || | |||||||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||||||||||| |||||||||||| ||||      | |||| |||||| |    |||   | || | | | ||  |  || | ||||  |    ||   |  | | ||| |  | ||| | ||
AGAAGTATTTATCCGGATATACCAAAGTTGACGATAACAGATATTCCATGAAGATATTTTTTGAAATCAGGAAGCAAAAATATCTTGAAGCACTTGATCGgtaa-----attttgtatctatat----tttggaagttctgtgtttgtatcaggagatactaaattgattaagtaatggagtgttgatttatctcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|209726114|gb|BW675288.1|BW675288
EST:     AAAATATTCTTTGAAATCAGGAAGCAAAAATATCTAGAAGCACTTGATGG                         GCAAGACAAAGCAAAGGCTGTTGAGATATTGGTGGGTGATTTAAAAGTTTT
genomic: AAAATATTCTTTGAAATCAGGAAGCAAAAATATCTAGAAGCACTTGATGGgtatctatta ... tctattttagGCAAGACAAAGCAAAGGCTGTTGAGATATTGGTGGGTGATTTAAAAGTTTT
EST: gi|209697859|gb|BW670102.1|BW670102
EST:     AAAATATTCTTTGAAATCAGGAAGCAAAAATATCTAGAAGCACTTGATGG                         GCAAGACAAAGCAAAGGCTGTTGAGATATTGGTGGGTGATTTAAAAGTTTT
genomic: AAAATATTCTTTGAAATCAGGAAGCAAAAATATCTAGAAGCACTTGATGGgtatctatta ... tctattttagGCAAGACAAAGCAAAGGCTGTTGAGATATTGGTGGGTGATTTAAAAGTTTT
EST: gi|213590590|gb|DB968126.1|DB968126
EST:     AAAATATTCTTTGAAATCAGGAAGCAAAAATATCTAGAAGCACTTGATGG                         GCAAGACAAAGCAAAGGCTGTTGAGATATTGGTGGGTGATTTAAAAGTTTT
genomic: AAAATATTCTTTGAAATCAGGAAGCAAAAATATCTAGAAGCACTTGATGGgtatctatta ... tctattttagGCAAGACAAAGCAAAGGCTGTTGAGATATTGGTGGGTGATTTAAAAGTTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGTACTTAACAGGGTTTACCAAAGTTGATGATAATAGATACTCCATGAAAATATTCTTTGAAATCAGGAAGCAAAAATATCTAGAAGCACTTGATGGgtatctattaatttgaatctatttgggattttctaattgtttttgtgcttatggtggtacttcacatgttttatctttggtgctcttctattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC