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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaagggcccttgtaattggttaacttctttaacatttattatattattgtgttcttatgttggtaccttctgtgtggctgtgatag

Basic information

species Glycine max
transcript GLYMA07G00430.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 17
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 17
CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaaggg---------cccttgtaattggttaacttctttaacatttattatattattgtgttctt-atgttggtaccttctgtgtgg---ctgtgatag
||||| || || |||||  |||| ||||| || || ||||| || ||||| || ||||| ||||| || ||||| ||||||||||| || |||||||||||||           |||||    |||||| | | || |  |  ||  | | | |  | ||| || |   | | ||||| ||  ||     | ||| ||
CTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttgttggctcccttcgttttggtttagtactct--ctctttctctctcaacgggttattcactcttgaaccttttggatgaattttttgacag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 17
CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaagggcccttgtaa----ttggttaa---------cttctttaacatttattatattattgtgttcttatgttggtaccttctgtgtggctgtgatag-------------------------------------------
||||| || || |||||||||||||||  |||||| || ||  |||| ||||||||||||||||| || || |||||||| |||||||| ||||| |||||||  ||    |||    ||| || |         | | |||||  ||| ||   ||| | | | ||||||||    | || | ||  | | |   |                                            
CTTGTCGGAAAAGATGCTTTAGCTGAAACAGATAAAATTACTCTAGAGACTGCAAAGCTTTTGAGGGAAGACTATCTTGCACAAAATGCATTTACCCCgtaagtcccagattaagtttttgattcaaattttcgtcctttttaatttttgtttacttactatttccttatgttc-ccctttttatgctggtctagaaattctttttccacttaatatatgtatctcatgtggctgtgacag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 17
--CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaag-ggcccttgtaattggttaa---cttctttaacatttattata--------ttattgtgttcttatg--ttggtaccttctgtgtggctgtgatag
  ||||| || ||||||||||| || |||   ||||| || ||  | || ||||||||||| ||||| ||||| ||||||||||||||||| || |||||||||| ||   ||||| ||  || |   |   |||   | | ||| ||        || |  | ||  ||    ||| ||  || | |    |  || || 
AGCTTGTTGGAAAGGATGCTTTGGCAGAAACGGATAAAATTACACTGGAGACTGCAAAGCTCTTGAGGGAGGACTATCTTGCTCAAAATGCTTTCACACCgtaagtggaaattgtacttaatttagaccccgtttggtagtgattctaaaaagcgtttttaatatttctaatacttgataatttttatcattcaatggta-

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|57575927|gb|CX548898.1|CX548898
EST:     ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC                         ATATGATAAATTTTGCCCCTTCTACTAGTCTGTTTGGATGATGCGCAACAT
genomic: ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaagggccc ... gctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|58021805|gb|CX708546.1|CX708546
EST:     ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC                         ATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaagggccc ... gctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|58018020|gb|CX704762.1|CX704762
EST:     ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC                         ATATGATAAATTTTGCCCCTTCTACTAGTCTGTTTGGATGATGCGCAACAT
genomic: ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaagggccc ... gctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|58020232|gb|CX706974.1|CX706974
EST:     ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC                         ATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaagggccc ... gctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|58024542|gb|CX711283.1|CX711283
EST:     ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC                         ATATGATAAATTTTGCCCCTTCTACTAGTCTGTTTGGATGATGCGCAACAT
genomic: ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaagggccc ... gctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|8286121|gb|BE023680.1|BE023680
EST:     ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC                         ATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaagggccc ... gctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|51345142|gb|CO985875.1|CO985875
EST:     ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC                         ATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaagggccc ... gctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|26268746|gb|CA819809.1|CA819809
EST:     AGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC                         ATATGATAAATTTTGCCCCTTCTACAATTCTGTTTGGATGATGCGCAACAT
genomic: AGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaagggccc ... gctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACCgtaagggcccttgtaattggttaacttctttaacatttattatattattgtgttcttatgttggtaccttctgtgtggctgtgatag

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT