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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcggtttagacggttgaattttcgttttggattttgaatttgaatttcgcggagcacaattgtgagaatttttgagtgttttggtatggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGGTAGAGGAGCGGAACCTTCTGTCGGTTGGGTACAAGAACGTGGTGGGTGC

Basic information

species Glycine max
transcript GLYMA05G29080.7
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G29080.7 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0003g01240.t01 (Vitis vinifera), 3'ss of exon 1
----------------------atttcgg--tttagacggttgaattttcgtt-ttggattttgaatttgaatttcgcggagcacaattgtgagaatttttgagtgttttggtatggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGGTAGAGGAGCGGAACCTTCTGTCGGTTGGGTACAAGAACGTGGTGGGTGC
                       ||  ||   |  ||       | | ||  | || || || |  |||  | ||  | || ||| |      |||||||    ||||||  | |  | |  |||||||||||||  | |||||||| |||||||||||  ||||||||||||| || |||||||||||||| || |||||||| |  ||||||||| | || ||
gtttccctctctctttctcctgtttgtggatctcggattaccccactctcactgttagagttagggtttccaattatctgatcactacct---gaattttactctgttttt-ttttttttggtagAAATGGTGGATTCCATGAAGAAAGTGGCGAAGCTGGACGTGGAATTGACCGTGGAGGAGCGGAACCTGCTCTCGGTTGGCTTTAAGAACGTGATCGGCGC

upper sequence: GLYMA05G29080.7 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0014g01420.t01 (Vitis vinifera), 3'ss of exon 1
atttcggtttagacggttgaattttcgttttggattttgaatttgaatttcgc--ggagcaca-attgtgagaatttttgagtgttttggtatggtgttt---tagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGGTAGAGGAGCGGAACCTTCTGTCGGTTGGGTACAAGAACGTGGTGGGTGC
 |    |||| | |  | |  ||   | | ||   ||| |||||   |   ||  ||    || ||| | |     ||| | | |||| |       |||    |||||||||||| || |||||||| |||||||||||  | ||||| ||||| || || ||||||||  | || ||||||||||||||||||||| | || ||
gtcagtgtttcgtccttcgctttccagatctgctgttttaatttcgctagggctagggtttcagattctaactggatttcactctttttgcgaaaattttgtgcagAAATGGTGGATGCGATGAAGAAAGTGGCGAAGCTGGATGTGGATTTGACTGTGGAAGAGCGGAATTTGCTTTCGGTTGGGTACAAGAACGTGATCGGAGC

upper sequence: GLYMA05G29080.7 (Glycine max), 3'ss of exon 1
lower sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 1
atttcggtttagacggttgaattttcgttttggattttgaatttgaatttcgcggagcacaattgtgagaatttttgagtgttttg-gtatggtg--ttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGGTAGAGGAGCGGAACCTTCTGTCGGTTGGGTACAAGAACGTGGTGGGTGC
 |||    || |  ||  ||    |   |  ||   |||     |     ||  |       | |||     |   | ||||  || || | |||  ||  ||| ||||||||  | |||||||| |||||||||||  |||||||  ||||||| |||||||| || || ||||| || || |||||||||||| | || ||
gtttgcagttgggaggcagagacgtgagtgcgg---ttgggcccggtgggcggcggttgtgttggtggatgatggagcgtgtggtgcgttttgtgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC

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|7686518|gb|AW757166.1|AW757166
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|193610352|gb|FK562066.1|FK562066
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|254328641|gb|GR833013.1|GR833013
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|298178990|gb|HO024725.1|HO024725
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAGTGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|193401573|gb|FK368038.1|FK368038
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|5058166|gb|AI736642.1|AI736642
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|298198736|gb|HO042099.1|HO042099
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|193301431|gb|FK266828.1|FK266828
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|193575189|gb|FK530300.1|FK530300
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|5666653|gb|AI930689.1|AI930689
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|193462492|gb|FK426879.1|FK426879
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|6502305|gb|AW203678.1|AW203678
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|21889084|gb|BQ742297.1|BQ742297
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|254333164|gb|GR850414.1|GR850414
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|298191378|gb|HO038857.1|HO038857
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|208175353|gb|GD975992.1|GD975992
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|254347253|gb|GR853502.1|GR853502
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|193327746|gb|FK296371.1|FK296371
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|208214053|gb|GE008842.1|GE008842
EST:     CCGAACAAGCCGAACGCTATGAAG                         AAACGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: CCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|19270324|gb|BM886580.1|BM886580
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|193475090|gb|FK439813.1|FK439813
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|254336492|gb|GR842671.1|GR842671
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|151394632|gb|EV264503.1|EV264503
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|10843848|gb|BF067096.1|BF067096
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|192309537|gb|FK000969.1|FK000969
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|10231553|gb|BE800441.1|BE800441
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
EST: gi|6482683|gb|AW201922.1|AW201922
EST:     AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAG                         AAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG
genomic: AAACTTCGTCTACGTCGCCAAGCTCGCCGAACAAGCCGAACGCTATGAAGgtataataat ... ggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcgcggagcacaattgtgagaatttttgagtgttttggtatggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGGTAGAGGAGCGGAACCTTCTGTCGGTTGGGTACAAGAACGTGGTGGGTGC
                      agaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcggtttagacggttgaattttcgttttggattttgaatttgaatttcgcggagcacaattgtgagaatttttgagtgttttggtatggtgttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGGTAGAGGAGCGGAACCTTCTGTCGGTTGGGTACAAGAACGTGGTGGGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG