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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTCTGCATGTCAAGATGCAGTAAATGGAGTACCGTCGAGAAGACCGGTTATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTGgtacttgaaacttcgtttaggaatgtcctcatatgttgttcagtcactggagctagtttcattactttgcttttaatgcatttgccacatttatgatgat...

Basic information

species Glycine max
transcript GLYMA02G06340.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G06340.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv04s0023g01790.t01 (Vitis vinifera), 5'ss of exon 12
CACTCTGCATGTCAAGATGCAGTAAATGGAGTACCGTCGAGAAGACCGGTTATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTGgtacttgaaacttcgtttagg-aatgtcctcatatgttgttcagt--cactggagctagtttcattactttgcttttaatgcatttgccacatttatgatgat-
  ||  || |||||||||||    |||||  || | ||  | || || |||||||||||| ||||||| ||   | ||||||| ||||||||||| |||||||||   ||||   | |    ||||   | |||| ||    | |  || | ||| || | | ||||  ||  | |   |   |||   ||  || |||     
GGCTTAGCTTGTCAAGATGCTTGGAATGGCCTATCATCACGGAGGCCTGTTATTGAGATGACAATTCCTTCTTCATTGGACAAGACTATTTCTCCTCCTGgtactatgaactgtatctgcctaatgcatttatatatttgctaatatcatttgaggta-tgttattaggttaatgtcttt---tttattactattgtgaaagga

upper sequence: GLYMA02G06340.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv04s0023g01780.t01 (Vitis vinifera), 5'ss of exon 12
CACTCTGCATGTCAAGATGCAGTAAATGGAGTACCGTCGAGAAGACCGGTTATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTGgtacttgaaacttcgtttaggaatgtcc-tcatatgttgttcagtcactggagctagtttcattactttgcttttaatgcatttgccacatttatgatgat---
 |||| ||  ||||||||||    |||||  |||| ||    |||||  |||| |||||| ||||||| ||  || ||||||| |||||||||||||||||||    || | || |   |     |   | |||| |  ||    ||  | |  | | |   ||  |||| | ||  |   ||     | ||| ||    |   
GACTCAGCTAGTCAAGATGCTACGAATGGCATACCATCACAGAGACCAATTATCGAGATGACAATTCCTTCTGTATTGGACAAGACTATTTCTCCACCTGgta---aaaccatcctcctgatgcatttatgatatttcatttc-ccatagcattttgctgtgtttgtttgatcttttttttttctaaccttttctggcattgca
















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|24135342|gb|BU925852.1|BU925852
EST:     TATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTG                         GTAAGCATGTGATCAACCTGTTTGTGCAGTATACACCCTACAAACCATTGG
genomic: TATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTGgtacttgaaa ... ttcttcacagGTAAGCATGTGATCAACCTGTTTGTGCAGTATACACCCTACAAACCATTGG
EST: gi|57574137|gb|CX547112.1|CX547112
EST:     TATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTG                         GTAAGCATGTGATCAACCTGTTTGTGCAGTATACACCCTACAAACCATTGG
genomic: TATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTGgtacttgaaa ... ttcttcacagGTAAGCATGTGATCAACCTGTTTGTGCAGTATACACCCTACAAACCATTGG
EST: gi|57574232|gb|CX547207.1|CX547207
EST:     TATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTG                         GTAAGCATGTGATCAACCTGTTTGTGCAGTATACACCCTACAAACCATTGG
genomic: TATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTGgtacttgaaa ... ttcttcacagGTAAGCATGTGATCAACCTGTTTGTGCAGTATACACCCTACAAACCATTGG
EST: gi|51335571|gb|CO979437.1|CO979437
EST:     TATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTG                         GTAAGCATGTGATCAACCTGTTTGTGCAGTATACACCCTACAAACCATTGG
genomic: TATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTGgtacttgaaa ... ttcttcacagGTAAGCATGTGATCAACCTGTTTGTGCAGTATACACCCTACAAACCATTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTCTGCATGTCAAGATGCAGTAAATGGAGTACCGTCGAGAAGACCGGTTATTGAGATGTCAATTCCCTCCATACTGGACAAAACTATTTCTCCACCTGgtacttgaaacttcgtttaggaatgtcctcatatgttgttcagtcactggagctagtttcattactttgcttttaatgcatttgccacatttatgatgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG