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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTTCAAGGTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaattgactaggcaaagaaactgtagttattatagtttctcctagtaaacatttttttctctataaaaacataatggtcattcttgtaaatctgttgccaggcttatgtaagtccagttctttcttcatttctgtaaatgtag

Basic information

species Glycine max
transcript GLYMA14G36280.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36280.1 (Glycine max), 5'ss of exon 10
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 5'ss of exon 10
GTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTTCAAGGTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaattgactaggcaaagaaactgtagtt-attat--agtttctcctagtaaacatttttttctct---ataaaaacataatggtcattcttgtaaatctgttgccaggcttatgtaagtccagttctttcttc-atttctgtaaatgtag
|||||||||||| |||| ||| || || ||||||||||||||||| |||||||||||||| |||||||||||  | ||  |||||||||| |||||||||||||  | ||  |      |  ||||||||  |  ||| |  | | | | |   | | |   |||  || |   || ||    || |      |  | |   |||  ||  |  ||| |  | |  |  ||   |  || |||| |   | | |||
GTATGACTATGAGGACAGAATTAATCAAGCTGTTTTTCCTGGACTGCAAGGTGGTCCACATAATCACACTATAACGGGTCTAGCAGTTGCTCTGAAGCAGgttcagtcatcaaacttttattgaaactgtgttccattgtctaatgtgttcgcatgatctcctttcactttctgattaaggtctactctaggattctcttggtct--tgtaactcttgttcatgatcttttgacttatcgatttgttctattatag

upper sequence: GLYMA14G36280.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 5'ss of exon 10
GTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTTCAAGGTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaattgactaggcaaagaaactgtagttattatagtttctcctagtaaacatttttttctctataaaaacataatggtcattcttgtaaatctgttgccaggcttatgtaagtccagttctttcttcatttctgtaaatgtag
||||||||||||||||||||| || |||||||| |||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||| |||| |||||| ||||  |        |||| |  |  |  |   |||   | |  | |    |||||  |||       |     | |  |   | |    | ||||| |                                              
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGAAACAGgttatttatct--------aaagtatttccaactggaatacaattttttggatctcatttcattcaaagctgattttgattcatttctttgactattctgtggttgtag----------------------------------------

upper sequence: GLYMA14G36280.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 10
GTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTTCAAGGTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaattgactaggcaaagaaactgtagttattatagtttctcc---tagtaaacatttttttctctataaaaacataatggt-cattcttgtaaatctgttgccaggcttatgtaagtccagttctttcttcatttctgtaaatgtag
 || ||||||||||||||||| ||    ||||||||||| ||||| ||||| ||||| ||||| ||||| ||| ||||  | || |||||  |||| |||||    |  ||    | || |  |          |  |||  |  ||    | | ||| |  |||      || ||||   ||   | ||   || | |||                                                    
CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaact--ttcgtcatgcgatcatttaacgaggagcataactcatcgatattggaaagaggtttaagcgaatcaaaatgcaaaacttcaccttttttaatg---------------------------------------------------

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|19269481|gb|BM885737.1|BM885737
EST:     GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAG                         GCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
genomic: GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaat ... gtaaatgtagGCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
EST: gi|192312199|gb|FK003920.1|FK003920
EST:     GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAG                         GCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCA-CTGC
genomic: GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaat ... gtaaatgtagGCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
EST: gi|6915301|gb|AW396831.1|AW396831
EST:     GTGGTCCACACAATCACACTATTTCAGGCTTATCAGTTGCACTGAAGCAG                         GCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
genomic: GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaat ... gtaaatgtagGCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
EST: gi|7796703|gb|AW782097.1|AW782097
EST:     GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAG                         GCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
genomic: GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaat ... gtaaatgtagGCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
EST: gi|19348549|gb|BM893081.1|BM893081
EST:     GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAG                         GCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
genomic: GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaat ... gtaaatgtagGCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
EST: gi|151409184|gb|EV278992.1|EV278992
EST:     GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCGCTGAAGCAG                         GCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
genomic: GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaat ... gtaaatgtagGCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
EST: gi|192315079|gb|FK010449.1|FK010449
EST:     GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAG                         GCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
genomic: GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaat ... gtaaatgtagGCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
EST: gi|13240115|gb|BG359424.1|BG359424
EST:     GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAG                         GCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
genomic: GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaat ... gtaaatgtagGCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
EST: gi|192312198|gb|FK003919.1|FK003919
EST:     GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAG                         GCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCA-CTGC
genomic: GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaat ... gtaaatgtagGCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
EST: gi|192298247|gb|FG992067.1|FG992067
EST:     GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAG                         GCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC
genomic: GTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaat ... gtaaatgtagGCTATGACACCAGAATTCAAGAATTACCAAAAGCAAGTACTTAGCAACTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTTCAAGGTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaattgactaggcaaagaaactgtagttattatagtttctcctagtaaacatttttttctctataaaaacataatggtcattcttgtaaatctgttgccaggcttatgtaagtccagttctttcttcatttctgtaaatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC